[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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