VMD-L Mailing List

From: Boris Steipe (boris.steipe_at_utoronto.ca)
Date: Tue Nov 20 2012 - 11:20:04 CST

Although chain C has a number of potential problems (atom numbers going over 9999, residue numbers going over 999, B-values exceeding 99.9 ...), the problem is elsewhere. There is a close approach between the sidechain NZ of LYS 103 (atom 4336) and the backbone nitrogen of LEU 64 (1.61 Å). VMD draws a bond between the two. Deleting atom 4336 from chain C restores the ability to display the entire secondary structure of the chain.

Here is a minimal example. The coordinates display oK in all bond-centric views (lines, licorice etc.), but all backbone centric views (tube, trace, cartoon) show only the first segment of two residues.

ATOM 3997 N LEU C 64 87.333 -31.436 42.210 1.00102.28 N
ATOM 3998 CA LEU C 64 87.588 -30.951 43.567 1.00 99.94 C
ATOM 3999 C LEU C 64 86.495 -31.326 44.578 1.00 99.46 C
ATOM 4000 O LEU C 64 85.302 -31.160 44.317 1.00 98.87 O
ATOM 4001 CB LEU C 64 87.805 -29.437 43.561 1.00 90.91 C
ATOM 4002 CG LEU C 64 89.226 -28.967 43.256 1.00 98.18 C
ATOM 4003 CD1 LEU C 64 89.296 -27.454 43.121 1.00 84.17 C
ATOM 4004 CD2 LEU C 64 90.170 -29.452 44.340 1.00102.48 C
ATOM 4328 N LYS C 103 89.888 -35.608 42.924 1.00123.76 N
ATOM 4329 CA LYS C 103 89.510 -36.956 42.527 1.00125.42 C
ATOM 4330 C LYS C 103 90.069 -37.295 41.153 1.00134.94 C
ATOM 4331 O LYS C 103 89.817 -36.600 40.169 1.00136.29 O
ATOM 4332 CB LYS C 103 87.988 -37.107 42.528 1.00122.89 C
ATOM 4333 CG LYS C 103 87.244 -35.890 43.053 1.00113.89 C
ATOM 4334 CD LYS C 103 86.311 -35.316 41.999 1.00112.18 C
ATOM 4335 CE LYS C 103 87.011 -34.262 41.157 1.00111.89 C
ATOM 4336 NZ LYS C 103 86.867 -32.899 41.739 1.00107.40 N

The Stride warning arises from an unrelated bug. Coloring by secondary structure works for chain C and no warning is generated. But secondary structure assignment fails for the full file (and cartoon representations show everything as tube). The complex is large, and there may will be over 10,000 H-bonds ... I would expect that increasing the hard-wired limit should fix this.

Hope this helps for fixing the bugs.
Boris

On 2012-11-19, at 9:03 PM, Martin, Erik W wrote:

> I actually enjoy a good mystery, and downloaded this structure, wrote the C chain to its own pdb and loaded it alone to see if it would solve the problem... it did not (hence my not posting anything). There are also no odd indicies or names that would obviously cause a stride error. I'm stumped, and am really curious to see if anyone comes up with an explanation.
> ________________________________________
> From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Bennion, Brian [Bennion1_at_llnl.gov]
> Sent: Monday, November 19, 2012 5:30 PM
> To: Larry Guy; vmd-l_at_ks.uiuc.edu
> Subject: RE: vmd-l: VMD can't display new PDB secondary structure properly ( pyMol, jMol can). .
>
> Could it be that stride gives and error if the selection is too big? There is a limit of 10000 hbonds. Not sure how the other viewers calculate the cartoons.
>
> brian
>
>
> ________________________________
> From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] on behalf of Larry Guy [gglarry0_at_gmail.com]
> Sent: Monday, November 19, 2012 2:00 PM
> To: vmd-l_at_ks.uiuc.edu
> Subject: vmd-l: VMD can't display new PDB secondary structure properly (pyMol, jMol can)
>
> Hi all,
>
> I hope that somebody here can help me solve a mystery regarding a newly released pdb 4G7O. Chain C of this protein can't be visualized using the ribbons or cartoon representations. Some smaller sections of chain C that I have removed and put in to a new pdb files show up fine in new cartoon representation. pyMol, jMol and other visualization software packages handle this structure with no problems, displaying all of chain C.
>
> What could be happening in VMD that would cause this kind of problem in the cartoon representation of chain C?
>
>
> Thanks in advance for your help!
>
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