Re: [PyMOL] loading electrostatic maps generated with apbs
Hi,
(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...
This won't work. For now, PyMOL needs to be recompiled for my DX-related
code to work.
(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)...
(I think you mean the current CVS version of PyMOL .. the code on my
webpage is synchronized with that, rather than 0.95)
This, on the other hand, should work. The fact that the recompiled PyMOL
works is a good sign.
(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.
I think you're right.
However, the process invariably dies with the following error stream:
PyMOLload_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'
This is very strange. I know you said that you installed all of the files
I listed, but are you *sure* that you installed my version of importing.py
as modules/pymol/importing.py? The error here is that it can't find
importing.loadable.DX, but if you have my version of importing.py, that
shouldn't be a problem.
If really do have an up-to-date version of my code, we should probably
figure out what's wrong off-list.
Thanks,
-michael
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
Re: [PyMOL] loading electrostatic maps generated with apbs
hi Michael,
I finally got the APBS plugin to work
(http://mccammon.ucsd.edu/~cmura/PYMOL_examples/apbs_plugin.html).
I'm not sure what I did differently this time, but I did rebuilt PyMOL
from scratch and re-downloaded your python modules and modified source
files. The only catch was that I had to make the following changes near
line 500 of your layer4/Cmd.c in order to build the CVS version of PyMOL:
[cm...@chemcca35 pymol]# diff -uNr
/u1/cmura/PYMOL/MGLerner_APBSplugin/Cmd.c layer4/Cmd.c
--- /u1/cmura/PYMOL/MGLerner_APBSplugin/Cmd.c 2004-05-13
14:18:02.0 -0700
+++ layer4/Cmd.c2004-05-14 09:49:26.0 -0700
@@ -501,12 +501,12 @@
int ok=true;
char *str1;
OrthoLineType s1;
- int int1,int2,int3,int4,int5;
- ok =
PyArg_ParseTuple(args,si,str1,int1,int2,int3,int4,int5);
+ int int1,int2,int3,int4,int5,int6;
+ ok =
PyArg_ParseTuple(args,si,str1,int1,int2,int3,int4,int5,int6);
if(ok) {
SelectorGetTmp(str1,s1);
APIEntry();
-ok = ExecutiveSmooth(s1,int1,int2,int3,int4,int5);
+ok = ExecutiveSmooth(s1,int1,int2,int3,int4,int5,int6);
APIExit();
SelectorFreeTmp(s1);
}
Thanks again,
Cameron
=== Michael George Lerner wrote (on 05/14/2004 07:01 AM): ===
Hi,
(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...
This won't work. For now, PyMOL needs to be recompiled for my DX-related
code to work.
(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)...
(I think you mean the current CVS version of PyMOL .. the code on my
webpage is synchronized with that, rather than 0.95)
This, on the other hand, should work. The fact that the recompiled PyMOL
works is a good sign.
(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.
I think you're right.
However, the process invariably dies with the following error stream:
PyMOLload_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'
This is very strange. I know you said that you installed all of the files
I listed, but are you *sure* that you installed my version of importing.py
as modules/pymol/importing.py? The error here is that it can't find
importing.loadable.DX, but if you have my version of importing.py, that
shouldn't be a problem.
If really do have an up-to-date version of my code, we should probably
figure out what's wrong off-list.
Thanks,
-michael
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
--
Cameron Mura
UCSD
Re: [PyMOL] loading electrostatic maps generated with apbs
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:
PyMOLload_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
---BeginMessage---
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:
PyMOLload_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
