Re: [PyMOL] pymol and gromacs

2018-05-19 Thread Thomas Holder 
Hi Paul,

Looks like they are working on a new version of the plugin:
https://github.com/makson96/Dynamics/pull/95

You could give this modified version a try:
https://github.com/speleo3/Dynamics/blob/no-tk-mainloop/pymol_plugin_dynamics.py

Cheers,
  Thomas

> On May 17, 2018, at 1:50 PM, Paul Buscemi <busce...@umn.edu> wrote:
> 
> 
> Dear Users,
> 
> I’ve been able to use Pymol 1.7 with Gromacs plugin ( ppa download and 
> install ), but have not found a  plugin/method to use version2.1.1 ( 
> Schrodinger maintained ).
> Is a plugin for v 2.1.1 available ?
> 
> System is linux Mint 18.1
> 
> Regards
> Paul

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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[PyMOL] Pymol and Gromacs XTC

2012-02-08 Thread Raúl Mera 
Dear all,

I think there is no easy way of reading Gromacs xtc trajectories into PyMOL,

At least in the version compiled for Debian, which I don't think
includes the vmd plugins.

I should have probably asked about this before, but now I just coded a
little script that loads xtc in pymol.  It has a part in C,
and it requires a Gromacs installation to compile and run. It probably
only works for Linux (And I would guess Mac) but getting it to run in
other SO should be easy,  just signal how to find/link the gromacs
libraries in the setup.py file.

If someone is interested,  it is in
https://github.com/rmera/xtc-python/downloads

It there was an easy way already, just ignore this :-)

Cheers!

Raúl

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Re: [PyMOL] Pymol and Gromacs XTC

2012-02-08 Thread Thomas Holder 

Hi Raúl,

the pymol 1.2r1 package in Ubuntu (lucid) loads xtc files fine, it has 
the VMD plugins enabled. As far as I know this is the same package as in 
debian (at least in squeeze, http://packages.debian.org/squeeze/pymol).


If you compile from source, you can apply the attached patch.

Cheers,
  Thomas

On 02/08/2012 02:18 PM, Raúl Mera wrote:

Dear all,

I think there is no easy way of reading Gromacs xtc trajectories into PyMOL,

At least in the version compiled for Debian, which I don't think
includes the vmd plugins.

I should have probably asked about this before, but now I just coded a
little script that loads xtc in pymol.  It has a part in C,
and it requires a Gromacs installation to compile and run. It probably
only works for Linux (And I would guess Mac) but getting it to run in
other SO should be easy,  just signal how to find/link the gromacs
libraries in the setup.py file.

If someone is interested,  it is in
https://github.com/rmera/xtc-python/downloads

It there was an easy way already, just ignore this :-)

Cheers!

Raúl


--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
Index: setup.py
===
--- setup.py	(revision 3975)
+++ setup.py	(working copy)
@@ -132,8 +132,8 @@
   /usr/include/freetype2,
 # /users/warren/ext/include,
 # VMD plugin support
-#  contrib/uiuc/plugins/include,
-#  contrib/uiuc/plugins/molfile_plugin/src,
+  contrib/uiuc/plugins/include,
+  contrib/uiuc/plugins/molfile_plugin/src,
   modules/cealign/src,
 	  modules/cealign/src/tnt, ]
 libs=[GL,GLU,glut,png,z,freetype, GLEW,
@@ -153,7 +153,7 @@
 # Numeric Python support
 #(_PYMOL_NUMPY,None),
 # VMD plugin support   
-#   (_PYMOL_VMD_PLUGINS,None)
+   (_PYMOL_VMD_PLUGINS,None),
 		(NO_MMLIBS,None),
 ]
 ext_comp_args=[-ffast-math,-funroll-loops,-O3,-g]
@@ -307,7 +307,7 @@
 layer5/main.c
 # VMD plugin support
 # switch the 0 to 1 to activate the additional source code
-] + 0 * [
+] + 1 * [
 # (incomplete support -- only TRJ, TRR, XTC, DCD so far...)
 'contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c',
 'contrib/uiuc/plugins/molfile_plugin/src/avsplugin.cpp',
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