VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Dec 10 2003 - 00:42:08 CST

Hi Tyler,
  The problem is rooted in the fixed field sizes of the PDB file format,
which is what Stride takes as input. Unfortunately its easy for a large
macromolecule to overrun both the atom index and residue ID fields and
thus cause Stride to bomb. We've done a number of tests (Jordi actually)
and the fix is somewhat non-trivial if we want to continue to use a
standard Stride compilation. You're right that changing the Stride
source (along with VMD) altering field widths and formatting to something
other than strict PDB could be an expedient solution. Another method would
be to split up the Stride calculation into numerous calls remapping atom
IDs etc. Yet another option would be to interface VMD to other secondary
structure prediction packages/routines. I haven't determined which route
I want to take yet, but I hope to address this for the next rev of VMD.
As soon as I've got something that works I'll let people know so they can
test it.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Dec 08, 2003 at 11:36:03AM -0700, Tyler Luchko wrote:
> Hello,
>
> I've recently run into a problem using stride via the cartoon
> representation where I get the error:
>
> File /usr/tmp/filen0BRs1 has no coordinates
> Error reading PDB file /usr/tmp/filen0BRs1
>
> I tracked down the temp file to look at it and all the coordinates were
> there. However, I noticed a slight formatting problem in an extra space
> after the residue name. I changed this with sed from
>
> ATOM 69526 N MET 23175 36.212 6.640 12.342
>
> to
>
> ATOM 69526 N MET 23175 36.212 6.640 12.342
>
> and stride worked fine from the command line. I believe this would
> correspond to changing line 49 of Stride.C from
>
> "ATOM %5d %4s %-4s %4d %8.3f%8.3f%8.3f\n",
>
> to
>
> "ATOM %5d %4s %-4s%4d %8.3f%8.3f%8.3f\n",
>
> I haven't compiled this to test it but I think this should work.
>
> Thanks,
>
> Tyler 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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