VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Sep 24 2002 - 14:19:01 CDT

Dear Craig,
  At present VMD assumes that PDB files containing multiple structures
are a trajectory of sorts, but I agree completely that this is not necessarily
ideal in all cases, as others have run into the same limitation that you have.
We could probably make a change to VMD that would allow one to load a
multi-structure PDB as separate molecules, but we'll have to figure out
what the user interface issues associated with this will be, and how best
to change the code for this purpose. That being the case, it will be a little
while before we'd be able to implement this.

Alternately, one could easily write a very short C program that would
split out a multi-structure PDB file and make it into a group of individual
files which could then be trivially loaded into VMD by a script. I would
think that this could be done by keying off of the "END" records in the
multi-structure file. I suspect that one could write the C code and a
small Tcl or Python script to drive it and do the loading with a relatively
small amount of effort, much smaller than what it will take us to implement
this natively in VMD itself. If you or someone else wants to give this
a try, I'd be happy to help you get it done. Someone that knows C and Tcl
can probably write the code to parse and generate new files in 30 minutes
or less. If no one volunteers let me know and I'll help out.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

> From: "Craig Morton" <craig_at_medstv.unimelb.edu.au>
> To: <vmd-l_at_ks.uiuc.edu>
> Subject: Multiple entry PDB loading
>
> Hi all,
>
> I've been using VMD to inspect docking runs from AutoDock, where the input
> file is in PDB format with multiple entries for the different docked
> conformations. It works beautifully using the animation tool to scroll back
> and forth through the hits.
>
> Now I want to do something very similar and read a multiple entry PDB file
> that I've generated using OpenEye's FRED to screen a database (and yes, I
> know I can do it in Vida, but I like to use VMD for its graphical
> capabilities). Unfortunately VMD assumes that a multiple entry PDB file is a
> trajectory - or at least is mutiple copies of the same structure. It rejects
> any entries in the list that don't have the same number of atoms as the
> first entry, and insists on using the connectivity it found in the first
> entry for any other entry of the same size, regardless of conect records or
> geometry.
>
> I can see why the animation reading tool was written that way, but is there
> some other way I could convince it to read in a multiple entry file where
> the structures are different? It would be very annoying to have to load them
> all individually.
>
> Cheers,
>
> Craig.
>
> Dr Craig Morton Ph: +61 3 9288 2519
> Biota Structural Biology Laboratory Fx: +61 3 9416 2676
> St. Vincent's Institute of email: craig_at_medstv.unimelb.edu.au
> Medical Research. http://www.svimr.unimelb.edu.au 

-- 
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              
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