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Re: [ccp4bb]: Recompiling CNS ??

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  • Edward A. Berry
    cd to directory ???/cns_solve_1.1/source supposing MAXA is a parameter and being aware that fortran is case-insensitive, you: grep -i MAXA * |grep -i parameter
    Message 1 of 8 , Jul 9, 2002
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      cd to directory ???/cns_solve_1.1/source
      supposing MAXA is a parameter and being aware that fortran is case-insensitive, you:

      grep -i MAXA * |grep -i parameter

      which gives:

      angledb.inc: PARAMETER (MAXANGLEDBCLASSES = 200)
      cnst.inc: PARAMETER (MAXA2=MAX_ATOM)
      coord.inc: PARAMETER (MAXAT3=MAX_ATOM)
      coordc.inc: PARAMETER (MAXAT4=MAX_ATOM)
      deriv.inc: PARAMETER (MAXAT5=MAX_ATOM)
      genic.f: & 'exceeded MAXA parameter --> recompile program')
      genic.f: & 'exceeded MAXA parameter --> recompile program')
      * mtf.inc: PARAMETER (MAXA=MAX_ATOM)
      mtfio.f: & 'MAXA parameter exceeded --> recompile program')
      mtfio.f: & 'MAXA parameter exceeded --> recompile program')
      psfio.f: & 'exceeded MAXA parameter --> recompile program')
      rtf.inc: PARAMETER (MAXAT2=1000)
      rtfio.f: & 'exceeded MAXAT2 (RTF) parameter --> recompile program')
      xmaxl.f: PARAMETER (MAXARG = 250.0D0, MINVAL = 10.0D0, MAXVAL = 250.0D0)
      xmaxl.f: PARAMETER (MAXARG = 250.0D0, MINVAL = 10.0D0, MAXVAL = 250.0D0)
      xpeakpik.f: & 'exceeded MAXA parameter --> recompile program')

      The 8'th line shows MAXA is set to MAX_ATOM in mtf.f
      So you grep for a parameter MAX_ATOM:

      grep -i MAX_ATOM * | grep -i parameter

      And the very first occurrence gives:

      cns.inc: PARAMETER (MAX_ATOM=40000)

      So you edit cns.inc and in the line above change 40000 to some larger number.
      Hope that's the only place it gets set.
      then cd .. to the main cns directory and "make" the installation as when you
      first installed. If someone else installed originally you might ask her to
      help with this. If that person is on vacation and you don't have write access
      to the directories, or you are concerned about possibly corrupting a good
      install of CNS, you can cp -r the directory to your own disk space and
      follow the instructions in the Readme:

      Please see the HTML documentation for detailed installation instructions
      and trouble shooting information. To install on any platform:

      - cd to the CNSsolve directory
      - modify the file cns_solve_env to define the location of CNSsolve
      - type 'make install'
      - source cns_solve_env prior to using CNSsolve

      Now you have two cns installations. You determine which is effective by which
      cns_solve_env you source in your .tcshrc or wherever.

      Hope that helps,
      Ed

      Rajeswari Edayathumangalam wrote:
      >
      > *** For details on how to be removed from this list visit the ***
      > *** CCP4 home page http://www.ccp4.ac.uk ***
      >
      > Hello Everyone,
      > Sorry, this is a non-CCP4 query....
      > I am trying to merge 2 molecules using the CNS
      > script,'merge_structures,inp'.
      > However, the MAXA parameter (I think, the max. no. of atoms) has been
      > set to 40000 and my molecules when merged exceed that limit.
      > CNS gives me a message saying that the "MAXA parameter has been exceeded
      > ---> recompile program".
      > CNS FAQ also suggests that I recompile the program but it's not apparent
      > to me as to how and where I can do it.....
      > Would someone know where and how I can recompile the MAXA parameter?? I
      > can't find it in the merge_structures.inp file.
      > Thanks a ton for your help.
      > Raji
    • Joe Krahn
      ... You can also copy just the source directory (assuming it is configured): cp -Lr $CNS_SOURCE cns_src # Use -L to copy files instead of the links cd cns_src
      Message 2 of 8 , Jul 9, 2002
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        "Edward A. Berry" wrote:
        > ... you can cp -r the directory to your own disk space and
        > follow the instructions in the Readme:
        >
        > Please see the HTML documentation for detailed installation instructions
        > and trouble shooting information. To install on any platform:
        >
        > - cd to the CNSsolve directory
        > - modify the file cns_solve_env to define the location of CNSsolve
        > - type 'make install'
        > - source cns_solve_env prior to using CNSsolve
        >
        > Now you have two cns installations. You determine which is effective by which
        > cns_solve_env you source in your .tcshrc or wherever.
        >
        > Hope that helps,
        > Ed
        You can also copy just the source directory (assuming it is configured):
        cp -Lr $CNS_SOURCE cns_src # Use -L to copy files instead of the links
        cd cns_src
        vi cns.inc # Change MAX_ATOM
        make cns_solve

