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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