VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Nov 17 2006 - 12:50:31 CST

Hi,
  STRIDE (the program that VMD calls to calculate secondary structure)
has various limitations that prevent it from working on some very
large structures. Since we didn't write STRIDE and don't have time or
to write our own secondary structure prediction tool from
scratch, we try to use STRIDE despite it's limitations. STRIDE uses the
PDB file format for communication, so some of the limitations are inherent
just due to limitations of the PDB format itself.
VMD does a few things to try and assist STRIDE with these structures,
but some of the new ribosome structures out there still give STRIDE trouble.
I'm planning to try some experiments changing the way VMD communicates
with STRIDE, to reduce the size of the substructures it analyzes to avoid
this problem, but I haven't had time to work on it yet. One solution may be
to send STRIDE individual protein fragments, another way would be to
automatically split up the structure into groups of fragments that are
still within STRIDE's size limits. I'll be working on this soon and will
get back to you when I've made progress. In the mean time, one solution may
be to make an atom selection and save just the protein portions of the
structure to a PDB file, load that structure in a separate molecule, and
then use one when you want a NewRibbons display of secondary structure.
The STRIDE error should not have any effect on the nucleic acid portions
of your structure, so you can ignore it if you've selected "nucleic" when
displaying NewRibbons etc. Let me know if you need more help with this.

Regarding the VDW representation, no there are no limits of any kind
in VMD itself, only your patience. Drawing a 150,000 atoms with a
space filling representation such as VDW spheres will make
the graphics card work VERY hard, and so it will likely be slow, but
VMD will do what you ask. The faster your graphics card, the better
the rendering performance for such a representation.

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Nov 17, 2006 at 11:33:52PM +0530, Sathyapriya R wrote:
>
> Hi,
> I am trying to load the complete ribosome structure
> (~150000) atoms. It loads perfectly fine with line
> representation but on selecting the NewCartoon it
> gives the following error:
> Error reading PDB file
> ERROR) Unable to find Stride output file:
> ERROR) Stride::read_stride_record: unable to read output
> file from Stride
> ERROR) Call to Stride program failed
>
> Also, is there any limit for the maximum number of
> residues that can be loaded as VDW representation in the
> atom_select window?
>
> Technical details:
> VMD-1.8.5
> OS-Mandrake10.1
> Video Card:GeForce4 MX 440SE with AGP8X/AGP/SSE2 (64MB RAM)
>
> Thanks for any suggestions..
> Sathyapriya 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078