Re: writing back coordinates of waters that cross the unit cell

From: Thomas Evangelidis (tevang3_at_gmail.com)
Date: Fri Nov 26 2010 - 08:19:19 CST

Just for the record, Truncate Trajectory was developed in VMD 1.8.6 with the
goal to become a plugin. We have tried to incorporate it in the plugin tree
of a beta release of VMD 1.8.7, if I remember correctly in January 2009, but
due to unexpected behaviour it wasn't eventually included in the stable
release. As far as I remember there was a problem with the GUI (Axel pointed
this out) while switching from frame to frame, thus I had to add command
line options and run it from the console, as well as psfgen related issues.
Since then I haven't touched the code again, waiting for the new features of
VMD (namely saving bonds, angles, dihedrals etc into objects) that would
render psfgen usage redundant. It is in my TODO list to finalise a stable
version for the current VMD release hopefully within 2011.

To get a flavour of what it could do have a look at:

https://sites.google.com/site/thomasevangelidishomepage/truncate-trajectory-plugin-for-vmd

PS: Hi Dr. Glykos, hope everything is well.

On 25 November 2010 17:53, Nicholas M Glykos <glykos_at_mbg.duth.gr> wrote:

>
>
> > For further work I wold like to cut out different water spheres around
> the
> > protein from a snapshot, So I would need a buffer of water around the
> > protein.
>
> Thomas Evangelidis had once upon a time written a VMD script (named
> 'trunctraj') which was supposed to apply PBC translations in order to
> generate a new DCD file containing a specified number of waters around the
> protein component. The script is still there (in something like
> /usr/local/lib/vmd/plugins/noarch/tcl/trunctraj1.5/) _but_ I have never
> used it and (obviously) can not promise that it will do the trick.
>
> Nicholas
>
>
> --
>
>
> Dr Nicholas M. Glykos, Department of Molecular Biology
> and Genetics, Democritus University of Thrace, University Campus,
> Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
> Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/>
>
>

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