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wa 0.0 in cns 1.2 linux version

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  • amitd_01
    Hello everybody, When using refine.inp of CNS ver 1.2 the rsmd bonds and angles outputs are 0.000 and very low values of wa=2x10-2 and rweight= 0.02 resptly.
    Message 1 of 11 , Feb 4, 2010
      Hello everybody,
      When using refine.inp of CNS ver 1.2 the rsmd bonds and angles outputs are 0.000 and very low values of wa=2x10-2 and rweight= 0.02 resptly. Using optimize_wa.inp gives wa=0.0 for all the cycles and optimize_rweight.inp gives 0.2 as best value. I recreated a new refine.inp and ran it but I get the same result. The R- and R-free are near 20%. There are a few anions and metal ions (but used as neutral) along with waters and protein chain in the input pdb.
      I had refined with only protein and waters, with and without the ions but with no luck. Fixing the wa= 0.3 to 1.5 increases the R- to very high values.
      I would appreciate any help to get proper rsmds and wa values.
      Thanks in advance,
      Amit Das.
    • Ed Pozharski
      Just to verify, you are using the *latest* version, 1.21 (not 1.2)? This is really strange. Do both R and Rfree go up when you weaken restraints? And how
      Message 2 of 11 , Feb 5, 2010
        Just to verify, you are using the *latest* version, 1.21 (not 1.2)?

        This is really strange. Do both R and Rfree go up when you weaken
        restraints? And how high they go? You see, normally you would expect
        that with weaker restraints Rfree may go up, but R should go down.
        What's the resolution?

        How do the maps look? Can you get anything else refined (which would
        indicate that the issue is this particular dataset). If you try other
        refinement programs (refmac, phenix), do you still have the problem?

        On Fri, 2010-02-05 at 07:42 +0000, amitd_01 wrote:
        >
        > Hello everybody,
        > When using refine.inp of CNS ver 1.2 the rsmd bonds and angles outputs
        > are 0.000 and very low values of wa=2x10-2 and rweight= 0.02 resptly.
        > Using optimize_wa.inp gives wa=0.0 for all the cycles and
        > optimize_rweight.inp gives 0.2 as best value. I recreated a new
        > refine.inp and ran it but I get the same result. The R- and R-free are
        > near 20%. There are a few anions and metal ions (but used as neutral)
        > along with waters and protein chain in the input pdb.
        > I had refined with only protein and waters, with and without the ions
        > but with no luck. Fixing the wa= 0.3 to 1.5 increases the R- to very
        > high values.
        > I would appreciate any help to get proper rsmds and wa values.
        > Thanks in advance,
        > Amit Das.
        >
        >
        >
        >
        >
        --
        Edwin Pozharski, PhD, Assistant Professor
        University of Maryland, Baltimore
        ----------------------------------------------
        When the Way is forgotten duty and justice appear;
        Then knowledge and wisdom are born along with hypocrisy.
        When harmonious relationships dissolve then respect and devotion arise;
        When a nation falls to chaos then loyalty and patriotism are born.
        ------------------------------ / Lao Tse /
      • amitd_01
        Yes I am using 1.21 version. Forcing the wa to higher than automatic value of wa= 7.230911E-02, increases the r and rfree to above 50! ... rweight= 0.0100 r=
        Message 3 of 11 , Feb 7, 2010
          Yes I am using 1.21 version. Forcing the wa to higher than automatic value of wa= 7.230911E-02, increases the r and rfree to above 50!

          The opt_rweight output is :
          ------> initial rweight estimate= 0.1000

          rweight= 0.0100 r= 0.1685 free_r= 0.2128 rms B(bond)= 3.8780 rms B(angle)= 4.7275
          rweight= 0.0200 r= 0.1685 free_r= 0.2128 rms B(bond)= 3.8205 rms B(angle)= 4.6736
          rweight= 0.0500 r= 0.1687 free_r= 0.2127 rms B(bond)= 3.5794 rms B(angle)= 4.4422
          rweight= 0.1000 r= 0.1688 free_r= 0.2126 rms B(bond)= 3.4538 rms B(angle)= 4.3251
          rweight= 0.2000 r= 0.1691 free_r= 0.2121 rms B(bond)= 3.0403 rms B(angle)= 3.9464
          rweight= 0.5000 r= 0.1699 free_r= 0.2123 rms B(bond)= 2.5454 rms B(angle)= 3.4242
          rweight= 1.0000 r= 0.1716 free_r= 0.2127 rms B(bond)= 1.9617 rms B(angle)= 2.7739
          rweight= 2.0000 r= 0.1734 free_r= 0.2135 rms B(bond)= 1.5863 rms B(angle)= 2.3047
          rweight= 5.0000 r= 0.1781 free_r= 0.2169 rms B(bond)= 1.0437 rms B(angle)= 1.5197

          ------> lowest free_r for target "mlf" with rweight= 0.2000 (with wa= 4.41916)

          The opt_wa output is:
          ------> initial wa estimate= 0

          wa= 0.0000 r= 0.1689 free_r= 0.2126 rmsd bonds= 0.000000 rmsd angles= 0.00000
          wa= 0.0000 r= 0.1688 free_r= 0.2126 rmsd bonds= 0.000000 rmsd angles= 0.00000
          wa= 0.0000 r= 0.1688 free_r= 0.2126 rmsd bonds= 0.000000 rmsd angles= 0.00000
          wa= 0.0000 r= 0.1688 free_r= 0.2126 rmsd bonds= 0.000000 rmsd angles= 0.00000
          wa= 0.0000 r= 0.1688 free_r= 0.2126 rmsd bonds= 0.000000 rmsd angles= 0.00000
          wa= 0.0000 r= 0.1687 free_r= 0.2126 rmsd bonds= 0.000000 rmsd angles= 0.00000
          wa= 0.0000 r= 0.1687 free_r= 0.2126 rmsd bonds= 0.000000 rmsd angles= 0.00000
          wa= 0.0000 r= 0.1686 free_r= 0.2127 rmsd bonds= 0.000000 rmsd angles= 0.00000
          wa= 0.0000 r= 0.1684 free_r= 0.2128 rmsd bonds= 0.000000 rmsd angles= 0.00000
          wa= 0.0000 r= 0.1680 free_r= 0.2129 rmsd bonds= 0.000000 rmsd angles= 0.00000
          wa= 0.0000 r= 0.1675 free_r= 0.2129 rmsd bonds= 0.000000 rmsd angles= 0.00000
          wa= 0.0000 r= 0.1666 free_r= 0.2131 rmsd bonds= 0.000000 rmsd angles= 0.00000

          ------> lowest free_r for target mlf with wa= 0

          ------> The best value for wa is one that produces a low
          free_r value and also good model geometry. As a general
          guide, good geometry is indicated by rms deviations from
          ideal values of less than:
          bonds -> 0.01 A
          angles -> 2.00 degrees

          The rsmds are bad since the planarity of the rings are distorted although R and Rfree are good.
          Thanks
          Amit.


          --- In cnsbb@yahoogroups.com, Ed Pozharski <epozh001@...> wrote:
          >
          > Just to verify, you are using the *latest* version, 1.21 (not 1.2)?
          >
          > This is really strange. Do both R and Rfree go up when you weaken
          > restraints? And how high they go? You see, normally you would expect
          > that with weaker restraints Rfree may go up, but R should go down.
          > What's the resolution?
          >
          > How do the maps look? Can you get anything else refined (which would
          > indicate that the issue is this particular dataset). If you try other
          > refinement programs (refmac, phenix), do you still have the problem?
          >
          > On Fri, 2010-02-05 at 07:42 +0000, amitd_01 wrote:
          > >
          > > Hello everybody,
          > > When using refine.inp of CNS ver 1.2 the rsmd bonds and angles outputs
          > > are 0.000 and very low values of wa=2x10-2 and rweight= 0.02 resptly.
          > > Using optimize_wa.inp gives wa=0.0 for all the cycles and
          > > optimize_rweight.inp gives 0.2 as best value. I recreated a new
          > > refine.inp and ran it but I get the same result. The R- and R-free are
          > > near 20%. There are a few anions and metal ions (but used as neutral)
          > > along with waters and protein chain in the input pdb.
          > > I had refined with only protein and waters, with and without the ions
          > > but with no luck. Fixing the wa= 0.3 to 1.5 increases the R- to very
          > > high values.
          > > I would appreciate any help to get proper rsmds and wa values.
          > > Thanks in advance,
          > > Amit Das.
          > >
          > >
          > >
          > >
          > >
          > --
          > Edwin Pozharski, PhD, Assistant Professor
          > University of Maryland, Baltimore
          > ----------------------------------------------
          > When the Way is forgotten duty and justice appear;
          > Then knowledge and wisdom are born along with hypocrisy.
          > When harmonious relationships dissolve then respect and devotion arise;
          > When a nation falls to chaos then loyalty and patriotism are born.
          > ------------------------------ / Lao Tse /
          >
        • AMIT
          Yes I was puzzled. I tried the same refinements using CNS 1.1 (I switched to this version now) which works fine gives following pdb output file: REMARK
          Message 4 of 11 , Feb 11, 2010
            Yes I was puzzled. I tried the same refinements using CNS 1.1 (I switched to this version now) which works fine gives following pdb output file:

            REMARK starting r= 0.1854 free_r= 0.2018
            REMARK final    r= 0.1830 free_r= 0.2026
            REMARK rmsd bonds= 0.008089  rmsd angles=  1.45742 ..........
            REMARK target= mlf  final wa= 0.6668
            REMARK final rweight=  0.1204 (with wa= 0.6668)

            Actually the refine.out used earlier says CNS ver 1.2. I assume that refine.inp works for both 1.2 and 1.21 because I created a fresh refine.inp for 1.21 from web and ran but the rsmds are still become 0.000.
            Actually the same input pdb in refmac 5.5 gives proper rsmds as is now given by CNS 1.1.

            Regards
            Amit Das.



            On Mon, Feb 8, 2010 at 8:29 PM, Ed Pozharski <epozh001@...> wrote:
            This is obviously abnormal.  It's hard to diagnose what the problem is
            without further details.  I assume that your installation of CNS works
            with other datasets/models, so it's something with the data.  If you can
            send me the data/model I will take a look and will treat this
            confidentially.  Otherwise, consider trying other refinement programs
            and checking the original data for signs of twinning (although I don't
            see how twinning can produce this behavior)

            Ed.