        This will make cns_solve-***.exe, then try to copy it to ../bin.
        All you need is that .exe file. Rename it to something like cns_big
        and put it in your path. Then, you don't need two whole CNS
        installations. Just run cns_big when needed.

        Of course, if you can copy the whole CNS distribution if you run
        into problems. But, only the cns*.exe is needed when you're done.

        Joe Krahn
      • Qian Xu
        Dear all, I am trying to refine multiple conformations of certain protein residues in CNS, but always failed. My pdb file is like following, ... ATOM 2479 N
        Message 3 of 8 , Jul 11, 2002
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          Dear all,

          I am trying to refine multiple conformations of certain protein residues
          in CNS, but always failed. My pdb file is like following,

          ...
          ATOM 2479 N GLU B 46 14.708 58.904 9.808 1.00 31.91 B
          ATOM 2480 CA GLU B 46 15.140 57.662 10.460 1.00 33.22 B
          ATOM 2481 CB AGLU B 46 15.810 56.715 9.455 0.50 36.75 B
          ATOM 2481 CB BGLU B 46 15.710 56.686 9.429 0.50 36.75 B
          ATOM 2482 CG AGLU B 46 14.883 56.055 8.445 0.50 42.35 B
          ATOM 2482 CG BGLU B 46 16.389 55.469 10.036 0.50 42.35 B
          ATOM 2483 CD AGLU B 46 14.108 57.053 7.595 0.50 45.27 B
          ATOM 2483 CD BGLU B 46 16.909 54.508 8.985 0.50 45.27 B
          ATOM 2484 OE1AGLU B 46 14.738 57.973 7.028 0.50 45.49 B
          ATOM 2484 OE1BGLU B 46 16.738 54.794 7.781 0.50 45.49 B
          ATOM 2485 OE2AGLU B 46 12.868 56.908 7.486 0.50 46.85 B
          ATOM 2485 OE2BGLU B 46 17.488 53.468 9.365 0.50 46.85 B
          ATOM 2486 C GLU B 46 16.147 57.983 11.563 1.00 32.88 B
          ATOM 2487 O GLU B 46 16.048 57.488 12.691 1.00 32.66 B
          ...
          ATOM 3642 N GLU B 192 17.421 93.373 12.756 1.00 28.01 B
          ATOM 3643 CA GLU B 192 16.076 92.956 13.122 1.00 28.27 B
          ATOM 3644 CB GLU B 192 15.058 93.599 12.178 1.00 31.94 B
          ATOM 3645 CG AGLU B 192 15.415 95.038 11.783 0.50 37.66 B
          ATOM 3645 CG BGLU B 192 15.179 95.127 12.098 0.50 37.66 B
          ATOM 3646 CD AGLU B 192 16.470 95.112 10.662 0.50 42.41 B
          ATOM 3646 CD BGLU B 192 15.095 95.811 13.476 0.50 42.41 B
          ATOM 3647 OE1AGLU B 192 17.103 94.065 10.377 0.50 44.67 B
          ATOM 3647 OE1BGLU B 192 14.544 95.185 14.414 0.50 44.67 B
          ATOM 3648 OE2AGLU B 192 16.668 96.212 10.076 0.50 37.78 B
          ATOM 3648 OE2BGLU B 192 15.571 96.972 13.615 0.50 37.78 B
          ATOM 3649 C GLU B 192 15.909 91.441 13.155 1.00 28.35 B
          ATOM 3650 O GLU B 192 16.777 90.706 12.680 1.00 27.66 B
          ...

