Hi, I just checked the apbs download page and I couldn't find apbs binaries available for windows. The only way I've seen (through previous mailing lists posts) is to compile it using cygwin, but the performance is less than optimal.
So if you or someone else has compiled apbs for windows, the binary location is the path to the apbs executable. For example "apbs" on your windows system may be in c:\cygwin\usr\local\apbs\bin\i686\apbs . Furthermore the psize.py should be located at: c:\cygwin\usr\local\apbs\tools\manip\psize.py ..maybe something like that. Yes the plugin is asking for the .dx electrostatic map. By default the electrostatic map is placed into %TEMP% (maybe c:\documents and settings\you\temp or c:\windows\temp). You can check what %TEMP% or %TMP% is set to by going to control panels -> system -> "advanced" tab -> environment variables. Otherwise you can directly specify where the pymol-generated.dx file should go by changing it in the "Temporary File Locations" tab of the APBS tools (e.g. Temporary DX file: c:\mydir\pymol-generated.dx). Also may I suggest that for a fast overall electrostatics calculation, without having to compile anything, to look into GRASP2 for windows. It is at http://trantor.bioc.columbia.edu/grasp2/ . You can import the .phi maps from grasp into many applications including pymol and visualize them also. Hope that helps, Sabuj Pattanayek migalepa wrote: > I've been trying to generate an electrostatic potential map of the surface of > a protein using Pymol but haven't been successful. I'm working with the latest > version of pymol (0.98, windows version), which brings the APBS plugin (I have > as well installed the APBS plugin "apbs_tools.py") that is supposed to do the > necessary calculation in a straightforward way, according to the guidelines > provided in http://www-personal.umich.edu/~mlerner/Pymol/. I've follewed them > but the plugin asks for an "APBS binary location". I do not know what a > "binary location" is or where to find it. I'm using PDB files converted to PQR > files, as indicated in > http://www.csb.yale.edu/userguides/graphics/pymol/electro.html., and run the > APBS tool selecting a ramdonly chosen "APBS binary location". The program > seems to do calculations on the surface of the protein although does not > generate any figure representing the results. By clicking on visualization > the plugin warms that at least a molecule and a map must be loaded. Is the > plugin asking for the calculated electrostatic surface map? Is so, how do I > find it? Does it have to be with the "APBS binary location" issue? Well, lots > of questions... > > Thank you beforehand... > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: NEC IT Guy Games. How far can you shotput > a projector? How fast can you ride your desk chair down the office luge track? > If you want to score the big prize, get to know the little guy. > Play to win an NEC 61" plasma display: http://www.necitguy.com/?r=20 > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