            On Mon, 2010-02-08 at 04:30 +0000, amitd_01 wrote:
            >
            > Yes I am using 1.21 version. Forcing the wa to higher than automatic
            > value of wa= 7.230911E-02, increases the r and rfree to above 50!
            >
            > The opt_rweight output is :
            > ------> initial rweight estimate= 0.1000
            >
            > rweight= 0.0100 r= 0.1685 free_r= 0.2128 rms B(bond)= 3.8780 rms
            > B(angle)= 4.7275
            > rweight= 0.0200 r= 0.1685 free_r= 0.2128 rms B(bond)= 3.8205 rms
            > B(angle)= 4.6736
            > rweight= 0.0500 r= 0.1687 free_r= 0.2127 rms B(bond)= 3.5794 rms
            > B(angle)= 4.4422
            > rweight= 0.1000 r= 0.1688 free_r= 0.2126 rms B(bond)= 3.4538 rms
            > B(angle)= 4.3251
            > rweight= 0.2000 r= 0.1691 free_r= 0.2121 rms B(bond)= 3.0403 rms
            > B(angle)= 3.9464
            > rweight= 0.5000 r= 0.1699 free_r= 0.2123 rms B(bond)= 2.5454 rms
            > B(angle)= 3.4242
            > rweight= 1.0000 r= 0.1716 free_r= 0.2127 rms B(bond)= 1.9617 rms
            > B(angle)= 2.7739
            > rweight= 2.0000 r= 0.1734 free_r= 0.2135 rms B(bond)= 1.5863 rms
            > B(angle)= 2.3047
            > rweight= 5.0000 r= 0.1781 free_r= 0.2169 rms B(bond)= 1.0437 rms
            > B(angle)= 1.5197
            >
            > ------> lowest free_r for target "mlf" with rweight= 0.2000 (with wa=
            > 4.41916)
            >
            > The opt_wa output is:
            > ------> initial wa estimate= 0
            >
            > wa= 0.0000 r= 0.1689 free_r= 0.2126 rmsd bonds= 0.000000 rmsd angles=
            > 0.00000
            > wa= 0.0000 r= 0.1688 free_r= 0.2126 rmsd bonds= 0.000000 rmsd angles=
            > 0.00000
            > wa= 0.0000 r= 0.1688 free_r= 0.2126 rmsd bonds= 0.000000 rmsd angles=
            > 0.00000
            > wa= 0.0000 r= 0.1688 free_r= 0.2126 rmsd bonds= 0.000000 rmsd angles=
            > 0.00000
            > wa= 0.0000 r= 0.1688 free_r= 0.2126 rmsd bonds= 0.000000 rmsd angles=
            > 0.00000
            > wa= 0.0000 r= 0.1687 free_r= 0.2126 rmsd bonds= 0.000000 rmsd angles=
            > 0.00000
            > wa= 0.0000 r= 0.1687 free_r= 0.2126 rmsd bonds= 0.000000 rmsd angles=
            > 0.00000
            > wa= 0.0000 r= 0.1686 free_r= 0.2127 rmsd bonds= 0.000000 rmsd angles=
            > 0.00000
            > wa= 0.0000 r= 0.1684 free_r= 0.2128 rmsd bonds= 0.000000 rmsd angles=
            > 0.00000
            > wa= 0.0000 r= 0.1680 free_r= 0.2129 rmsd bonds= 0.000000 rmsd angles=
            > 0.00000
            > wa= 0.0000 r= 0.1675 free_r= 0.2129 rmsd bonds= 0.000000 rmsd angles=
            > 0.00000
            > wa= 0.0000 r= 0.1666 free_r= 0.2131 rmsd bonds= 0.000000 rmsd angles=
            > 0.00000
            >
            > ------> lowest free_r for target mlf with wa= 0
            >
            > ------> The best value for wa is one that produces a low
            > free_r value and also good model geometry. As a general
            > guide, good geometry is indicated by rms deviations from
            > ideal values of less than:
            > bonds -> 0.01 A
            > angles -> 2.00 degrees
            >
            > The rsmds are bad since the planarity of the rings are distorted
            > although R and Rfree are good.
            > Thanks
            > Amit.
            >
            > --- In cnsbb@yahoogroups.com, Ed Pozharski <epozh001@...> wrote:
            > >
            > > Just to verify, you are using the *latest* version, 1.21 (not 1.2)?
            > >
            > > This is really strange. Do both R and Rfree go up when you weaken
            > > restraints? And how high they go? You see, normally you would expect
            > > that with weaker restraints Rfree may go up, but R should go down.
            > > What's the resolution?
            > >
            > > How do the maps look? Can you get anything else refined (which would
            > > indicate that the issue is this particular dataset). If you try
            > other
            > > refinement programs (refmac, phenix), do you still have the problem?
            > >
            > > On Fri, 2010-02-05 at 07:42 +0000, amitd_01 wrote:
            > > >
            > > > Hello everybody,
            > > > When using refine.inp of CNS ver 1.2 the rsmd bonds and angles
            > outputs
            > > > are 0.000 and very low values of wa=2x10-2 and rweight= 0.02
            > resptly.
            > > > Using optimize_wa.inp gives wa=0.0 for all the cycles and
            > > > optimize_rweight.inp gives 0.2 as best value. I recreated a new
            > > > refine.inp and ran it but I get the same result. The R- and R-free
            > are
            > > > near 20%. There are a few anions and metal ions (but used as
            > neutral)
            > > > along with waters and protein chain in the input pdb.
            > > > I had refined with only protein and waters, with and without the
            > ions
            > > > but with no luck. Fixing the wa= 0.3 to 1.5 increases the R- to
            > very
            > > > high values.
            > > > I would appreciate any help to get proper rsmds and wa values.
            > > > Thanks in advance,
            > > > Amit Das.
            > > >
            > > >
            > > >
            > > >
            > > >
            > > --
            > > Edwin Pozharski, PhD, Assistant Professor
            > > University of Maryland, Baltimore
            > > ----------------------------------------------
            > > When the Way is forgotten duty and justice appear;
            > > Then knowledge and wisdom are born along with hypocrisy.
            > > When harmonious relationships dissolve then respect and devotion
            > arise;
            > > When a nation falls to chaos then loyalty and patriotism are born.
            > > ------------------------------ / Lao Tse /
            > >
            >
            >
            >
            >
            >


            --
            Edwin Pozharski, PhD, Assistant Professor
            University of Maryland, Baltimore
            ----------------------------------------------
            When the Way is forgotten duty and justice appear;
            Then knowledge and wisdom are born along with hypocrisy.
            When harmonious relationships dissolve then respect and devotion arise;
            When a nation falls to chaos then loyalty and patriotism are born.
            ------------------------------   / Lao Tse /





            --
            AMIT DAS,
            PROTEIN CRYSTALLOGRAPHY SECTION,
            SOLID STATE PHYSICS DIVISION, BARC, TROMBAY,
            MUMBAI-400085.
            INDIA.
            Alt E-mail:amitdas@...
            PHONE:+91-22-25594688/4063
            FAX:+91-22-25505151
          • Axel Brunger
            This could be a compilation problem. Please try the pre-compiled linux binaries that you can download from the CNS download site. Axel Brunger ... Axel T.
            Message 5 of 11 , Feb 11, 2010
              This could be a compilation problem. Please try the pre-compiled
              linux binaries that you can download from the CNS download site.

              Axel Brunger

              On Feb 11, 2010, at 12:23 AM, AMIT wrote:

              Yes I was puzzled. I tried the same refinements using CNS 1.1 (I switched to this version now) which works fine gives following pdb output file:

              REMARK starting r= 0.1854 free_r= 0.2018
              REMARK final    r= 0.1830 free_r= 0.2026
              REMARK rmsd bonds= 0.008089  rmsd angles=  1.45742 ..........
              REMARK target= mlf  final wa= 0.6668
              REMARK final rweight=  0.1204 (with wa= 0.6668)

              Actually the refine.out used earlier says CNS ver 1.2. I assume that refine.inp works for both 1.2 and 1.21 because I created a fresh refine.inp for 1.21 from web and ran but the rsmds are still become 0.000.
              Actually the same input pdb in refmac 5.5 gives proper rsmds as is now given by CNS 1.1.

              Regards 
              Amit Das.



              On Mon, Feb 8, 2010 at 8:29 PM, Ed Pozharski <epozh001@umaryland. edu> wrote:
              This is obviously abnormal.  It's hard to diagnose what the problem is
              without further details.  I assume that your installation of CNS works
              with other datasets/models, so it's something with the data.  If you can
              send me the data/model I will take a look and will treat this
              confidentially.  Otherwise, consider trying other refinement programs
              and checking the original data for signs of twinning (although I don't
              see how twinning can produce this behavior)

              Ed.

              On Mon, 2010-02-08 at 04:30 +0000, amitd_01 wrote:
              >
              > Yes I am using 1.21 version. Forcing the wa to higher than automatic
              > value of wa= 7.230911E-02, increases the r and rfree to above 50!
              >
              > The opt_rweight output is :
              > ------> initial rweight estimate= 0.1000
              >
              > rweight= 0.0100 r= 0.1685 free_r= 0.2128 rms B(bond)= 3.8780 rms
              > B(angle)= 4.7275
              > rweight= 0.0200 r= 0.1685 free_r= 0.2128 rms B(bond)= 3.8205 rms
              > B(angle)= 4.6736
              > rweight= 0.0500 r= 0.1687 free_r= 0.2127 rms B(bond)= 3.5794 rms
              > B(angle)= 4.4422
              > rweight= 0.1000 r= 0.1688 free_r= 0.2126 rms B(bond)= 3.4538 rms
              > B(angle)= 4.3251
              > rweight= 0.2000 r= 0.1691 free_r= 0.2121 rms B(bond)= 3.0403 rms
              > B(angle)= 3.9464
              > rweight= 0.5000 r= 0.1699 free_r= 0.2123 rms B(bond)= 2.5454 rms
              > B(angle)= 3.4242
              > rweight= 1.0000 r= 0.1716 free_r= 0.2127 rms B(bond)= 1.9617 rms
              > B(angle)= 2.7739
              > rweight= 2.0000 r= 0.1734 free_r= 0.2135 rms B(bond)= 1.5863 rms
              > B(angle)= 2.3047
              > rweight= 5.0000 r= 0.1781 free_r= 0.2169 rms B(bond)= 1.0437 rms
              > B(angle)= 1.5197
              >
              > ------> lowest free_r for target "mlf" with rweight= 0.2000 (with wa=
              > 4.41916)
              >
              > The opt_wa output is:
              > ------> initial wa estimate= 0
              >
              > wa= 0.0000 r= 0.1689 free_r= 0.2126 rmsd bonds= 0.000000 rmsd angles=
              > 0.00000
              > wa= 0.0000 r= 0.1688 free_r= 0.2126 rmsd bonds= 0.000000 rmsd angles=
              > 0.00000
              > wa= 0.0000 r= 0.1688 free_r= 0.2126 rmsd bonds= 0.000000 rmsd angles=
              > 0.00000
              > wa= 0.0000 r= 0.1688 free_r= 0.2126 rmsd bonds= 0.000000 rmsd angles=
              > 0.00000
              > wa= 0.0000 r= 0.1688 free_r= 0.2126 rmsd bonds= 0.000000 rmsd angles=
              > 0.00000
              > wa= 0.0000 r= 0.1687 free_r= 0.2126 rmsd bonds= 0.000000 rmsd angles=
              > 0.00000
              > wa= 0.0000 r= 0.1687 free_r= 0.2126 rmsd bonds= 0.000000 rmsd angles=
              > 0.00000
              > wa= 0.0000 r= 0.1686 free_r= 0.2127 rmsd bonds= 0.000000 rmsd angles=
              > 0.00000
              > wa= 0.0000 r= 0.1684 free_r= 0.2128 rmsd bonds= 0.000000 rmsd angles=
              > 0.00000
              > wa= 0.0000 r= 0.1680 free_r= 0.2129 rmsd bonds= 0.000000 rmsd angles=
              > 0.00000
              > wa= 0.0000 r= 0.1675 free_r= 0.2129 rmsd bonds= 0.000000 rmsd angles=
              > 0.00000
              > wa= 0.0000 r= 0.1666 free_r= 0.2131 rmsd bonds= 0.000000 rmsd angles=
              > 0.00000
              >
              > ------> lowest free_r for target mlf with wa= 0
              >
              > ------> The best value for wa is one that produces a low
              > free_r value and also good model geometry. As a general
              > guide, good geometry is indicated by rms deviations from
              > ideal values of less than:
              > bonds -> 0.01 A
              > angles -> 2.00 degrees
              >
              > The rsmds are bad since the planarity of the rings are distorted
              > although R and Rfree are good.
              > Thanks
              > Amit.
              >
              > --- In cnsbb@yahoogroups. com, Ed Pozharski <epozh001@...> wrote:
              > >
              > > Just to verify, you are using the *latest* version, 1.21 (not 1.2)?
              > >
              > > This is really strange. Do both R and Rfree go up when you weaken
              > > restraints? And how high they go? You see, normally you would expect
              > > that with weaker restraints Rfree may go up, but R should go down.
              > > What's the resolution?
              > >
              > > How do the maps look? Can you get anything else refined (which would
              > > indicate that the issue is this particular dataset). If you try
              > other
              > > refinement programs (refmac, phenix), do you still have the problem?
              > >
              > > On Fri, 2010-02-05 at 07:42 +0000, amitd_01 wrote:
              > > >
              > > > Hello everybody,
              > > > When using refine.inp of CNS ver 1.2 the rsmd bonds and angles
              > outputs
              > > > are 0.000 and very low values of wa=2x10-2 and rweight= 0.02
              > resptly.
              > > > Using optimize_wa. inp gives wa=0.0 for all the cycles and
              > > > optimize_rweight. inp gives 0.2 as best value. I recreated a new
              > > > refine.inp and ran it but I get the same result. The R- and R-free
              > are
              > > > near 20%. There are a few anions and metal ions (but used as
              > neutral)
              > > > along with waters and protein chain in the input pdb.
              > > > I had refined with only protein and waters, with and without the
              > ions
              > > > but with no luck. Fixing the wa= 0.3 to 1.5 increases the R- to
              > very
              > > > high values.
              > > > I would appreciate any help to get proper rsmds and wa values.
              > > > Thanks in advance,
              > > > Amit Das.
              > > >
              > > >
              > > >
              > > >
              > > >
              > > --
              > > Edwin Pozharski, PhD, Assistant Professor
              > > University of Maryland, Baltimore
              > > ------------ --------- --------- --------- -------
              > > When the Way is forgotten duty and justice appear;
              > > Then knowledge and wisdom are born along with hypocrisy.
              > > When harmonious relationships dissolve then respect and devotion
              > arise;
              > > When a nation falls to chaos then loyalty and patriotism are born.
              > > ------------ --------- --------- / Lao Tse /
              > >
              >
              >
              >
              >
              > 


