Re: [PyMOL] pymol and gromacs
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 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. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] pymol and gromacs
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 -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Pymol and Gromacs XTC
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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[PyMOL] Pymol and Gromacs XTC
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 -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
