VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jun 21 2005 - 16:01:12 CDT

Chris,
  I looked at the structures you included and I get the expected
number of fragments when I load them. I did notice that inside
your script, you're using 'unset temp' rather than '$temp delete'
to free your atom selections. Regarding the ordering of output,
previous revs of VMD didn't explicitly sync the output of Tcl
with the internal VMD messages such as the molecule info printout,
so the out of order printing of output is not unusual. I do think
the weird fragment count is unusual, but you might be leaking
memory with those undeleted atom selections, and/or there may be
some interesting bug you've found that's causing that. Do you get
the unusual fragment count if you load those PDB files manually?

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jun 17, 2005 at 02:02:57PM -0600, Chang, Christopher wrote:
> Hi all,
>
> I am using VMD to process snapshots from a Brownian dynamics run. So, I have a set of input PDB files with filenames A0001.pdb through A0100.pdb generated by the BD program. VMD reads one in at a time, selects a subset of atoms, then writes out a new PDB file with name #.pdb, where "#" ranges from 1 to 100. This is all in the attached BDanimate.tcl script.
> When this script gets to file A0096.pdb (attached, along with A0095.pdb), the strange output in the attached file VMD.strange is generated. For some reason, VMD sees 599 fragments, whereas for the other 99 structures it sees 5 fragments. There is also an "atomselect 99" line, but I would have expected "atomselect 95" at this point, assuming VMD selections number from 0. The output PDB files (attached, for 95.pdb and 96.pdb)seem fine, though.
> Anyone know what's going on?
>
> Thanks,
>
> Chris
> Christopher H. Chang, Ph.D.
> Research Associate
> National Renewable Energy Laboratory
> 1617 Cole Blvd., Mail Stop 1608
> Golden, CO 80401
> Phone (303) 275-3751
> Fax (303) 275-4007
>
> <<95.pdb>> <<96.pdb>> <<A0095.pdb>> <<A0096.pdb>> <<BDanimate.tcl>> <<VMD.strange>> 

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