              --
              Edwin Pozharski, PhD, Assistant Professor
              University of Maryland, Baltimore
              ------------ --------- --------- --------- -------
              When the Way is forgotten duty and justice appear;
              Then knowledge and wisdom are born along with hypocrisy.
              When harmonious relationships dissolve then respect and devotion arise;
              When a nation falls to chaos then loyalty and patriotism are born.
              ------------ --------- ---------   / Lao Tse /





              -- 
              AMIT DAS, 
              PROTEIN CRYSTALLOGRAPHY SECTION, 
              SOLID STATE PHYSICS DIVISION, BARC, TROMBAY, 
              MUMBAI-400085.
              INDIA.
              Alt E-mail:amitdas@ barc.gov. in
              PHONE:+91-22- 25594688/ 4063
              FAX:+91-22-25505151


              Axel T. Brunger
              Investigator,  Howard Hughes Medical Institute
              Professor of Molecular and Cellular Physiology
              Stanford University

              Email:  brunger@...      
              Phone:  +1 650-736-1031
              Fax:    +1 650-745-1463






            • Ed Pozharski
              OK, this clearly indicates that there is something wrong with the CNS 1.21 binaries that you use. Where did you get them and what OS you are running? ... --
              Message 6 of 11 , Feb 12, 2010
                OK, this clearly indicates that there is something wrong with the CNS
                1.21 binaries that you use. Where did you get them and what OS you are
                running?

                On Thu, 2010-02-11 at 13:53 +0530, AMIT wrote:
                > Yes I was puzzled. I tried the same refinements using CNS 1.1 (I
                > switched to this version now) which works fine gives following pdb
                > output file:
                >
                > REMARK starting r= 0.1854 free_r= 0.2018
                > REMARK final r= 0.1830 free_r= 0.2026
                > REMARK rmsd bonds= 0.008089 rmsd angles= 1.45742 ..........
                > REMARK target= mlf final wa= 0.6668
                > REMARK final rweight= 0.1204 (with wa= 0.6668)
                >
                > Actually the refine.out used earlier says CNS ver 1.2. I assume that
                > refine.inp works for both 1.2 and 1.21 because I created a fresh
                > refine.inp for 1.21 from web and ran but the rsmds are still become
                > 0.000.
                > Actually the same input pdb in refmac 5.5 gives proper rsmds as is now
                > given by CNS 1.1.
                >
                > Regards
                > Amit Das.
                >
                >
                >
                > On Mon, Feb 8, 2010 at 8:29 PM, Ed Pozharski <epozh001@...>
                > wrote:
                > This is obviously abnormal. It's hard to diagnose what the
                > problem is
                > without further details. I assume that your installation of
                > CNS works
                > with other datasets/models, so it's something with the data.
                > If you can
                > send me the data/model I will take a look and will treat this
                > confidentially. Otherwise, consider trying other refinement
                > programs
                > and checking the original data for signs of twinning (although
                > I don't
                > see how twinning can produce this behavior)
                >
                > Ed.
                >
                >
                > On Mon, 2010-02-08 at 04:30 +0000, amitd_01 wrote:
                > >
                > > Yes I am using 1.21 version. Forcing the wa to higher than
                > automatic
                > > value of wa= 7.230911E-02, increases the r and rfree to
                > above 50!
                > >
                > > The opt_rweight output is :
                > > ------> initial rweight estimate= 0.1000
                > >
                > > rweight= 0.0100 r= 0.1685 free_r= 0.2128 rms B(bond)= 3.8780
                > rms
                > > B(angle)= 4.7275
                > > rweight= 0.0200 r= 0.1685 free_r= 0.2128 rms B(bond)= 3.8205
                > rms
                > > B(angle)= 4.6736
                > > rweight= 0.0500 r= 0.1687 free_r= 0.2127 rms B(bond)= 3.5794
                > rms
                > > B(angle)= 4.4422
                > > rweight= 0.1000 r= 0.1688 free_r= 0.2126 rms B(bond)= 3.4538
                > rms
                > > B(angle)= 4.3251
                > > rweight= 0.2000 r= 0.1691 free_r= 0.2121 rms B(bond)= 3.0403
                > rms
                > > B(angle)= 3.9464
                > > rweight= 0.5000 r= 0.1699 free_r= 0.2123 rms B(bond)= 2.5454
                > rms
                > > B(angle)= 3.4242
                > > rweight= 1.0000 r= 0.1716 free_r= 0.2127 rms B(bond)= 1.9617
                > rms
                > > B(angle)= 2.7739
                > > rweight= 2.0000 r= 0.1734 free_r= 0.2135 rms B(bond)= 1.5863
                > rms
                > > B(angle)= 2.3047
                > > rweight= 5.0000 r= 0.1781 free_r= 0.2169 rms B(bond)= 1.0437
                > rms
                > > B(angle)= 1.5197
                > >
                > > ------> lowest free_r for target "mlf" with rweight= 0.2000
                > (with wa=
                > > 4.41916)
                > >
                > > The opt_wa output is:
                > > ------> initial wa estimate= 0
                > >
                > > wa= 0.0000 r= 0.1689 free_r= 0.2126 rmsd bonds= 0.000000
                > rmsd angles=
                > > 0.00000
                > > wa= 0.0000 r= 0.1688 free_r= 0.2126 rmsd bonds= 0.000000
                > rmsd angles=
                > > 0.00000
                > > wa= 0.0000 r= 0.1688 free_r= 0.2126 rmsd bonds= 0.000000
                > rmsd angles=
                > > 0.00000
                > > wa= 0.0000 r= 0.1688 free_r= 0.2126 rmsd bonds= 0.000000
                > rmsd angles=
                > > 0.00000
                > > wa= 0.0000 r= 0.1688 free_r= 0.2126 rmsd bonds= 0.000000
                > rmsd angles=
                > > 0.00000
                > > wa= 0.0000 r= 0.1687 free_r= 0.2126 rmsd bonds= 0.000000
                > rmsd angles=
                > > 0.00000
                > > wa= 0.0000 r= 0.1687 free_r= 0.2126 rmsd bonds= 0.000000
                > rmsd angles=
                > > 0.00000
                > > wa= 0.0000 r= 0.1686 free_r= 0.2127 rmsd bonds= 0.000000
                > rmsd angles=
                > > 0.00000
                > > wa= 0.0000 r= 0.1684 free_r= 0.2128 rmsd bonds= 0.000000
                > rmsd angles=
                > > 0.00000
                > > wa= 0.0000 r= 0.1680 free_r= 0.2129 rmsd bonds= 0.000000
                > rmsd angles=
                > > 0.00000
                > > wa= 0.0000 r= 0.1675 free_r= 0.2129 rmsd bonds= 0.000000
                > rmsd angles=
                > > 0.00000
                > > wa= 0.0000 r= 0.1666 free_r= 0.2131 rmsd bonds= 0.000000
                > rmsd angles=
                > > 0.00000
                > >
                > > ------> lowest free_r for target mlf with wa= 0
                > >
                > > ------> The best value for wa is one that produces a low
                > > free_r value and also good model geometry. As a general
                > > guide, good geometry is indicated by rms deviations from
                > > ideal values of less than:
                > > bonds -> 0.01 A
                > > angles -> 2.00 degrees
                > >
                > > The rsmds are bad since the planarity of the rings are
                > distorted
                > > although R and Rfree are good.
                > > Thanks
                > > Amit.
                > >
                > > --- In cnsbb@yahoogroups.com, Ed Pozharski <epozh001@...>
                > wrote:
                > > >
                > > > Just to verify, you are using the *latest* version, 1.21
                > (not 1.2)?
                > > >
                > > > This is really strange. Do both R and Rfree go up when you
                > weaken
                > > > restraints? And how high they go? You see, normally you
                > would expect
                > > > that with weaker restraints Rfree may go up, but R should
                > go down.
                > > > What's the resolution?
                > > >
                > > > How do the maps look? Can you get anything else refined
                > (which would
                > > > indicate that the issue is this particular dataset). If
                > you try
                > > other
                > > > refinement programs (refmac, phenix), do you still have
                > the problem?
                > > >
                > > > On Fri, 2010-02-05 at 07:42 +0000, amitd_01 wrote:
                > > > >
                > > > > Hello everybody,
                > > > > When using refine.inp of CNS ver 1.2 the rsmd bonds and
                > angles
                > > outputs
                > > > > are 0.000 and very low values of wa=2x10-2 and rweight=
                > 0.02
                > > resptly.
                > > > > Using optimize_wa.inp gives wa=0.0 for all the cycles
                > and
                > > > > optimize_rweight.inp gives 0.2 as best value. I
                > recreated a new
                > > > > refine.inp and ran it but I get the same result. The R-
                > and R-free
                > > are
                > > > > near 20%. There are a few anions and metal ions (but
                > used as
                > > neutral)
                > > > > along with waters and protein chain in the input pdb.
                > > > > I had refined with only protein and waters, with and
                > without the
                > > ions
                > > > > but with no luck. Fixing the wa= 0.3 to 1.5 increases
                > the R- to
                > > very
                > > > > high values.
                > > > > I would appreciate any help to get proper rsmds and wa
                > values.
                > > > > Thanks in advance,
                > > > > Amit Das.
                > > > >
                > > > >
                > > > >
                > > > >
                > > > >
                > > > --
                > > > Edwin Pozharski, PhD, Assistant Professor
                > > > University of Maryland, Baltimore
                > > > ----------------------------------------------
                > > > When the Way is forgotten duty and justice appear;
                > > > Then knowledge and wisdom are born along with hypocrisy.
                > > > When harmonious relationships dissolve then respect and
                > devotion
                > > arise;
                > > > When a nation falls to chaos then loyalty and patriotism
                > are born.
                > > > ------------------------------ / Lao Tse /
                > > >
                > >
                > >
                > >
                > >
                > >
                >
                >
                >
                >
                > --
                > Edwin Pozharski, PhD, Assistant Professor
                > University of Maryland, Baltimore
                > ----------------------------------------------
                > When the Way is forgotten duty and justice appear;
                > Then knowledge and wisdom are born along with hypocrisy.
                > When harmonious relationships dissolve then respect and
                > devotion arise;
                > When a nation falls to chaos then loyalty and patriotism are
                > born.
                > ------------------------------ / Lao Tse /
                >
                >
                >
                >
                >
                >
                > --
                > AMIT DAS,
                > PROTEIN CRYSTALLOGRAPHY SECTION,
                > SOLID STATE PHYSICS DIVISION, BARC, TROMBAY,
                > MUMBAI-400085.
                > INDIA.
                > Alt E-mail:amitdas@...
                > PHONE:+91-22-25594688/4063
                > FAX:+91-22-25505151


