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)
with
words = 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
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Andreas Henschel
Bioinformatics Group
TU Dresden
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Phone: +49 351 463 40063
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psize.py
Description: application/python
