VMD-L Mailing List

From: Stéphane Teletchéa (steletch_at_biomedicale.univ-paris5.fr)
Date: Wed Sep 25 2002 - 03:17:31 CDT

Assuming the structures in the pdb file are of the same lenghth, one could
easily generate noew files with the command split :
split -n 1544 my_pdb.pdb
Would provide :
aa
ab
ac
...
As much as needed ..
Stef

Le Mardi 24 Septembre 2002 21:19, John Stone a écrit :
> 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