                --
                Edwin Pozharski, PhD, Assistant Professor
                University of Maryland, Baltimore
                ----------------------------------------------
                When the Way is forgotten duty and justice appear;
                Then knowledge and wisdom are born along with hypocrisy.
                When harmonious relationships dissolve then respect and devotion arise;
                When a nation falls to chaos then loyalty and patriotism are born.
                ------------------------------ / Lao Tse /
              • AMIT
                CNS is downloaded from the yale website and installed in a linux workstation , ver is RHEL WS4.0. The one which is working fine is CNS ver 1.1 installed on a
                Message 7 of 11 , Feb 13, 2010
                  CNS is downloaded from the yale website and installed in a linux workstation , ver is RHEL WS4.0. The one which is working fine is CNS ver 1.1 installed on a Windows PC having Win XP OS.
                  Thanks
                  Amit.
                   

                   
                  On Sat, Feb 13, 2010 at 3:47 AM, Ed Pozharski <epozh001@...> wrote:
                  OK, this clearly indicates that there is something wrong with the CNS
                  1.21 binaries that you use.  Where did you get them and what OS you are
                  running?

                  On Thu, 2010-02-11 at 13:53 +0530, AMIT wrote:
                  > Yes I was puzzled. I tried the same refinements using CNS 1.1 (I
                  > switched to this version now) which works fine gives following pdb
                  > output file:
                  >
                  > REMARK starting r= 0.1854 free_r= 0.2018
                  > REMARK final    r= 0.1830 free_r= 0.2026
                  > REMARK rmsd bonds= 0.008089  rmsd angles=  1.45742 ..........
                  > REMARK target= mlf  final wa= 0.6668
                  > REMARK final rweight=  0.1204 (with wa= 0.6668)
                  >
                  > Actually the refine.out used earlier says CNS ver 1.2. I assume that
                  > refine.inp works for both 1.2 and 1.21 because I created a fresh
                  > refine.inp for 1.21 from web and ran but the rsmds are still become
                  > 0.000.
                  > Actually the same input pdb in refmac 5.5 gives proper rsmds as is now
                  > given by CNS 1.1.
                  >
                  > Regards
                  > Amit Das.
                  >
                  >
                  >
                  > On Mon, Feb 8, 2010 at 8:29 PM, Ed Pozharski <epozh001@...>
                  > wrote:
                  >         This is obviously abnormal.  It's hard to diagnose what the
                  >         problem is
                  >         without further details.  I assume that your installation of
                  >         CNS works
                  >         with other datasets/models, so it's something with the data.
                  >          If you can
                  >         send me the data/model I will take a look and will treat this
                  >         confidentially.  Otherwise, consider trying other refinement
                  >         programs
                  >         and checking the original data for signs of twinning (although
                  >         I don't
                  >         see how twinning can produce this behavior)
                  >
                  >         Ed.
                  >
                  >
                  >         On Mon, 2010-02-08 at 04:30 +0000, amitd_01 wrote:
                  >         >
                  >         > Yes I am using 1.21 version. Forcing the wa to higher than
                  >         automatic
                  >         > value of wa= 7.230911E-02, increases the r and rfree to
                  >         above 50!
                  >         >
                  >         > The opt_rweight output is :
                  >         > ------> initial rweight estimate= 0.1000
                  >         >
                  >         > rweight= 0.0100 r= 0.1685 free_r= 0.2128 rms B(bond)= 3.8780
                  >         rms
                  >         > B(angle)= 4.7275
                  >         > rweight= 0.0200 r= 0.1685 free_r= 0.2128 rms B(bond)= 3.8205
                  >         rms
                  >         > B(angle)= 4.6736
                  >         > rweight= 0.0500 r= 0.1687 free_r= 0.2127 rms B(bond)= 3.5794
                  >         rms
                  >         > B(angle)= 4.4422
                  >         > rweight= 0.1000 r= 0.1688 free_r= 0.2126 rms B(bond)= 3.4538
                  >         rms
                  >         > B(angle)= 4.3251
                  >         > rweight= 0.2000 r= 0.1691 free_r= 0.2121 rms B(bond)= 3.0403
                  >         rms
                  >         > B(angle)= 3.9464
                  >         > rweight= 0.5000 r= 0.1699 free_r= 0.2123 rms B(bond)= 2.5454
                  >         rms
                  >         > B(angle)= 3.4242
                  >         > rweight= 1.0000 r= 0.1716 free_r= 0.2127 rms B(bond)= 1.9617
                  >         rms
                  >         > B(angle)= 2.7739
                  >         > rweight= 2.0000 r= 0.1734 free_r= 0.2135 rms B(bond)= 1.5863
                  >         rms
                  >         > B(angle)= 2.3047
                  >         > rweight= 5.0000 r= 0.1781 free_r= 0.2169 rms B(bond)= 1.0437
                  >         rms
                  >         > B(angle)= 1.5197
                  >         >
                  >         > ------> lowest free_r for target "mlf" with rweight= 0.2000
                  >         (with wa=
                  >         > 4.41916)
                  >         >
                  >         > The opt_wa output is:
                  >         > ------> initial wa estimate= 0
                  >         >
                  >         > wa= 0.0000 r= 0.1689 free_r= 0.2126 rmsd bonds= 0.000000
                  >         rmsd angles=
                  >         > 0.00000
                  >         > wa= 0.0000 r= 0.1688 free_r= 0.2126 rmsd bonds= 0.000000
                  >         rmsd angles=
                  >         > 0.00000
                  >         > wa= 0.0000 r= 0.1688 free_r= 0.2126 rmsd bonds= 0.000000
                  >         rmsd angles=
                  >         > 0.00000
                  >         > wa= 0.0000 r= 0.1688 free_r= 0.2126 rmsd bonds= 0.000000
                  >         rmsd angles=
                  >         > 0.00000
                  >         > wa= 0.0000 r= 0.1688 free_r= 0.2126 rmsd bonds= 0.000000
                  >         rmsd angles=
                  >         > 0.00000
                  >         > wa= 0.0000 r= 0.1687 free_r= 0.2126 rmsd bonds= 0.000000
                  >         rmsd angles=
                  >         > 0.00000
                  >         > wa= 0.0000 r= 0.1687 free_r= 0.2126 rmsd bonds= 0.000000
                  >         rmsd angles=
                  >         > 0.00000
                  >         > wa= 0.0000 r= 0.1686 free_r= 0.2127 rmsd bonds= 0.000000
                  >         rmsd angles=
                  >         > 0.00000
                  >         > wa= 0.0000 r= 0.1684 free_r= 0.2128 rmsd bonds= 0.000000
                  >         rmsd angles=
                  >         > 0.00000
                  >         > wa= 0.0000 r= 0.1680 free_r= 0.2129 rmsd bonds= 0.000000
                  >         rmsd angles=
                  >         > 0.00000
                  >         > wa= 0.0000 r= 0.1675 free_r= 0.2129 rmsd bonds= 0.000000
                  >         rmsd angles=
                  >         > 0.00000
                  >         > wa= 0.0000 r= 0.1666 free_r= 0.2131 rmsd bonds= 0.000000
                  >         rmsd angles=
                  >         > 0.00000
                  >         >
                  >         > ------> lowest free_r for target mlf with wa= 0
                  >         >
                  >         > ------> The best value for wa is one that produces a low
                  >         > free_r value and also good model geometry. As a general
                  >         > guide, good geometry is indicated by rms deviations from
                  >         > ideal values of less than:
                  >         > bonds -> 0.01 A
                  >         > angles -> 2.00 degrees
                  >         >
                  >         > The rsmds are bad since the planarity of the rings are
                  >         distorted
                  >         > although R and Rfree are good.
                  >         > Thanks
                  >         > Amit.
                  >         >
                  >         > --- In cnsbb@yahoogroups.com, Ed Pozharski <epozh001@...>
                  >         wrote:
                  >         > >
                  >         > > Just to verify, you are using the *latest* version, 1.21
                  >         (not 1.2)?
                  >         > >
                  >         > > This is really strange. Do both R and Rfree go up when you
                  >         weaken
                  >         > > restraints? And how high they go? You see, normally you
                  >         would expect
                  >         > > that with weaker restraints Rfree may go up, but R should
                  >         go down.
                  >         > > What's the resolution?
                  >         > >
                  >         > > How do the maps look? Can you get anything else refined
                  >         (which would
                  >         > > indicate that the issue is this particular dataset). If
                  >         you try
                  >         > other
                  >         > > refinement programs (refmac, phenix), do you still have
                  >         the problem?
                  >         > >
                  >         > > On Fri, 2010-02-05 at 07:42 +0000, amitd_01 wrote:
                  >         > > >
                  >         > > > Hello everybody,
                  >         > > > When using refine.inp of CNS ver 1.2 the rsmd bonds and
                  >         angles
                  >         > outputs
                  >         > > > are 0.000 and very low values of wa=2x10-2 and rweight=
                  >         0.02
                  >         > resptly.
                  >         > > > Using optimize_wa.inp gives wa=0.0 for all the cycles
                  >         and
                  >         > > > optimize_rweight.inp gives 0.2 as best value. I
                  >         recreated a new
                  >         > > > refine.inp and ran it but I get the same result. The R-
                  >         and R-free
                  >         > are
                  >         > > > near 20%. There are a few anions and metal ions (but
                  >         used as
                  >         > neutral)
                  >         > > > along with waters and protein chain in the input pdb.
                  >         > > > I had refined with only protein and waters, with and
                  >         without the
                  >         > ions
                  >         > > > but with no luck. Fixing the wa= 0.3 to 1.5 increases
                  >         the R- to
                  >         > very
                  >         > > > high values.
                  >         > > > I would appreciate any help to get proper rsmds and wa
                  >         values.
                  >         > > > Thanks in advance,
                  >         > > > Amit Das.
                  >         > > >
                  >         > > >
                  >         > > >
                  >         > > >
                  >         > > >
                  >         > > --
                  >         > > Edwin Pozharski, PhD, Assistant Professor
                  >         > > University of Maryland, Baltimore
                  >         > > ----------------------------------------------
                  >         > > When the Way is forgotten duty and justice appear;
                  >         > > Then knowledge and wisdom are born along with hypocrisy.
                  >         > > When harmonious relationships dissolve then respect and
                  >         devotion
                  >         > arise;
                  >         > > When a nation falls to chaos then loyalty and patriotism
                  >         are born.
                  >         > > ------------------------------ / Lao Tse /
                  >         > >
                  >         >
                  >         >
                  >         >
                  >         >
                  >         >
                  >
                  >
                  >
                  >
                  >         --
                  >         Edwin Pozharski, PhD, Assistant Professor
                  >         University of Maryland, Baltimore
                  >         ----------------------------------------------
                  >         When the Way is forgotten duty and justice appear;
                  >         Then knowledge and wisdom are born along with hypocrisy.
                  >         When harmonious relationships dissolve then respect and
                  >         devotion arise;
                  >         When a nation falls to chaos then loyalty and patriotism are
                  >         born.
                  >         ------------------------------   / Lao Tse /
                  >
                  >
                  >
                  >
                  >
                  >
                  > --
                  > AMIT DAS,
                  > PROTEIN CRYSTALLOGRAPHY SECTION,
                  > SOLID STATE PHYSICS DIVISION, BARC, TROMBAY,
                  > MUMBAI-400085.
                  > INDIA.
                  > Alt E-mail:amitdas@...
                  > PHONE:+91-22-25594688/4063
                  > FAX:+91-22-25505151


