Hi Anastassis, I got the same error with a few pdb files.The problem is the following. The B-factor in the pymol-generated pdb file is somtimes set to values larger than 100 (119.63 in your case) thus occupying all its columns of the lovely PDB-format and not leaving any space to the preceding occupancy column (1.00 in your case). The script psize.py however parses these lines by splitting on white-spaces and crashes when converting the merged field ...
The remedy is to modify psize.py like this: around line 108, replace words = string.split(subline) withwords = line[30:38], line[38:46], line[46:54], line[54:60], line[60:66], line[72:76], line[76:78] ## PDB-format is fixed-space!
Hope that works for you, in any case attached is my debugged psize.py file.Another error occurs when calculating the electrostatics of pdb 1F88, a transmembrane protein. The same thing happens on the pdb2pqr Server (http://nbcr.net/pdb2pqr): 'NoneType' object has no attribute 'getCoords'
looks a bit like strange atom name problem, I get the script working by inserting:
if not nextatom: return 0 in line 608, however I am not 100% sure whether its still sound... Cheers, Andreas Peter Adrian Meyer wrote:
Hi,parseInput self.parseLines(file.readlines()) File "/usr/local/apbs-0.4.0/tools/manip/psize.py", line 116, in parseLines self.q = self.q + float(words[3]) ValueError: invalid literal for float(): 1.00119.63 Any clues ?It looks like it's reading from a pdb file when it's expecting a pqr file, and that the split statement didn't produce the expected input due to the B factor in the pdb file being too large. Possibly you have to generate a pqr file before setting the grid (I'm not farmilar enough with the apbs-pymol plugin to remember offhand). Good luck, Pete Pete Meyer Fu Lab BMCB grad student Cornell University ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
-- Andreas Henschel Bioinformatics Group TU Dresden Tatzberg 47-51 01307 Dresden, Germany Phone: +49 351 463 40063 EMail: a...@biotec.tu-dresden.de
psize.py
Description: application/python
