VMD-L Mailing List

From: Debostuti Ghoshdastidar (debostutighosh_at_gmail.com)
Date: Fri May 06 2022 - 01:18:10 CDT

Thank you John...this worked!!!

On Fri, May 6, 2022 at 9:51 AM John Stone <johns_at_ks.uiuc.edu> wrote:

> 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/
> 

-- 
Debostuti Ghosh Dastidar
Research Associate
PDB-India