hi Michael et al.,
I'm still unable to visualize DX-formatted electrostatics maps in PyMOL,
as described in my earlier email (attached). I've tried various
scenarios to get this to work, including the following:
(1) fresh, clean install of the pymol-0.95-1.rh90.py22 RPM, downloading
the various electrostatics.py, dx.py, etc. modules from your website and
then using the load_dx() function with DX maps already calculated in a
standalone APBS run...
(2) rebuilding PyMOL 0.95 from CVS version, incorporating the new and
modified source such as ObjectMap.{h,c}, PMGApp.py, etc. exactly as
described on your website (the recompiled PyMOL works fine)...
(3) both of the above steps with either a pre-calculated dx map or for
one generated on-the-fly in PyMOL via the apbs_tools wizard, for both a
small protein and a large one
Based on the ~60-sec delay and increased processor usage after issuing a
PyMOL command like 'load_dx("some_file.dx","mapa")', I think the DX file
is actually being read. However, the process invariably dies with the
following error stream:
PyMOL>load_dx some_file.dx
Traceback (most recent call last):
File "modules/pymol/parser.py", line 139, in parse
result=apply(kw[nest][0],args[nest],kw_args[nest])
File "/usr/lib/python2.2/site-packages/pymol/modules/pymol/dx.py",
line 1034, in load_dx
importing.load_object(importing.loadable.DX, thing, mapName)
AttributeError: class loadable has no attribute 'DX'
The "line 139" parser.py error sometimes shows up as line 255, and this
error behavior also results if I perform more explicit function calls
such as 'load_dx("some_file.dx","mapa")'.
If anyone has any ideas about solving this problem, please let me know....
Thanks,
Cameron
PS. This is all on a Red Hat 9 Linux PC utilizing the following Python
packages:
CHEMCCA35:NFkB[8] rpm -qa | egrep -i python
python-2.2.2-26
python-optik-1.4-2
rpm-python-4.2-1
python-devel-2.2.2-26
gnome-python2-canvas-1.99.14-5
gnome-python2-gtkhtml2-1.99.14-5
gnome-python2-bonobo-1.99.14-5
python-numeric-devel-22.0-2mdk
libxml2-python-2.5.4-3.rh9
gnome-python2-1.99.14-5
python-numeric-22.0-2mdk
=== Michael George Lerner wrote (on 05/13/2004 09:55 AM): ===
Hi,
My code should work again. The parsing errors were probably caused by the
fact that my code was out of date with respect to the current CVS version
of PyMOL. Please let me know if it doesn't work!
Thanks,
-michael
Has anyone had luck with loading DX format electrostatic potential maps
that were generated by APBS? I tried to use the electrostatics wizard and
load_dx function created by Michael Lerner
(http://www-personal.umich.edu/~mlerner/Pymol/) but I get parsing errors
when I try to load a map calculated by standalone APBS. The maps are very
large (small grid spacing and a very large molecule) - could that be the
problem? Please help.
Ken
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--
Cameron Mura
UCSD
--- Begin Message ---
hi Michael,
quick question about your APBS/PyMOL stuff-- if I've already created an
OpenDX file as output of APBS (all indpendent of PyMOL) and simply want
to display it in PyMOL along with the molecule, is there a minimal
protocol for doing this (i.e. without recompiling PyMOL)??
So far, I've done the following:
(1) downloaded "electrostatics.py" and placed it in
modules/pymol/wizard/, as per instructions on your PyMOL page; also
modified the Tk window thing (PMGApp.py) with the Wizard menu item...
(2) downloaded your "dx.py" in local directory and loaded it into PyMOL
via "run dx.py" on PyMOL command line (no errors)
(3) tried "load_dx('sample.dx','mapa')", where 'sample.dx' is an
electrostatics map already output by APBS. PyMOL then number crunches
for a bit, and ends with following error:
PyMOL>load_dx('sample.dx','mapa')
Traceback (most recent call last):
File "modules/pymol/parser.py", line 255, in parse
exec(com2[nest]+"\n",pymol_names,pymol_names)
File "<string>", line 1, in ?
File "dx.py", line 1033, in load_dx
importing.load_object(importing.loadable.DX, thing, mapName)
AttributeError: class loadable has no attribute 'DX'
I'm too impatient to read everything in detail right now, so I was
wondering if I also need to load in apbs_tools.py, your modified
psize.py, replace the PyMOL files ObjectMap.h, etc. with your's,
recompile, so on and so forth just to read in a pre-computed dx map?
This is all in PyMOL v0.95, btw.
Thansk for any advice,
Cameron
--- End Message ---
