From: Cameron M. <cm...@uc...> - 2004-05-14 21:15:38
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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: > [cmura@chemcca35 pymol]# diff -uNr > /u1/cmura/PYMOL/MGLerner_APBSplugin/Cmd.c layer4/Cmd.c > --- /u1/cmura/PYMOL/MGLerner_APBSplugin/Cmd.c 2004-05-13 > 14:18:02.000000000 -0700 > +++ layer4/Cmd.c 2004-05-14 09:49:26.000000000 -0700 > @@ -501,12 +501,12 @@ > int ok=true; > char *str1; > OrthoLineType s1; > - int int1,int2,int3,int4,int5; > - ok = > PyArg_ParseTuple(args,"siiiii",&str1,&int1,&int2,&int3,&int4,&int5); > + int int1,int2,int3,int4,int5,int6; > + ok = > PyArg_ParseTuple(args,"siiiii",&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: >> >> >> >>>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' >>> >>> > >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 |