From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu May 09 2013 - 10:41:28 CDT

The GUI always returns a canonical file name. With the current setup you can have relative paths stored in scripting. Forcing those to be canonicalized inside of VMD removes that option. In scripting you always can adjust your script.

If I remember correctly the current behavior was adopted because there were requests from people that were dissatisfied with the behavior you are asking for.

Axel.
--
Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.

-----Original Message-----
From: Christopher MacDermaid <chris.macdermaid_at_gmail.com>
Date: Thu, 9 May 2013 11:32:35
To: Axel Kohlmeyer<akohlmey_at_gmail.com>
Cc: <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: molinfo top get filename, dialogue vs. "mol new"

Hi Axel,

On Thu, May 9, 2013 at 10:21 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> **
> Why not simply canonicalize the file name yourself before calling mol new?
>

Of course, which is the workaround. However, this doesn't change that fact
that molinfo returns different things depending on how the mol was loaded.
I think it's pretty clear that the expectation should be that the absolute
path is always returned. What's the advantage the way it currently is?


> Axel
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
> ------------------------------
> *From: * Christopher MacDermaid <chris.macdermaid_at_gmail.com>
> *Sender: * owner-vmd-l_at_ks.uiuc.edu
> *Date: *Thu, 9 May 2013 09:30:13 -0400
> *To: *<vmd-l_at_ks.uiuc.edu>
> *Subject: *vmd-l: molinfo top get filename, dialogue vs. "mol new"
>
> Hello,
>
> When calling "molinfo top get filename", the filename returned is
> different depending on the method in which I choose to load the molecule.
>
> If I use the file browser dialogue, molinfo returns the absolute path,
> however if I use the console with "mol new" it returns the relative path:
>
> vmd> mol new ../../../../test/test.pdb
>
> vmd > molinfo top get filename
> ../../../../test/test.pdb
>
> detrimental in the event that I want to reload the molecule like so and if
> I've changed working directories...
>
> proc reload { mol } {
> lassign {*}[molinfo $mol get filename] psf dcd
> mol delete $mol
> mol new $psf type psf waitfor all
> mol addfile $dcd waitfor all
> }
>
> Can this be fixed such that "mol new" will set the correct file name to
> one that is the absolute path of the loaded files. I realize this may
> present complications since mol new can be used to create an empty
> molecule, but the behavior regarding the file names is rather unexpected.
>
> Thanks!
>
> Dr. Chris MacDermaid, Postdoctoral Fellow
> Institute for Computational Molecular Science
> Temple University, Philadelphia, PA
>
>


--
--
C

Dr. Chris MacDermaid, Postdoctoral Fellow
Institute for Computational Molecular Science
Temple University, Philadelphia, PA