VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Mar 29 2005 - 14:56:46 CST

Josh,
  That's good to know. I'll see about running Purify and Valgrind on
VMD when loading your structure files with the corplugin, it might just
be that corplugin is doing something nasty.

  John

On Tue, Mar 29, 2005 at 03:47:27PM -0500, Josh Ward wrote:
> John,
> It is working properly when I load a pdb file, using webpdb at least.
> We are running Debian Sarge linux on a Pentium 4 chips in our linux
> boxes here. The behavior is the same on all of them. Not sure what
> else to lookup. Playing around with it some more, I also noticed that
> the lines representation seems to work properly, while ribbons and
> cartoon fouls up on the even numbered molid molecules.
>
> After checking the output from loading the COR file, I did notice an
> error while loading molids 2 and 4. The alternating warning shows up
> after it reports the number of water molecules and is:
>
> Warning) Unusual bond between residues 63 and 64
>
> Here is the output to the console, including startup so you can see what
> graphics settings I am using:
>
>
> Info) VMD for LINUX, version 1.8.3 (February 15, 2005)
> Info) http://www.ks.uiuc.edu/Research/vmd/
> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> Info) Please include this reference in published work using VMD:
> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> Info) Multithreading available, 4 CPUs detected.
> Info) OpenGL renderer: Quadro NVS/PCI/SSE2
> Info) Features: STENCIL RN MDE CVA MTX PP PS GLSL(OV)
> Info) GLSL rendering mode is NOT available.
> Info) Textures: 2-D (2048x2048), 3-D (64x64x64), Multitexture (2)
> vmd > Info) Using plugin cor for structure file
> /pablo/wardjm/charmm/martin/smi3
> /cor/3.c.a.700-1000.avg.cor
> Info) Using plugin cor for coordinates from file
> /pablo/wardjm/charmm/martin/smi
> 3/cor/3.c.a.700-1000.avg.cor
> Info) Determining bond structure from distance search ...
> Info) Analyzing structure ...
> Info) Atoms: 1725
> Info) Residues: 106
> Info) Waters: 0
> Info) Segments: 2
> Info) Fragments: 2 Protein: 2 Nucleic: 0
> Info) Finished with coordinate file
> /pablo/wardjm/charmm/martin/smi3/cor/3.c.a.7
> 00-1000.avg.cor.
> Info) Using plugin cor for structure file
> /pablo/wardjm/charmm/martin/smi3/cor/3
> .c.a.700-1000.avg.cor
> Info) Using plugin cor for coordinates from file
> /pablo/wardjm/charmm/martin/smi
> 3/cor/3.c.a.700-1000.avg.cor
> Info) Determining bond structure from distance search ...
> Info) Analyzing structure ...
> Info) Atoms: 1725
> Info) Residues: 106
> Info) Waters: 0
> Info) Segments: 2
> Info) Fragments: 2 Protein: 2 Nucleic: 0
> Info) Finished with coordinate file
> /pablo/wardjm/charmm/martin/smi3/cor/3.c.a.7
> 00-1000.avg.cor.
> Info) Using plugin cor for structure file
> /pablo/wardjm/charmm/martin/smi3/cor/3
> .c.a.700-1000.avg.cor
> Info) Using plugin cor for coordinates from file
> /pablo/wardjm/charmm/martin/smi
> 3/cor/3.c.a.700-1000.avg.cor
> Info) Determining bond structure from distance search ...
> Info) Analyzing structure ...
> Info) Atoms: 1725
> Info) Residues: 106
> Info) Waters: 0
> Warning) Unusual bond between residues 63 and 64
> Info) Segments: 283
> Info) Fragments: 2 Protein: 2 Nucleic: 0
> Info) Finished with coordinate file
> /pablo/wardjm/charmm/martin/smi3/cor/3.c.a.7
> 00-1000.avg.cor.
> Info) Using plugin cor for structure file
> /pablo/wardjm/charmm/martin/smi3/cor/3
> .c.a.700-1000.avg.cor
> Info) Using plugin cor for coordinates from file
> /pablo/wardjm/charmm/martin/smi
> 3/cor/3.c.a.700-1000.avg.cor
> Info) Determining bond structure from distance search ...
> Info) Analyzing structure ...
> Info) Atoms: 1725
> Info) Residues: 106
> Info) Waters: 0
> Info) Segments: 2
> Info) Fragments: 2 Protein: 2 Nucleic: 0
> Info) Finished with coordinate file
> /pablo/wardjm/charmm/martin/smi3/cor/3.c.a.7
> 00-1000.avg.cor.
> Info) Using plugin cor for structure file
> /pablo/wardjm/charmm/martin/smi3/cor/3
> .c.a.700-1000.avg.cor
> Info) Using plugin cor for coordinates from file
> /pablo/wardjm/charmm/martin/smi
> 3/cor/3.c.a.700-1000.avg.cor
> Info) Determining bond structure from distance search ...
> Info) Analyzing structure ...
> Info) Atoms: 1725
> Info) Residues: 106
> Info) Waters: 0
> Warning) Unusual bond between residues 63 and 64
> Info) Segments: 283
> Info) Fragments: 2 Protein: 2 Nucleic: 0
> Info) Finished with coordinate file
> /pablo/wardjm/charmm/martin/smi3/cor/3.c.a.7
> 00-1000.avg.cor.
>
> John Stone wrote:
>
> >Josh,
> > I just loaded the structure you sent me 5 times as you described, but
> >it worked fine for me (see transcript below). Can you tell me more about
> >your machine? Do you get different results if you load the structure as
> >a PDB rather than as a COR file? I'll check this out on some machines here
> >and see if I'm able to reproduce your problem on one of the other machines.
> >
> >vmd > mol new 3.c.a.700-1000.avg.cor
> >vmd > mol new 3.c.a.700-1000.avg.cor
> >vmd > mol new 3.c.a.700-1000.avg.cor
> >vmd > mol new 3.c.a.700-1000.avg.cor
> >vmd > mol new 3.c.a.700-1000.avg.cor
> >vmd > set a0 [atomselect 0 "name CA"]
> >atomselect0
> >vmd > set a1 [atomselect 1 "name CA"]
> >atomselect1
> >vmd > set a2 [atomselect 2 "name CA"]
> >atomselect2
> >vmd > set a3 [atomselect 3 "name CA"]
> >atomselect3
> >vmd > set a4 [atomselect 4 "name CA"]
> >atomselect4
> >vmd > llength [$a0 get index]
> >106
> >vmd > llength [$a1 get index]
> >106
> >vmd > llength [$a2 get index]
> >106
> >vmd > llength [$a3 get index]
> >106
> >vmd > llength [$a4 get index]
> >106
> >
> >Can you just do that and tell me what happens on your machine?
> >Do you get any warnings when VMD loads the structure?
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Tue, Mar 29, 2005 at 11:28:34AM -0500, Josh Ward wrote:
> >
> >
> >>John,
> >>Yes, after it repeatedly messed up trying to align a pair of pdb files,
> >>I checked that problem by loading the same file into each molecule
> >>slot. I am attaching that file in CHARMM CRD format.
> >>
> >>Josh
> >>
> >>John Stone wrote:
> >>
> >>
> >>
> >
> >
>
> --
> Josh Ward
> Graduate Research Assistant
> Purdue University
> Department of Medicinal Chemistry and Molecular Pharmacology
> Lily Hall of Life Sciences
> Phone: (765) 494-2191 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
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