VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Mar 27 2013 - 14:54:02 CDT

Hi,
  I was able to load and display secondary structure reps for 2WRN on
the test versions of VMD 1.9.2. Can you try one of the test versions
of VMD 1.9.2 on your machine and see if it will display 2WRN correctly?
Also, for your existing VMD install, do you get any errors in the VMD
terminal/text console when you try to display the cartoon rep?
The text below is what I see in VMD 1.9.2 on my machine:

Info) VMD for LINUX, version 1.9.2a20 (March 12, 2013)
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) Free system memory: 4794MB (60%)
Info) Creating CUDA device pool and initializing hardware...
Info) Detected 3 available CUDA accelerators:
Info) [0] GeForce GTX 285 30 SM_1.3 @ 1.48 GHz, 1.0GB RAM, KTO, OIO, ZCP
Info) [1] Tesla C870 16 SM_1.0 @ 1.35 GHz, 1.5GB RAM
Info) [2] Tesla C870 16 SM_1.0 @ 1.35 GHz, 1.5GB RAM
Info) OpenGL renderer: GeForce GTX 285/PCI/SSE2
Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVFG)
Info) Full GLSL rendering mode is available.
Info) Textures: 2-D (8192x8192), 3-D (2048x2048x2048), Multitexture (4)
Info) Dynamically loaded 2 plugins in directory:
Info) /Projects/vmd/pub/linux/lib/vmd192a20/plugins/LINUX/molfile
Info) Dynamically loaded 1 plugins in directory:
Info) /home/johns/plugins/compile/lib_LINUX/molfile
vmd > mol new 2WRN
  The PDB is supported by RCSB, the NSF, US PHS, NIH, NCRP, NIGMS, NLM,
and US DoE, who are not liable for the data. PDB files shall not be
sold. See ftp://ftp.rcsb.org/advisory.doc for full details.
Info) Using plugin webpdb for structure file 2WRN
Info) Using plugin webpdb for coordinates from file 2WRN
Info) Determining bond structure from distance search ...
Info) Analyzing structure ...
Info) Atoms: 59677
Info) Bonds: 64507
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 4523
Info) Waters: 0
Warning) Unusual bond between residues: 240 (protein) and 241 (none)
Warning) Unusual bond between residues: 207 (protein) and 208 (none)
Warning) Unusual bond between residues: 154 (protein) and 155 (none)
Warning) Unusual bond between residues: 100 (protein) and 101 (none)
Warning) Unusual bond between residues: 128 (protein) and 129 (none)
Warning) Unusual bond between residues: 125 (protein) and 126 (none)
Warning) Unusual bond between residues: 83 (protein) and 84 (none)
Warning) Unusual bond between residues: 100 (protein) and 101 (none)
Warning) Unusual bond between residues: 81 (protein) and 82 (none)
Warning) Unusual bond between residues: 25 (protein) and 26 (none)
Warning) Unusual bond between residues: 76 (nucleic) and 77 (protein)
Info) Segments: 1
Info) Fragments: 35 Protein: 23 Nucleic: 5
0
Info) Finished with coordinate file 2WRN.
vmd > Info) In any publication of scientific results based in part or
Info) completely on the use of the program STRIDE, please reference:
Info) Frishman,D & Argos,P. (1995) Knowledge-based secondary structure
Info) assignment. Proteins: structure, function and genetics, 23, 566-579.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Mar 21, 2013 at 08:54:27PM -0400, Juan Antonio Raygoza Garay wrote:
> I just did and nothing happened to the secondary structure, just for curiosity i loaded ubiquitin and it showed the secondary structure so i'm guessing that it is something with the pdb (2WRN), has anyone seen this and solved it?
>
> Thanks
>
>
> On Mar 21, 2013, at 7:34 PM, Jack Bulat wrote:
>
> > Hi Juan,
> >
> > Have you tried adjusting the Aspect Ratio or Thickness in the Graphical Representations menu box? Sometimes those default to the minimum, which makes the protein look coiled without showing ribbons.
> >
> > Hope that works,
> > Jack Bulat
> > Grad student,
> > UC Berkeley
> >
> >
> >
> >
> > On Mar 21, 2013, at 2:42 PM, Juan Antonio Raygoza Garay <raygozag_at_psu.edu> wrote:
> >
> >> Hi, i'm using VMD 1.9.1 on mac os and whenever I load any pdb with protein in it, it won't show the secondary structure of the protein in new cartoon, it only shows the proteins as coils, i already installed stride and restarted vmd but keeps showing me the same result.
> >>
> >> thanks
> >>
> >>
> >>
> >>
> >
> 

-- 
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