                  --
                  Edwin Pozharski, PhD, Assistant Professor
                  University of Maryland, Baltimore
                  ----------------------------------------------
                  When the Way is forgotten duty and justice appear;
                  Then knowledge and wisdom are born along with hypocrisy.
                  When harmonious relationships dissolve then respect and devotion arise;
                  When a nation falls to chaos then loyalty and patriotism are born.
                  ------------------------------   / Lao Tse /





                  --
                  AMIT DAS,
                  PROTEIN CRYSTALLOGRAPHY SECTION,
                  SOLID STATE PHYSICS DIVISION, BARC, TROMBAY,
                  MUMBAI-400085.
                  INDIA.
                  Alt E-mail:amitdas@...
                  PHONE:+91-22-25594688/4063
                  FAX:+91-22-25505151
                • Axel Brunger
                  Please try the pre-compiled linux binary (follow instructions in the Installation section of the cns website). Axel Brunger ... Axel T. Brunger Investigator,
                  Message 8 of 11 , Feb 13, 2010
                    Please try the pre-compiled linux binary (follow
                    instructions in the Installation section of the
                    cns website).

                    Axel Brunger

                    On Feb 13, 2010, at 5:57 AM, AMIT wrote:


                    CNS is downloaded from the yale website and installed in a linux workstation , ver is RHEL WS4.0. The one which is working fine is CNS ver 1.1 installed on a Windows PC having Win XP OS.
                    Thanks
                    Amit.
                     

                     
                    On Sat, Feb 13, 2010 at 3:47 AM, Ed Pozharski <epozh001@umaryland. edu> wrote:
                    OK, this clearly indicates that there is something wrong with the CNS
                    1.21 binaries that you use.  Where did you get them and what OS you are
                    running?

                    On Thu, 2010-02-11 at 13:53 +0530, AMIT wrote:
                    > Yes I was puzzled. I tried the same refinements using CNS 1.1 (I
                    > switched to this version now) which works fine gives following pdb
                    > output file:
                    >
                    > REMARK starting r= 0.1854 free_r= 0.2018
                    > REMARK final    r= 0.1830 free_r= 0.2026
                    > REMARK rmsd bonds= 0.008089  rmsd angles=  1.45742 ..........
                    > REMARK target= mlf  final wa= 0.6668
                    > REMARK final rweight=  0.1204 (with wa= 0.6668)
                    >
                    > Actually the refine.out used earlier says CNS ver 1.2. I assume that
                    > refine.inp works for both 1.2 and 1.21 because I created a fresh
                    > refine.inp for 1.21 from web and ran but the rsmds are still become
                    > 0.000.
                    > Actually the same input pdb in refmac 5.5 gives proper rsmds as is now
                    > given by CNS 1.1.
                    >
                    > Regards
                    > Amit Das.
                    >
                    >
                    >
                    > On Mon, Feb 8, 2010 at 8:29 PM, Ed Pozharski <epozh001@umaryland. edu>
                    > wrote:
                    >         This is obviously abnormal.  It's hard to diagnose what the
                    >         problem is
                    >         without further details.  I assume that your installation of
                    >         CNS works
                    >         with other datasets/models, so it's something with the data.
                    >          If you can
                    >         send me the data/model I will take a look and will treat this
                    >         confidentially.  Otherwise, consider trying other refinement
                    >         programs
                    >         and checking the original data for signs of twinning (although
                    >         I don't
                    >         see how twinning can produce this behavior)
                    >
                    >         Ed.
                    >
                    >
                    >         On Mon, 2010-02-08 at 04:30 +0000, amitd_01 wrote:
                    >         >
                    >         > Yes I am using 1.21 version. Forcing the wa to higher than
                    >         automatic
                    >         > value of wa= 7.230911E-02, increases the r and rfree to
                    >         above 50!
                    >         >
                    >         > The opt_rweight output is :
                    >         > ------> initial rweight estimate= 0.1000
                    >         >
                    >         > rweight= 0.0100 r= 0.1685 free_r= 0.2128 rms B(bond)= 3.8780
                    >         rms
                    >         > B(angle)= 4.7275
                    >         > rweight= 0.0200 r= 0.1685 free_r= 0.2128 rms B(bond)= 3.8205
                    >         rms
                    >         > B(angle)= 4.6736
                    >         > rweight= 0.0500 r= 0.1687 free_r= 0.2127 rms B(bond)= 3.5794
                    >         rms
                    >         > B(angle)= 4.4422
                    >         > rweight= 0.1000 r= 0.1688 free_r= 0.2126 rms B(bond)= 3.4538
                    >         rms
                    >         > B(angle)= 4.3251
                    >         > rweight= 0.2000 r= 0.1691 free_r= 0.2121 rms B(bond)= 3.0403
                    >         rms
                    >         > B(angle)= 3.9464
                    >         > rweight= 0.5000 r= 0.1699 free_r= 0.2123 rms B(bond)= 2.5454
                    >         rms
                    >         > B(angle)= 3.4242
                    >         > rweight= 1.0000 r= 0.1716 free_r= 0.2127 rms B(bond)= 1.9617
                    >         rms
                    >         > B(angle)= 2.7739
                    >         > rweight= 2.0000 r= 0.1734 free_r= 0.2135 rms B(bond)= 1.5863
                    >         rms
                    >         > B(angle)= 2.3047
                    >         > rweight= 5.0000 r= 0.1781 free_r= 0.2169 rms B(bond)= 1.0437
                    >         rms
                    >         > B(angle)= 1.5197
                    >         >
                    >         > ------> lowest free_r for target "mlf" with rweight= 0.2000
                    >         (with wa=
                    >         > 4.41916)
                    >         >
                    >         > The opt_wa output is:
                    >         > ------> initial wa estimate= 0
                    >         >
                    >         > wa= 0.0000 r= 0.1689 free_r= 0.2126 rmsd bonds= 0.000000
                    >         rmsd angles=
                    >         > 0.00000
                    >         > wa= 0.0000 r= 0.1688 free_r= 0.2126 rmsd bonds= 0.000000
                    >         rmsd angles=
                    >         > 0.00000
                    >         > wa= 0.0000 r= 0.1688 free_r= 0.2126 rmsd bonds= 0.000000
                    >         rmsd angles=
                    >         > 0.00000
                    >         > wa= 0.0000 r= 0.1688 free_r= 0.2126 rmsd bonds= 0.000000
                    >         rmsd angles=
                    >         > 0.00000
                    >         > wa= 0.0000 r= 0.1688 free_r= 0.2126 rmsd bonds= 0.000000
                    >         rmsd angles=
                    >         > 0.00000
                    >         > wa= 0.0000 r= 0.1687 free_r= 0.2126 rmsd bonds= 0.000000
                    >         rmsd angles=
                    >         > 0.00000
                    >         > wa= 0.0000 r= 0.1687 free_r= 0.2126 rmsd bonds= 0.000000
                    >         rmsd angles=
                    >         > 0.00000
                    >         > wa= 0.0000 r= 0.1686 free_r= 0.2127 rmsd bonds= 0.000000
                    >         rmsd angles=
                    >         > 0.00000
                    >         > wa= 0.0000 r= 0.1684 free_r= 0.2128 rmsd bonds= 0.000000
                    >         rmsd angles=
                    >         > 0.00000
                    >         > wa= 0.0000 r= 0.1680 free_r= 0.2129 rmsd bonds= 0.000000
                    >         rmsd angles=
                    >         > 0.00000
                    >         > wa= 0.0000 r= 0.1675 free_r= 0.2129 rmsd bonds= 0.000000
                    >         rmsd angles=
                    >         > 0.00000
                    >         > wa= 0.0000 r= 0.1666 free_r= 0.2131 rmsd bonds= 0.000000
                    >         rmsd angles=
                    >         > 0.00000
                    >         >
                    >         > ------> lowest free_r for target mlf with wa= 0
                    >         >
                    >         > ------> The best value for wa is one that produces a low
                    >         > free_r value and also good model geometry. As a general
                    >         > guide, good geometry is indicated by rms deviations from
                    >         > ideal values of less than:
                    >         > bonds -> 0.01 A
                    >         > angles -> 2.00 degrees
                    >         >
                    >         > The rsmds are bad since the planarity of the rings are
                    >         distorted
                    >         > although R and Rfree are good.
                    >         > Thanks
                    >         > Amit.
                    >         >
                    >         > --- In cnsbb@yahoogroups. com, Ed Pozharski <epozh001@...>
                    >         wrote:
                    >         > >
                    >         > > Just to verify, you are using the *latest* version, 1.21
                    >         (not 1.2)?
                    >         > >
                    >         > > This is really strange. Do both R and Rfree go up when you
                    >         weaken
                    >         > > restraints? And how high they go? You see, normally you
                    >         would expect
                    >         > > that with weaker restraints Rfree may go up, but R should
                    >         go down.
                    >         > > What's the resolution?
                    >         > >
                    >         > > How do the maps look? Can you get anything else refined
                    >         (which would
                    >         > > indicate that the issue is this particular dataset). If
                    >         you try
                    >         > other
                    >         > > refinement programs (refmac, phenix), do you still have
                    >         the problem?
                    >         > >
                    >         > > On Fri, 2010-02-05 at 07:42 +0000, amitd_01 wrote:
                    >         > > >
                    >         > > > Hello everybody,
                    >         > > > When using refine.inp of CNS ver 1.2 the rsmd bonds and
                    >         angles
                    >         > outputs
                    >         > > > are 0.000 and very low values of wa=2x10-2 and rweight=
                    >         0.02
                    >         > resptly.
                    >         > > > Using optimize_wa. inp gives wa=0.0 for all the cycles
                    >         and
                    >         > > > optimize_rweight. inp gives 0.2 as best value. I
                    >         recreated a new
                    >         > > > refine.inp and ran it but I get the same result. The R-
                    >         and R-free
                    >         > are
                    >         > > > near 20%. There are a few anions and metal ions (but
                    >         used as
                    >         > neutral)
                    >         > > > along with waters and protein chain in the input pdb.
                    >         > > > I had refined with only protein and waters, with and
                    >         without the
                    >         > ions
                    >         > > > but with no luck. Fixing the wa= 0.3 to 1.5 increases
                    >         the R- to
                    >         > very
                    >         > > > high values.
                    >         > > > I would appreciate any help to get proper rsmds and wa
                    >         values.
                    >         > > > Thanks in advance,
                    >         > > > Amit Das.
                    >         > > >
                    >         > > >
                    >         > > >
                    >         > > >
                    >         > > >
                    >         > > --
                    >         > > Edwin Pozharski, PhD, Assistant Professor
                    >         > > University of Maryland, Baltimore
                    >         > > ------------ --------- --------- --------- -------
                    >         > > When the Way is forgotten duty and justice appear;
                    >         > > Then knowledge and wisdom are born along with hypocrisy.
                    >         > > When harmonious relationships dissolve then respect and
                    >         devotion
                    >         > arise;
                    >         > > When a nation falls to chaos then loyalty and patriotism
                    >         are born.
                    >         > > ------------ --------- --------- / Lao Tse /
                    >         > >
                    >         >
                    >         >
                    >         >
                    >         >
                    >         > 
                    >
                    >
                    >
                    >
                    >         --
                    >         Edwin Pozharski, PhD, Assistant Professor
                    >         University of Maryland, Baltimore
                    >         ------------ --------- --------- --------- -------
                    >         When the Way is forgotten duty and justice appear;
                    >         Then knowledge and wisdom are born along with hypocrisy.
                    >         When harmonious relationships dissolve then respect and
                    >         devotion arise;
                    >         When a nation falls to chaos then loyalty and patriotism are
                    >         born.
                    >         ------------ --------- ---------   / Lao Tse /
                    >
                    >
                    >
                    >
                    >
                    >
                    > --
                    > AMIT DAS,
                    > PROTEIN CRYSTALLOGRAPHY SECTION,
                    > SOLID STATE PHYSICS DIVISION, BARC, TROMBAY,
                    > MUMBAI-400085.
                    > INDIA.
                    > Alt E-mail:amitdas@ barc.gov. in
                    > PHONE:+91-22- 25594688/ 4063
                    > FAX:+91-22-25505151


