VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Sep 26 2019 - 13:48:38 CDT

Patrik,
  As Axel has already stated, the best way to resolve problems like this
is to send us examples of .mdf / .car files that you're having trouble
loading in VMD, ideally accompanied by a version of the same structure
as PDB or another format that actually loads _correctly_. That would allow
us to do detailed comparisons of how the files are parsed and how information
gets sent by the particular file reader plugins into VMD itself. Problems
like these can be very tricky to track down, and without collecting
good example cases, it's not possible to proceed further.

The emails you referenced from 2011/2012 didn't provide us with any
structures for comparison. Have you tried using OpenBabel to
convert the .car / .mdf files to something like a PDB or another
format that VMD definitely reads without any difficulties?

Since XenoView seems to have dropped out of ongoing development sometime
back in 2008 and its source code isn't available, I can't say much about
whether the files it writes are always correctly formatted or how their
structure compares with what the VMD plugins are expecting. The problem
you have loading XenoView output might be on the VMD side, but it might
also be that these files have a formatting irregularity that the carplugin
and mdfplugin implementations for VMD won't accept.

Best regards,
  John Stone

On Tue, Sep 24, 2019 at 12:20:18PM -0400, Axel Kohlmeyer wrote:
> On Tue, Sep 24, 2019 at 12:13 PM Patrik Molnár <pbadoo1995_at_gmail.com> wrote:
>
> > Dear VMD Team!
> >
> > I created a simple methane molecule in XenoView and saved in .car/.mdf
> > file.
> >
> > But whenever I try to open them in VMD, I get error message(s).
> >
>
> *what* error messages do your get?
> what is your VMD version? and what platform are you running on?
>
>
> > What did I do wrong? Can it be that the versions don't match?
> >
>
> versions of what?
>
>
> > I have already seen that other VMD users had problem with that plugins:
> >
> > http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/17736.html
> >
> > http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/21143.html
> >
> > What was the consequence?
> >
>
> you would have to ask the people posting the questions.
>
>
> > How could I solve this problem?
> >
>
> difficult to say. step one would be to provide sufficient information to
> reproduce the situation, e.g. by posting a set of small(!) files that
> reproduce the errors.
>
> axel.
>
>
> >
> > Best regards,
> >
> > Patrik Molnar
> >
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy. 

-- 
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/