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@cgl.ucsf.edu> wrote:
Hi Bala, Two reasons, both related to PDB file format:
< http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.htm...
(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@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