[Chimera-users] display ribbon for CA atoms

Bala subramanian bala.biophysics at gmail.com
Tue Oct 21 09:25:25 PDT 2014


Hi Elaine,

Thank you for the information. Replacing the residue names resolved my
problem.

Bala

On Tue, Oct 21, 2014 at 6:08 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Bala,
> Two reasons, both related to PDB file format:
>
> <
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html
> >
>
> (1) Column spacing:  spaces are important in PDB format, but there is a
> missing space before "A" on the line for atom 25, and one too many spaces
> before the "A" on the lines for atoms 23,29,30,31,33,34.  It is hard to see
> this if you are viewing with a varying-width font, but clear if you view in
> constant-width font.  Viewing/editing PDB files should be done using
> constant-width font.
>
> (2) Nonstandard residue names:  the ones with three-letter residue names
> not normally used for regular amino acids are not automatically connected.
> If I replace "ATOM  " (two spaces after the word) with "HETATM" on those
> lines, it fixes the problem.
>
> You could try applying these fixes yourself, but since I did them already,
> I attached the result below.   Chimera only shows the thin "licorice"
> ribbon because this is a CA-only structure.  I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>
>
> Attached above, pasted below, but again should really be viewed with
> constant-width font:
>
> MODEL       1
> ATOM    240  CA  VAL A  15      -4.028 -10.131 -14.981  1.00  0.00
> HETATM  256  CA  ASA A  16      -1.059  -7.963 -15.984  1.00  0.00
> ATOM    268  CA  LEU A  17      -1.498  -5.735 -12.905  1.00  0.00
> ATOM    287  CA  ALA A  18      -1.837  -8.694 -10.513  1.00  0.00
> ATOM    297  CA  VAL A  19       1.521 -10.149 -11.590  1.00  0.00
> ATOM    313  CA  ALA A  20       3.129  -6.662 -11.574  1.00  0.00
> ATOM    323  CA  VAL A  21       1.979  -5.898  -8.009  1.00  0.00
> ATOM    339  CA  VAL A  22       3.318  -9.266  -6.779  1.00  0.00
> ATOM    355  CA  ILE A  23       6.792  -8.806  -8.282  1.00  0.00
> ATOM    374  CA  GLY A  24       6.953  -5.077  -7.492  1.00  0.00
> ATOM    381  CA  THR A  25       5.978  -5.469  -3.854  1.00  0.00
> ATOM    395  CA  ALA A  26       8.113  -8.578  -3.252  1.00  0.00
> HETATM  405  CA  AHE A  27      11.502  -6.829  -3.607  1.00  0.00
> ATOM    425  CA  THR A  28      10.411  -3.957  -1.319  1.00  0.00
> ATOM    439  CA  ALA A  29       8.727  -6.289   1.217  1.00  0.00
> ATOM    449  CA  LEU A  30      11.626  -8.763   1.549  1.00  0.00
> ATOM    468  CA  VAL A  31      14.332  -6.060   1.884  1.00  0.00
> ATOM    484  CA  THR A  32      12.244  -3.984   4.372  1.00  0.00
> ATOM    498  CA  LYS A  33      11.589  -7.104   6.477  1.00  0.00
> HETATM  520  CA  AHE A  34      15.337  -7.950   6.374  1.00  0.00
> ATOM    540  CA  THR A  35      16.415  -4.418   7.456  1.00  0.00
> HETATM  554  CA  ASA A  36      13.895  -4.173  10.321  1.00  0.00
> ATOM    566  CA  SER A  37      14.420  -7.770  11.568  1.00  0.00
> ATOM    577  CA  ILE A  38      18.204  -8.185  11.182  1.00  0.00
> ATOM    596  CA  ILE A  39      20.091  -4.967  10.349  1.00  0.00
> ATOM    615  CA  THR A  40      18.515  -2.454  12.798  1.00  0.00
> END
>
>
> On Oct 21, 2014, at 2:27 AM, Bala subramanian <bala.biophysics at gmail.com>
> wrote:
>
> > Friends,
> > I am trying to visualize a helical structure containing only the CA
> atoms. Chimera doesnt display ribbon for some of atoms, a reason which i
> dnt understand.
> >
> > I have tried to visualize in several versions 1.10, 1.9, 1.7 etc. I am
> pasting the coordinates below of my pdb. You insights would be of great
> help to resolve the problem.
> >
> > MODEL       1
> > ATOM    240  CA  VAL A  15      -4.028 -10.131 -14.981  1.00  0.00
> > ATOM    256  CA  ASA A  16      -1.059  -7.963 -15.984  1.00  0.00
> > ATOM    268  CA  LEU A  17      -1.498  -5.735 -12.905  1.00  0.00
> > ATOM    287  CA  ALA A  18      -1.837  -8.694 -10.513  1.00  0.00
> > ATOM    297  CA  VAL A  19       1.521 -10.149 -11.590  1.00  0.00
> > ATOM    313  CA  ALA A  20       3.129  -6.662 -11.574  1.00  0.00
> > ATOM    323  CA  VAL A  21       1.979  -5.898  -8.009  1.00  0.00
> > ATOM    339  CA  VAL A  22       3.318  -9.266  -6.779  1.00  0.00
> > ATOM    355  CA  ILE  A  23       6.792  -8.806  -8.282  1.00  0.00
> > ATOM    374  CA  GLY A  24       6.953  -5.077  -7.492  1.00  0.00
> > ATOM    381  CA  THRA  25       5.978  -5.469  -3.854  1.00  0.00
> > ATOM    395  CA  ALA A  26       8.113  -8.578  -3.252  1.00  0.00
> > ATOM    405  CA  AHE A  27      11.502  -6.829  -3.607  1.00  0.00
> > ATOM    425  CA  THR A  28      10.411  -3.957  -1.319  1.00  0.00
> > ATOM    439  CA  ALA  A  29       8.727  -6.289   1.217  1.00  0.00
> > ATOM    449  CA  LEU  A  30      11.626  -8.763   1.549  1.00  0.00
> > ATOM    468  CA  VAL  A  31      14.332  -6.060   1.884  1.00  0.00
> > ATOM    484  CA  THR A  32      12.244  -3.984   4.372  1.00  0.00
> > ATOM    498  CA  LYS  A  33      11.589  -7.104   6.477  1.00  0.00
> > ATOM    520  CA  AHE  A  34      15.337  -7.950   6.374  1.00  0.00
> > ATOM    540  CA  THR A  35      16.415  -4.418   7.456  1.00  0.00
> > ATOM    554  CA  ASA A  36      13.895  -4.173  10.321  1.00  0.00
> > ATOM    566  CA  SER A  37      14.420  -7.770  11.568  1.00  0.00
> > ATOM    577  CA  ILE A  38      18.204  -8.185  11.182  1.00  0.00
> > ATOM    596  CA  ILE A  39      20.091  -4.967  10.349  1.00  0.00
> > ATOM    615  CA  THR A  40      18.515  -2.454  12.798  1.00  0.00
> > END
> >
>
>
>


-- 
C. Balasubramanian
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