                    --
                    Edwin Pozharski, PhD, Assistant Professor
                    University of Maryland, Baltimore
                    ------------ --------- --------- --------- -------
                    When the Way is forgotten duty and justice appear;
                    Then knowledge and wisdom are born along with hypocrisy.
                    When harmonious relationships dissolve then respect and devotion arise;
                    When a nation falls to chaos then loyalty and patriotism are born.
                    ------------ --------- ---------   / Lao Tse /





                    -- 
                    AMIT DAS, 
                    PROTEIN CRYSTALLOGRAPHY SECTION, 
                    SOLID STATE PHYSICS DIVISION, BARC, TROMBAY, 
                    MUMBAI-400085.
                    INDIA.
                    Alt E-mail:amitdas@ barc.gov. in
                    PHONE:+91-22- 25594688/ 4063
                    FAX:+91-22-25505151


                    Axel T. Brunger
                    Investigator,  Howard Hughes Medical Institute
                    Professor of Molecular and Cellular Physiology
                    Stanford University

                    Email:  brunger@...      
                    Phone:  +1 650-736-1031
                    Fax:    +1 650-745-1463








                    Axel T. Brunger
                    Investigator,  Howard Hughes Medical Institute
                    Professor of Molecular and Cellular Physiology
                    Stanford University

                    Email:  brunger@...      
                    Phone:  +1 650-736-1031
                    Fax:    +1 650-745-1463






                  • Ed Pozharski
                    Hmm... Is your Linux OS 64-bit or 32-bit? Did you compile your own binaries or used pre-compiled ones? On a side note, I highly recommend the parallel
                    Message 9 of 11 , Feb 13, 2010
                      Hmm... Is your Linux OS 64-bit or 32-bit? Did you compile your own
                      binaries or used pre-compiled ones? On a side note, I highly recommend
                      the parallel binaries, great if you have dual or quad processor.

                      On Sat, 2010-02-13 at 19:27 +0530, AMIT wrote:
                      >
                      > CNS is downloaded from the yale website and installed in a linux
                      > workstation , ver is RHEL WS4.0. The one which is working fine is CNS
                      > ver 1.1 installed on a Windows PC having Win XP OS.
                      > Thanks
                      > Amit.
                      >
                      >
                      >
                      > On Sat, Feb 13, 2010 at 3:47 AM, Ed Pozharski <epozh001@...>
                      > wrote:
                      > OK, this clearly indicates that there is something wrong with
                      > the CNS
                      > 1.21 binaries that you use. Where did you get them and what
                      > OS you are
                      > running?
                      >
                      >
                      > On Thu, 2010-02-11 at 13:53 +0530, AMIT wrote:
                      > > Yes I was puzzled. I tried the same refinements using CNS
                      > 1.1 (I
                      > > switched to this version now) which works fine gives
                      > following pdb
                      > > output file:
                      > >
                      > > REMARK starting r= 0.1854 free_r= 0.2018
                      > > REMARK final r= 0.1830 free_r= 0.2026
                      > > REMARK rmsd bonds= 0.008089 rmsd angles=
                      > 1.45742 ..........
                      > > REMARK target= mlf final wa= 0.6668
                      > > REMARK final rweight= 0.1204 (with wa= 0.6668)
                      > >
                      > > Actually the refine.out used earlier says CNS ver 1.2. I
                      > assume that
                      > > refine.inp works for both 1.2 and 1.21 because I created a
                      > fresh
                      > > refine.inp for 1.21 from web and ran but the rsmds are still
                      > become
                      > > 0.000.
                      > > Actually the same input pdb in refmac 5.5 gives proper rsmds
                      > as is now
                      > > given by CNS 1.1.
                      > >
                      > > Regards
                      > > Amit Das.
                      > >
                      > >
                      > >
                      > > On Mon, Feb 8, 2010 at 8:29 PM, Ed Pozharski
                      > <epozh001@...>
                      > > wrote:
                      > > This is obviously abnormal. It's hard to diagnose
                      > what the
                      > > problem is
                      > > without further details. I assume that your
                      > installation of
                      > > CNS works
                      > > with other datasets/models, so it's something with
                      > the data.
                      > > If you can
                      > > send me the data/model I will take a look and will
                      > treat this
                      > > confidentially. Otherwise, consider trying other
                      > refinement
                      > > programs
                      > > and checking the original data for signs of twinning
                      > (although
                      > > I don't
                      > > see how twinning can produce this behavior)
                      > >
                      > > Ed.
                      > >
                      > >
                      > > On Mon, 2010-02-08 at 04:30 +0000, amitd_01 wrote:
                      > > >
                      > > > Yes I am using 1.21 version. Forcing the wa to
                      > higher than
                      > > automatic
                      > > > value of wa= 7.230911E-02, increases the r and
                      > rfree to
                      > > above 50!
                      > > >
                      > > > The opt_rweight output is :
                      > > > ------> initial rweight estimate= 0.1000
                      > > >
                      > > > rweight= 0.0100 r= 0.1685 free_r= 0.2128 rms
                      > B(bond)= 3.8780
                      > > rms
                      > > > B(angle)= 4.7275
                      > > > rweight= 0.0200 r= 0.1685 free_r= 0.2128 rms
                      > B(bond)= 3.8205
                      > > rms
                      > > > B(angle)= 4.6736
                      > > > rweight= 0.0500 r= 0.1687 free_r= 0.2127 rms
                      > B(bond)= 3.5794
                      > > rms
                      > > > B(angle)= 4.4422
                      > > > rweight= 0.1000 r= 0.1688 free_r= 0.2126 rms
                      > B(bond)= 3.4538
                      > > rms
                      > > > B(angle)= 4.3251
                      > > > rweight= 0.2000 r= 0.1691 free_r= 0.2121 rms
                      > B(bond)= 3.0403
                      > > rms
                      > > > B(angle)= 3.9464
                      > > > rweight= 0.5000 r= 0.1699 free_r= 0.2123 rms
                      > B(bond)= 2.5454
                      > > rms
                      > > > B(angle)= 3.4242
                      > > > rweight= 1.0000 r= 0.1716 free_r= 0.2127 rms
                      > B(bond)= 1.9617
                      > > rms
                      > > > B(angle)= 2.7739
                      > > > rweight= 2.0000 r= 0.1734 free_r= 0.2135 rms
                      > B(bond)= 1.5863
                      > > rms
                      > > > B(angle)= 2.3047
                      > > > rweight= 5.0000 r= 0.1781 free_r= 0.2169 rms
                      > B(bond)= 1.0437
                      > > rms
                      > > > B(angle)= 1.5197
                      > > >
                      > > > ------> lowest free_r for target "mlf" with
                      > rweight= 0.2000
                      > > (with wa=
                      > > > 4.41916)
                      > > >
                      > > > The opt_wa output is:
                      > > > ------> initial wa estimate= 0
                      > > >
                      > > > wa= 0.0000 r= 0.1689 free_r= 0.2126 rmsd bonds=
                      > 0.000000
                      > > rmsd angles=
                      > > > 0.00000
                      > > > wa= 0.0000 r= 0.1688 free_r= 0.2126 rmsd bonds=
                      > 0.000000
                      > > rmsd angles=
                      > > > 0.00000
                      > > > wa= 0.0000 r= 0.1688 free_r= 0.2126 rmsd bonds=
                      > 0.000000
                      > > rmsd angles=
                      > > > 0.00000
                      > > > wa= 0.0000 r= 0.1688 free_r= 0.2126 rmsd bonds=
                      > 0.000000
                      > > rmsd angles=
                      > > > 0.00000
                      > > > wa= 0.0000 r= 0.1688 free_r= 0.2126 rmsd bonds=
                      > 0.000000
                      > > rmsd angles=
                      > > > 0.00000
                      > > > wa= 0.0000 r= 0.1687 free_r= 0.2126 rmsd bonds=
                      > 0.000000
                      > > rmsd angles=
                      > > > 0.00000
                      > > > wa= 0.0000 r= 0.1687 free_r= 0.2126 rmsd bonds=
                      > 0.000000
                      > > rmsd angles=
                      > > > 0.00000
                      > > > wa= 0.0000 r= 0.1686 free_r= 0.2127 rmsd bonds=
                      > 0.000000
                      > > rmsd angles=
                      > > > 0.00000
                      > > > wa= 0.0000 r= 0.1684 free_r= 0.2128 rmsd bonds=
                      > 0.000000
                      > > rmsd angles=
                      > > > 0.00000
                      > > > wa= 0.0000 r= 0.1680 free_r= 0.2129 rmsd bonds=
                      > 0.000000
                      > > rmsd angles=
                      > > > 0.00000
                      > > > wa= 0.0000 r= 0.1675 free_r= 0.2129 rmsd bonds=
                      > 0.000000
                      > > rmsd angles=
                      > > > 0.00000
                      > > > wa= 0.0000 r= 0.1666 free_r= 0.2131 rmsd bonds=
                      > 0.000000
                      > > rmsd angles=
                      > > > 0.00000
                      > > >
                      > > > ------> lowest free_r for target mlf with wa= 0
                      > > >
                      > > > ------> The best value for wa is one that produces
                      > a low
                      > > > free_r value and also good model geometry. As a
                      > general
                      > > > guide, good geometry is indicated by rms
                      > deviations from
                      > > > ideal values of less than:
                      > > > bonds -> 0.01 A
                      > > > angles -> 2.00 degrees
                      > > >
                      > > > The rsmds are bad since the planarity of the rings
                      > are
                      > > distorted
                      > > > although R and Rfree are good.
                      > > > Thanks
                      > > > Amit.
                      > > >
                      > > > --- In cnsbb@yahoogroups.com, Ed Pozharski
                      > <epozh001@...>
                      > > wrote:
                      > > > >
                      > > > > Just to verify, you are using the *latest*
                      > version, 1.21
                      > > (not 1.2)?
                      > > > >
                      > > > > This is really strange. Do both R and Rfree go
                      > up when you
                      > > weaken
                      > > > > restraints? And how high they go? You see,
                      > normally you
                      > > would expect
                      > > > > that with weaker restraints Rfree may go up, but
                      > R should
                      > > go down.
                      > > > > What's the resolution?
                      > > > >
                      > > > > How do the maps look? Can you get anything else
                      > refined
                      > > (which would
                      > > > > indicate that the issue is this particular
                      > dataset). If
                      > > you try
                      > > > other
                      > > > > refinement programs (refmac, phenix), do you
                      > still have
                      > > the problem?
                      > > > >
                      > > > > On Fri, 2010-02-05 at 07:42 +0000, amitd_01
                      > wrote:
                      > > > > >
                      > > > > > Hello everybody,
                      > > > > > When using refine.inp of CNS ver 1.2 the rsmd
                      > bonds and
                      > > angles
                      > > > outputs
                      > > > > > are 0.000 and very low values of wa=2x10-2 and
                      > rweight=
                      > > 0.02
                      > > > resptly.
                      > > > > > Using optimize_wa.inp gives wa=0.0 for all the
                      > cycles
                      > > and
                      > > > > > optimize_rweight.inp gives 0.2 as best value.
                      > I
                      > > recreated a new
                      > > > > > refine.inp and ran it but I get the same
                      > result. The R-
                      > > and R-free
                      > > > are
                      > > > > > near 20%. There are a few anions and metal
                      > ions (but
                      > > used as
                      > > > neutral)
                      > > > > > along with waters and protein chain in the
                      > input pdb.
                      > > > > > I had refined with only protein and waters,
                      > with and
                      > > without the
                      > > > ions
                      > > > > > but with no luck. Fixing the wa= 0.3 to 1.5
                      > increases
                      > > the R- to
                      > > > very
                      > > > > > high values.
                      > > > > > I would appreciate any help to get proper
                      > rsmds and wa
                      > > values.
                      > > > > > Thanks in advance,
                      > > > > > Amit Das.
                      > > > > >
                      > > > > >
                      > > > > >
                      > > > > >
                      > > > > >
                      > > > > --
                      > > > > Edwin Pozharski, PhD, Assistant Professor
                      > > > > University of Maryland, Baltimore
                      > > > > ----------------------------------------------
                      > > > > When the Way is forgotten duty and justice
                      > appear;
                      > > > > Then knowledge and wisdom are born along with
                      > hypocrisy.
                      > > > > When harmonious relationships dissolve then
                      > respect and
                      > > devotion
                      > > > arise;
                      > > > > When a nation falls to chaos then loyalty and
                      > patriotism
                      > > are born.
                      > > > > ------------------------------ / Lao Tse /
                      > > > >
                      > > >
                      > > >
                      > > >
                      > > >
                      > > >
                      > >
                      > >
                      > >
                      > >
                      > > --
                      > > Edwin Pozharski, PhD, Assistant Professor
                      > > University of Maryland, Baltimore
                      > > ----------------------------------------------
                      > > When the Way is forgotten duty and justice appear;
                      > > Then knowledge and wisdom are born along with
                      > hypocrisy.
                      > > When harmonious relationships dissolve then respect
                      > and
                      > > devotion arise;
                      > > When a nation falls to chaos then loyalty and
                      > patriotism are
                      > > born.
                      > > ------------------------------ / Lao Tse /
                      > >
                      > >
                      > >
                      > >
                      > >
                      > >
                      > > --
                      > > AMIT DAS,
                      > > PROTEIN CRYSTALLOGRAPHY SECTION,
                      > > SOLID STATE PHYSICS DIVISION, BARC, TROMBAY,
                      > > MUMBAI-400085.
                      > > INDIA.
                      > > Alt E-mail:amitdas@...
                      > > PHONE:+91-22-25594688/4063
                      > > FAX:+91-22-25505151
                      >
                      >
                      >
                      > --
                      >
                      > Edwin Pozharski, PhD, Assistant Professor
                      > University of Maryland, Baltimore
                      > ----------------------------------------------
                      > When the Way is forgotten duty and justice appear;
                      > Then knowledge and wisdom are born along with hypocrisy.
                      > When harmonious relationships dissolve then respect and
                      > devotion arise;
                      > When a nation falls to chaos then loyalty and patriotism are
                      > born.
                      > ------------------------------ / Lao Tse /
                      >
                      >
                      >
                      >
                      >
                      >
                      > --
                      > AMIT DAS,
                      > PROTEIN CRYSTALLOGRAPHY SECTION,
                      > SOLID STATE PHYSICS DIVISION, BARC, TROMBAY,
                      > MUMBAI-400085.
                      > INDIA.
                      > Alt E-mail:amitdas@...
                      > PHONE:+91-22-25594688/4063
                      > FAX:+91-22-25505151
                      >
                      >
                      >
                      >
                      --
                      Edwin Pozharski, PhD, Assistant Professor
                      University of Maryland, Baltimore
                      ----------------------------------------------
                      When the Way is forgotten duty and justice appear;
                      Then knowledge and wisdom are born along with hypocrisy.
                      When harmonious relationships dissolve then respect and devotion arise;
                      When a nation falls to chaos then loyalty and patriotism are born.
                      ------------------------------ / Lao Tse /
                    • AMIT
                      The linux OS is a 64-bit one. CNS was compiled on the machine. We have Xeon dual core processors. I will download the mp version and install it now to solve
                      Message 10 of 11 , Feb 14, 2010
                        The linux OS is a 64-bit one. CNS was compiled on the machine. We have Xeon dual core processors. I will download the mp version and install it now to solve the problem!

