Hi,
Note that there is also the 'nmwiz' keyword (and associated keywords)
for the 'diagmatrix' command that allows you to write files which can
be read by VMD's NMWiz plugin for generating "porcupine" plots. E.g.
runanalysis diagmatrix myCovar out evecs.dat vecs 5 name myEvecs \
nmwiz nmwizfile nmwiz.nmd nmwizvecs 5 nmwizmask <mask>
where <mask> corresponds to the mask used in generating the covariance matrix.
-Dan
On Thu, Oct 30, 2014 at 8:15 AM, Vlad Cojocaru
<vlad.cojocaru.mpi-muenster.mpg.de> wrote:
> Thanks Jason,
>
> Great ! This works nicely ....
>
> Vlad
>
>
> On 10/30/2014 12:33 PM, Jason Swails wrote:
>> On Thu, 2014-10-30 at 10:35 +0100, Vlad Cojocaru wrote:
>>> Dear Ambers,
>>>
>>> Can anybody recommend me a program to visualize the modes and
>>> projections created by cpptraj ? VMD used to have a plugin "IED" but
>>> this is quite old and doe not work with newest VMD versions ...
>> You can actually have cpptraj print out full trajectory files with the
>> "modes" command for this purpose.
>>
>> If you type "help modes" in the cpptraj command interpreter, it will
>> give you a list of "trajout" options that let you control how the
>> trajectory is printed.
>>
>> HTH,
>> Jason
>>
>
> --
> Dr. Vlad Cojocaru
> Computational Structural Biology Laboratory
> Department of Cell and Developmental Biology
> Max Planck Institute for Molecular Biomedicine
> Röntgenstrasse 20, 48149 Münster, Germany
> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
> http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
>
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
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Received on Thu Oct 30 2014 - 08:00:02 PDT
