Gilles, The PyMOL and APBS programs have differing views as to whether PDB & PQR files are column-based or space-delimited, respectively. We must eventually sort this out, because it causes continued grief for our users in common.
For now, however, the workaround is to make sure no B-factors exceed 100. alter all, b=min(b,99.9) should about do it. Cheers, Warren -----Original Message----- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Gilles Truan Sent: Wednesday, September 17, 2008 1:09 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Strange behaviour with APBS I have noticed a strange behaviour of the APBS module. I used it a lot recently and it works perfectly for 95% of the structures I analyzed. I usually fetch the pdb code, then remove waters, heteroatoms and so on. I also noticed that in some cases, when the b factor is quite big (over 100) APBS cannot work the pdb file because it mixes up the b factor and the number which is just before (occupancy). But I managed with that, I usually erase the b factor to 0 before doing the APBS calculation and everything works fine then. The other strange behavious is related to nothing I can pinpoint unfortunately. For some files (I always fetch them with the fetch command from Pymol), I can set the grid OK and when I launch APBS, I can see the file being processed (I see the select and hydrogens go on!) and then it stops with the following error message: ObjectMapLoadDXFile-Error: Unable to open file! ObjectMapLoadDXFile: Does 'pymol-generated.dx' exist? All the paths for APBS are correctly setup, the temp files are setup as well. If I then fetch a new file, APBS works, even for several files (one after another) and if I come back to the file I wanted to do first, it gives me the same error message (BTW, the pdb file is 1CJC). Any help would be greatly appreciated!!!