                        Is there any possiblity that CNS 1.21 will be available also for Win XP/ Win 7?

                        Thanks for the response,
                        Amit.

                        On Sun, Feb 14, 2010 at 12:45 PM, Ed Pozharski <epozh001@...> wrote:
                        Hmm... Is your Linux OS 64-bit or 32-bit?  Did you compile your own
                        binaries or used pre-compiled ones?  On a side note, I highly recommend
                        the parallel binaries, great if you have dual or quad processor.

                        On Sat, 2010-02-13 at 19:27 +0530, AMIT wrote:
                        >
                        > CNS is downloaded from the yale website and installed in a linux
                        > workstation , ver is RHEL WS4.0. The one which is working fine is CNS
                        > ver 1.1 installed on a Windows PC having Win XP OS.
                        > Thanks
                        > Amit.
                        >
                        >
                        >
                        > On Sat, Feb 13, 2010 at 3:47 AM, Ed Pozharski <epozh001@...>
                        > wrote:
                        >         OK, this clearly indicates that there is something wrong with
                        >         the CNS
                        >         1.21 binaries that you use.  Where did you get them and what
                        >         OS you are
                        >         running?
                        >
                        >
                        >         On Thu, 2010-02-11 at 13:53 +0530, AMIT wrote:
                        >         > Yes I was puzzled. I tried the same refinements using CNS
                        >         1.1 (I
                        >         > switched to this version now) which works fine gives
                        >         following pdb
                        >         > output file:
                        >         >
                        >         > REMARK starting r= 0.1854 free_r= 0.2018
                        >         > REMARK final    r= 0.1830 free_r= 0.2026
                        >         > REMARK rmsd bonds= 0.008089  rmsd angles=
                        >          1.45742 ..........
                        >         > REMARK target= mlf  final wa= 0.6668
                        >         > REMARK final rweight=  0.1204 (with wa= 0.6668)
                        >         >
                        >         > Actually the refine.out used earlier says CNS ver 1.2. I
                        >         assume that
                        >         > refine.inp works for both 1.2 and 1.21 because I created a
                        >         fresh
                        >         > refine.inp for 1.21 from web and ran but the rsmds are still
                        >         become
                        >         > 0.000.
                        >         > Actually the same input pdb in refmac 5.5 gives proper rsmds
                        >         as is now
                        >         > given by CNS 1.1.
                        >         >
                        >         > Regards
                        >         > Amit Das.
                        >         >
                        >         >
                        >         >
                        >         > On Mon, Feb 8, 2010 at 8:29 PM, Ed Pozharski
                        >         <epozh001@...>
                        >         > wrote:
                        >         >         This is obviously abnormal.  It's hard to diagnose
                        >         what the
                        >         >         problem is
                        >         >         without further details.  I assume that your
                        >         installation of
                        >         >         CNS works
                        >         >         with other datasets/models, so it's something with
                        >         the data.
                        >         >          If you can
                        >         >         send me the data/model I will take a look and will
                        >         treat this
                        >         >         confidentially.  Otherwise, consider trying other
                        >         refinement
                        >         >         programs
                        >         >         and checking the original data for signs of twinning
                        >         (although
                        >         >         I don't
                        >         >         see how twinning can produce this behavior)
                        >         >
                        >         >         Ed.
                        >         >
                        >         >
                        >         >         On Mon, 2010-02-08 at 04:30 +0000, amitd_01 wrote:
                        >         >         >
                        >         >         > Yes I am using 1.21 version. Forcing the wa to
                        >         higher than
                        >         >         automatic
                        >         >         > value of wa= 7.230911E-02, increases the r and
                        >         rfree to
                        >         >         above 50!
                        >         >         >
                        >         >         > The opt_rweight output is :
                        >         >         > ------> initial rweight estimate= 0.1000
                        >         >         >
                        >         >         > rweight= 0.0100 r= 0.1685 free_r= 0.2128 rms
                        >         B(bond)= 3.8780
                        >         >         rms
                        >         >         > B(angle)= 4.7275
                        >         >         > rweight= 0.0200 r= 0.1685 free_r= 0.2128 rms
                        >         B(bond)= 3.8205
                        >         >         rms
                        >         >         > B(angle)= 4.6736
                        >         >         > rweight= 0.0500 r= 0.1687 free_r= 0.2127 rms
                        >         B(bond)= 3.5794
                        >         >         rms
                        >         >         > B(angle)= 4.4422
                        >         >         > rweight= 0.1000 r= 0.1688 free_r= 0.2126 rms
                        >         B(bond)= 3.4538
                        >         >         rms
                        >         >         > B(angle)= 4.3251
                        >         >         > rweight= 0.2000 r= 0.1691 free_r= 0.2121 rms
                        >         B(bond)= 3.0403
                        >         >         rms
                        >         >         > B(angle)= 3.9464
                        >         >         > rweight= 0.5000 r= 0.1699 free_r= 0.2123 rms
                        >         B(bond)= 2.5454
                        >         >         rms
                        >         >         > B(angle)= 3.4242
                        >         >         > rweight= 1.0000 r= 0.1716 free_r= 0.2127 rms
                        >         B(bond)= 1.9617
                        >         >         rms
                        >         >         > B(angle)= 2.7739
                        >         >         > rweight= 2.0000 r= 0.1734 free_r= 0.2135 rms
                        >         B(bond)= 1.5863
                        >         >         rms
                        >         >         > B(angle)= 2.3047
                        >         >         > rweight= 5.0000 r= 0.1781 free_r= 0.2169 rms
                        >         B(bond)= 1.0437
                        >         >         rms
                        >         >         > B(angle)= 1.5197
                        >         >         >
                        >         >         > ------> lowest free_r for target "mlf" with
                        >         rweight= 0.2000
                        >         >         (with wa=
                        >         >         > 4.41916)
                        >         >         >
                        >         >         > The opt_wa output is:
                        >         >         > ------> initial wa estimate= 0
                        >         >         >
                        >         >         > wa= 0.0000 r= 0.1689 free_r= 0.2126 rmsd bonds=
                        >         0.000000
                        >         >         rmsd angles=
                        >         >         > 0.00000
                        >         >         > wa= 0.0000 r= 0.1688 free_r= 0.2126 rmsd bonds=
                        >         0.000000
                        >         >         rmsd angles=
                        >         >         > 0.00000
                        >         >         > wa= 0.0000 r= 0.1688 free_r= 0.2126 rmsd bonds=
                        >         0.000000
                        >         >         rmsd angles=
                        >         >         > 0.00000
                        >         >         > wa= 0.0000 r= 0.1688 free_r= 0.2126 rmsd bonds=
                        >         0.000000
                        >         >         rmsd angles=
                        >         >         > 0.00000
                        >         >         > wa= 0.0000 r= 0.1688 free_r= 0.2126 rmsd bonds=
                        >         0.000000
                        >         >         rmsd angles=
                        >         >         > 0.00000
                        >         >         > wa= 0.0000 r= 0.1687 free_r= 0.2126 rmsd bonds=
                        >         0.000000
                        >         >         rmsd angles=
                        >         >         > 0.00000
                        >         >         > wa= 0.0000 r= 0.1687 free_r= 0.2126 rmsd bonds=
                        >         0.000000
                        >         >         rmsd angles=
                        >         >         > 0.00000
                        >         >         > wa= 0.0000 r= 0.1686 free_r= 0.2127 rmsd bonds=
                        >         0.000000
                        >         >         rmsd angles=
                        >         >         > 0.00000
                        >         >         > wa= 0.0000 r= 0.1684 free_r= 0.2128 rmsd bonds=
                        >         0.000000
                        >         >         rmsd angles=
                        >         >         > 0.00000
                        >         >         > wa= 0.0000 r= 0.1680 free_r= 0.2129 rmsd bonds=
                        >         0.000000
                        >         >         rmsd angles=
                        >         >         > 0.00000
                        >         >         > wa= 0.0000 r= 0.1675 free_r= 0.2129 rmsd bonds=
                        >         0.000000
                        >         >         rmsd angles=
                        >         >         > 0.00000
                        >         >         > wa= 0.0000 r= 0.1666 free_r= 0.2131 rmsd bonds=
                        >         0.000000
                        >         >         rmsd angles=
                        >         >         > 0.00000
                        >         >         >
                        >         >         > ------> lowest free_r for target mlf with wa= 0
                        >         >         >
                        >         >         > ------> The best value for wa is one that produces
                        >         a low
                        >         >         > free_r value and also good model geometry. As a
                        >         general
                        >         >         > guide, good geometry is indicated by rms
                        >         deviations from
                        >         >         > ideal values of less than:
                        >         >         > bonds -> 0.01 A
                        >         >         > angles -> 2.00 degrees
                        >         >         >
                        >         >         > The rsmds are bad since the planarity of the rings
                        >         are
                        >         >         distorted
                        >         >         > although R and Rfree are good.
                        >         >         > Thanks
                        >         >         > Amit.
                        >         >         >
