Loading ...
Sorry, an error occurred while loading the content.

Re: [cnsbb] Re: wa 0.0 in cns 1.2 linux version

Expand Messages
  • 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 1 of 11 , Feb 13, 2010
    • 0 Attachment
      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 2 of 11 , Feb 13, 2010
      • 0 Attachment
        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 3 of 11 , Feb 14, 2010
        • 0 Attachment
          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 4 of 11 , Feb 16, 2010
          • 0 Attachment
            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 /
          Your message has been successfully submitted and would be delivered to recipients shortly.