VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu May 05 2022 - 23:21:28 CDT

Hi,
  On some platforms, the file browser will record the fully qualified
path for files that are loaded into VMD, and in such cases, if you
move all of your files around, it would cause trouble with loading
the saved state file. In such a case, the easiest thing to do is
open up the .vmd saved state file in a text editor (it's just a script)
and you can edit the filenames to remove the full path leaving just
the filename itself, or a relative path that happens to match your
new directory structure.

Best,
  John Stone

On Mon, May 02, 2022 at 11:56:46PM +0530, Debostuti Ghoshdastidar wrote:
> Hi John
> I'm sorry my earlier mail was confusing. I mentioned *.pdb to indicate
> that there re several pdb files with different names. Actually each file
> name is spelt out in the .vmd file as in 3g9i.pdb, 1glu.pdb, etc, 60 of
> them in all.
> Debostuti
> On Mon, 2 May 2022, 23:21 John Stone, <[1]johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> Â It looks like something unusual happened such that "*.pdb" was
> recorded in the saved state file load commands, but that shouldn't
> have happened. Normally it would list the files one-at-a-time.
>
> How did you originally load the 60 superimposed PDBs? Did you run
> a different script to do this?
> Did you edit the saved state file?
>
> I don't think the problem has anything to do with the fact
> that you had moved the files, but rather than "*" operator which
> will not be processed correctly except in combination with the
> Tcl "glob" command.
>
> Best,
> Â John Stone
>
> On Mon, May 02, 2022 at 05:47:12PM +0530, Debostuti Ghoshdastidar wrote:
> >Â Â Hi
> >Â Â I had created a project with ~60 superimposed crystal structures
> and was
> >Â Â able to load the visualization state until I moved the PDBs to
> another
> >Â Â directory by mistake. However, even though I restored the files
> back to
> >Â Â the correct path the visualization state is not loading and shows
> the
> >Â Â following errors sequentially for each of the PDB files:
> >Â Â >Could not read file *.pdb
> >Â Â >Unable to load file '*.pdb' using file type 'pdb'.
> >Â Â >No molecules loaded.mol operates on one molecule only
> >Â Â ....
> >Â Â Of course the PDB files were not edited, they were moved to
> another
> >Â Â directory and then moved back. Could someone please suggest a way
> for me
> >Â Â to recover the project?
> >Â Â Debostuti
> >Â Â --
> >Â Â Debostuti Ghosh Dastidar
> >Â Â Research Associate
> >Â Â PDB-India
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> [2]http://www.ks.uiuc.edu/~johns/Â Â Â Â Â Â Phone: 217-244-3349
> [3]http://www.ks.uiuc.edu/Research/vmd/Â Â Â
>
> References
>
> Visible links
> 1. mailto:johns_at_ks.uiuc.edu
> 2. http://www.ks.uiuc.edu/~johns/
> 3. http://www.ks.uiuc.edu/Research/vmd/ 

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