                        >         >         > --- In cnsbb@yahoogroups.com, Ed Pozharski
                        >         <epozh001@...>
                        >         >         wrote:
                        >         >         > >
                        >         >         > > Just to verify, you are using the *latest*
                        >         version, 1.21
                        >         >         (not 1.2)?
                        >         >         > >
                        >         >         > > This is really strange. Do both R and Rfree go
                        >         up when you
                        >         >         weaken
                        >         >         > > restraints? And how high they go? You see,
                        >         normally you
                        >         >         would expect
                        >         >         > > that with weaker restraints Rfree may go up, but
                        >         R should
                        >         >         go down.
                        >         >         > > What's the resolution?
                        >         >         > >
                        >         >         > > How do the maps look? Can you get anything else
                        >         refined
                        >         >         (which would
                        >         >         > > indicate that the issue is this particular
                        >         dataset). If
                        >         >         you try
                        >         >         > other
                        >         >         > > refinement programs (refmac, phenix), do you
                        >         still have
                        >         >         the problem?
                        >         >         > >
                        >         >         > > On Fri, 2010-02-05 at 07:42 +0000, amitd_01
                        >         wrote:
                        >         >         > > >
                        >         >         > > > Hello everybody,
                        >         >         > > > When using refine.inp of CNS ver 1.2 the rsmd
                        >         bonds and
                        >         >         angles
                        >         >         > outputs
                        >         >         > > > are 0.000 and very low values of wa=2x10-2 and
                        >         rweight=
                        >         >         0.02
                        >         >         > resptly.
                        >         >         > > > Using optimize_wa.inp gives wa=0.0 for all the
                        >         cycles
                        >         >         and
                        >         >         > > > optimize_rweight.inp gives 0.2 as best value.
                        >         I
                        >         >         recreated a new
                        >         >         > > > refine.inp and ran it but I get the same
                        >         result. The R-
                        >         >         and R-free
                        >         >         > are
                        >         >         > > > near 20%. There are a few anions and metal
                        >         ions (but
                        >         >         used as
                        >         >         > neutral)
                        >         >         > > > along with waters and protein chain in the
                        >         input pdb.
                        >         >         > > > I had refined with only protein and waters,
                        >         with and
                        >         >         without the
                        >         >         > ions
                        >         >         > > > but with no luck. Fixing the wa= 0.3 to 1.5
                        >         increases
                        >         >         the R- to
                        >         >         > very
                        >         >         > > > high values.
                        >         >         > > > I would appreciate any help to get proper
                        >         rsmds and wa
                        >         >         values.
                        >         >         > > > Thanks in advance,
                        >         >         > > > Amit Das.
                        >         >         > > >
                        >         >         > > >
                        >         >         > > >
                        >         >         > > >
                        >         >         > > >
                        >         >         > > --
                        >         >         > > Edwin Pozharski, PhD, Assistant Professor
                        >         >         > > University of Maryland, Baltimore
                        >         >         > > ----------------------------------------------
                        >         >         > > When the Way is forgotten duty and justice
                        >         appear;
                        >         >         > > Then knowledge and wisdom are born along with
                        >         hypocrisy.
                        >         >         > > When harmonious relationships dissolve then
                        >         respect and
                        >         >         devotion
                        >         >         > arise;
                        >         >         > > When a nation falls to chaos then loyalty and
                        >         patriotism
                        >         >         are born.
                        >         >         > > ------------------------------ / Lao Tse /
                        >         >         > >
                        >         >         >
                        >         >         >
                        >         >         >
                        >         >         >
                        >         >         >
                        >         >
                        >         >
                        >         >
                        >         >
                        >         >         --
                        >         >         Edwin Pozharski, PhD, Assistant Professor
                        >         >         University of Maryland, Baltimore
                        >         >         ----------------------------------------------
                        >         >         When the Way is forgotten duty and justice appear;
                        >         >         Then knowledge and wisdom are born along with
                        >         hypocrisy.
                        >         >         When harmonious relationships dissolve then respect
                        >         and
                        >         >         devotion arise;
                        >         >         When a nation falls to chaos then loyalty and
                        >         patriotism are
                        >         >         born.
                        >         >         ------------------------------   / Lao Tse /
                        >         >
                        >         >
                        >         >
                        >         >
                        >         >
                        >         >
                        >         > --
                        >         > AMIT DAS,
                        >         > PROTEIN CRYSTALLOGRAPHY SECTION,
                        >         > SOLID STATE PHYSICS DIVISION, BARC, TROMBAY,
                        >         > MUMBAI-400085.
                        >         > INDIA.
                        >         > Alt E-mail:amitdas@...
                        >         > PHONE:+91-22-25594688/4063
                        >         > FAX:+91-22-25505151
                        >
                        >
                        >
                        >         --
                        >
                        >         Edwin Pozharski, PhD, Assistant Professor
                        >         University of Maryland, Baltimore
                        >         ----------------------------------------------
                        >         When the Way is forgotten duty and justice appear;
                        >         Then knowledge and wisdom are born along with hypocrisy.
                        >         When harmonious relationships dissolve then respect and
                        >         devotion arise;
                        >         When a nation falls to chaos then loyalty and patriotism are
                        >         born.
                        >         ------------------------------   / Lao Tse /
                        >
                        >
                        >
                        >
                        >
                        >
                        > --
                        > AMIT DAS,
                        > PROTEIN CRYSTALLOGRAPHY SECTION,
                        > SOLID STATE PHYSICS DIVISION, BARC, TROMBAY,
                        > MUMBAI-400085.
                        > INDIA.
                        > Alt E-mail:amitdas@...
                        > PHONE:+91-22-25594688/4063
                        > FAX:+91-22-25505151
                        >
                        >
                        >
                        >
                        --
                        Edwin Pozharski, PhD, Assistant Professor
                        University of Maryland, Baltimore
                        ----------------------------------------------
                        When the Way is forgotten duty and justice appear;
                        Then knowledge and wisdom are born along with hypocrisy.
                        When harmonious relationships dissolve then respect and devotion arise;
                        When a nation falls to chaos then loyalty and patriotism are born.
                        ------------------------------   / Lao Tse /




                        --
                        AMIT DAS,
                        PROTEIN CRYSTALLOGRAPHY SECTION,
                        SOLID STATE PHYSICS DIVISION, BARC, TROMBAY,
                        MUMBAI-400085.
                        INDIA.
                        Alt E-mail:amitdas@...
                        PHONE:+91-22-25594688/4063
                        FAX:+91-22-25505151
                      • Ed Pozharski
                        Hope it works :) As for windows, I assume that you tried ms-dos binaries and they don t work? I always thought that CNS is the program which is not really
                        Message 11 of 11 , Feb 16, 2010
                          Hope it works :)

                          As for windows, I assume that you tried ms-dos binaries and they don't
                          work? I always thought that CNS is the program which is not really
                          suited for windows with its aversion to command line use. If you really
                          need it, you can try compiling your own binaries using windows version
                          of gfortran.

                          On Mon, 2010-02-15 at 12:52 +0530, AMIT wrote:
                          > The linux OS is a 64-bit one. CNS was compiled on the machine. We have
                          > Xeon dual core processors. I will download the mp version and install
                          > it now to solve the problem!
                          >
                          > Is there any possiblity that CNS 1.21 will be available also for Win
                          > XP/ Win 7?
                          >
                          > Thanks for the response,
                          > Amit.
                          >
                          >

                          --
                          Edwin Pozharski, PhD, Assistant Professor
                          University of Maryland, Baltimore
                          ----------------------------------------------
                          When the Way is forgotten duty and justice appear;
                          Then knowledge and wisdom are born along with hypocrisy.
                          When harmonious relationships dissolve then respect and devotion arise;
                          When a nation falls to chaos then loyalty and patriotism are born.
                          ------------------------------ / Lao Tse /
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