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

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Nov 26 2010 - 11:26:13 CST

tom,

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
   of data.

cheers,
   axel.

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:
>
> 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/
>>
>
>

-- 
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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