From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Nov 26 2010 - 11:26:13 CST
most of the issues have been resolved.
a) there is now the topotools plugin that acts as a frontend
to all kinds of bond manipulation and transfer between selections.
b) the improved bigdcd that i wrote, should take care most of where
you were getting deadlocks. this will become entirely obsolete
as soon as john finds the time to implement out-of-core processing
On Fri, Nov 26, 2010 at 9:19 AM, Thomas Evangelidis <tevang3_at_gmail.com> wrote:
> 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:
> 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.
>> 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/
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 Institute for Computational Molecular Science Temple University, Philadelphia PA, USA.
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