          When I did "generate", I noticed that the output pdb file contains only
          the second conformation of the above two residues.

          If I use the above pdb file (from O) and my old mtf file (generated from
          single conformation model) to do refinement, I got still only one
          conformation in output pdb, even if I already defined the alternate
          conforamtions in input file as following,

          {* select atoms in alternate conformation 1 *}
          {===>} conf_1=((segid B and (residue 46 or residue 192) and resname
          AGLU));

          {* select atoms in alternate conformation 2 *}
          {===>} conf_2=((segid B and (residue 46 or residue 192) and resname
          BGLU));

          {* select atoms in alternate conformation 3 *}
          {===>} conf_3=(none);

          {* select atoms in alternate conformation 4 *}
          {===>} conf_4=(none);

          So where am I wrong? Did I miss something?

          Any comments will be highly appreciated. Thanks in advance.

          regards,
          Q. Steve Xu, Ph.D. student
          Dept. of Physiology and Biophysics
          Boston Univ. School of Medicine
          Tel: (617)638-4083
          Fax: (617)638-4041
        • purnima khandelwal
          Hi I am trying to calculate an NMR ensemble plus an average structure using anneal.inp (there is simply a flag that needs to be set to true ). It does
          Message 4 of 8 , Jul 17, 2002
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            Hi

            I am trying to calculate an NMR ensemble plus an average structure using
            anneal.inp (there is simply a flag that needs to be set to 'true'). It
            does calculate the ensemble, but gives the following error while
            calculating the average. I looked at all the needed modules eg. initave,
            calcave etc. but couldn't figure out why it gave that error, nothing in
            those modules looks out of place to me. If you have come across this or
            can suggest some solution, it would be great. Thanks.

            Purnima.

            -------------------------------------------------------------------------------
            R.m.s. diff. between fitted set and comp. set for selected atoms = 1.8431
            Program version= 1.0 File version= 1.0
            MESSage=OFF
            ECHO=FALSe {OFF}
            Program version= 1.0 File version= 1.0
            MESSage=OFF
            ECHO=FALSe {OFF}
            %CNSsolve-ERR: unrecognized command:
            (
            ^
            %CNSsolve-ERR: unrecognized command:
            ( ave=
            ^^^
            %CNSsolve-ERR: unrecognized command:
            ( ave=&
            ^
            %WDSUB error encountered: can not obtain value of a compound symbol
            (CNS is in mode: SET ABORT=NORMal END)
            *****************************************************
            ABORT mode will terminate program execution.
            *****************************************************
            Program will stop immediately.
          • purnima khandelwal
            I have looked everywhere, for any typo, syntax error or anything not defined, everything seems fine. Do you know of any other program I can use to calculate an
            Message 5 of 8 , Jul 17, 2002
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              I have looked everywhere, for any typo, syntax error or anything not
              defined, everything seems fine. Do you know of any other program I can use
              to calculate an average structure starting from my ensemble?

              Thanks.
              Purnima.

              On Wed, 17 Jul 2002, Fred. Vellieux wrote:

              > Most likely a typo in your input file. Or in a macro, or a
              > script. These can be hard to detect!
              >
              > Fred.
              >
              > On Wed, 17 Jul 2002, purnima khandelwal wrote:
              >
              > > -------------------------------------------------------------------------------
              > > R.m.s. diff. between fitted set and comp. set for selected atoms = 1.8431
              > > Program version= 1.0 File version= 1.0
              > > MESSage=OFF
              > > ECHO=FALSe {OFF}
              > > Program version= 1.0 File version= 1.0
              > > MESSage=OFF
              > > ECHO=FALSe {OFF}
              > > %CNSsolve-ERR: unrecognized command:
              > > (
              > > ^
              > > %CNSsolve-ERR: unrecognized command:
              > > ( ave=
              > > ^^^
              > > %CNSsolve-ERR: unrecognized command:
              > > ( ave=&
              > > ^
              > > %WDSUB error encountered: can not obtain value of a compound symbol
              > > (CNS is in mode: SET ABORT=NORMal END)
              > > *****************************************************
              > > ABORT mode will terminate program execution.
              > > *****************************************************
              > > Program will stop immediately.
              > >
              >
              > --
              > s-mail: F.M.D. Vellieux (B.Sc., Ph.D.)
              > Institut de Biologie Structurale J.-P. Ebel CEA CNRS UJF
              > 41 rue Jules Horowitz
              > 38027 Grenoble Cedex 01
              > France
              > Tel: (+33) (0) 438789605
              > Fax: (+33) (0) 438785494
              > e-mail: vellieux@...
              > ==========================================================================
              > Don't even think of asking me: "I would Het leven is genieten
              > if I could, but I can't" (L.R., 1998) (to live is to enjoy)
              > ==========================================================================
              > BEGIN_ELECTRONIC_SIGNATURE
              > M/R-:@ZF:!H)4!":,+WW$O;CZMD.9)UDE'9=GB8HB/]>X><9JL0+B,:..\_@J
              > MP/H/0?*ZM_GS&C'30I,>S1G3UI>T-H;`!!>N'*JT1?[?;#OW[]UR'@YY2X`Z
              > MN)5"J6`$X-<O3Q/),4@]C=2$")KC"37!"Z1L]XW(-8E&KIE9/0[=K]@C3[-#
              > ?79H.\3W6F8,D<4WH4D.]E.>U+FCGZ3L6+P0_(.@T$```
              > END_ELECTRONIC_SIGNATURE
              >
            • Q. Steven Xu
              Dear all, The PDB deposition asks for the R factor, R work and R free values of the structure. The output from model_stats.inp gives only R work and R free,
              Message 6 of 8 , Jan 7, 2003
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                Dear all,

                The PDB deposition asks for the R factor, R work and R free values of the
                structure. The output from model_stats.inp gives only R work and R free,
                but not R factor for the whole data set, to my understanding. I tried to
                use the reflection file without test set array and the "residual"
                refinement target to calculate the overall R factor, but the caculation
                just kept aborting with the error message "%DEFSUBEXPA error encountered:
                Attemped to use an undefined parameter.". So my question is how to
                calculate the overall R factor in CNS or any other program can do it?

                Thanks in advance.

                regards,
                Q. Steven Xu
                Dept. of Physiology and Biophysics
                Boston Univ. School of Medicine
                Tel: (617)638-4083
                Fax: (617)638-4041
                E-mail: qian@...
              • Q. Steven Xu
                Hi, I am refining a DNA structure with 5-iodocytosines in it, but can t find its topology and parameter file in Hic-Up. Anybody out there can help me? Many
                Message 7 of 8 , Mar 21, 2003
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                  Hi,

                  I am refining a DNA structure with 5-iodocytosines in it, but can't find
                  its topology and parameter file in Hic-Up. Anybody out there can help me?
                  Many thanks in advance.

                  regards,
                  Q. Steven Xu
                  Dept. of Physiology and Biophysics
                  Boston Univ. School of Medicine
                  Tel: (617)638-4083
                  Fax: (617)638-4041
                  E-mail: qian@...
                • Gerard DVD Kleywegt
                  hi, do you have coordinates for this entity ? if so, use the HIC-Up or PRODRG server to generate CNS dictionaries. if not, copy your normal cytosine dictionary
                  Message 8 of 8 , Mar 21, 2003
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                    hi,

                    do you have coordinates for this entity ? if so, use the HIC-Up or PRODRG
                    server to generate CNS dictionaries. if not, copy your normal cytosine
                    dictionary and add the iodine atom, a bond C5-I (~2.1 A ?), two angle
                    restraints, a flatness improper for C5, and a NONB line for the iodine. you
                    can use a related compound's dictionary as a guide, e.g.
                    http://xray.bmc.uu.se/hicup/5IU

                    --gerard

                    ******************************************************************
                    Gerard J. Kleywegt
                    [Research Fellow of the Royal Swedish Academy of Sciences]
                    Dept. of Cell & Molecular Biology University of Uppsala
                    Biomedical Centre Box 596
                    SE-751 24 Uppsala SWEDEN

                    http://xray.bmc.uu.se/gerard/ mailto:gerard@...
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