From: Anastassis P. <a.p...@nk...> - 2006-11-24 15:18:44
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Hi - I installed apbs and tools (0.4.0) in a Linux box. I then specified the location of psize.py and apbs executable. when i load a protein and click on 'set grid' according to instructions I get on a new window a rather cryptic response: Error: 6 ValueError Exception in Tk callback Function: <function <lambda> at 0x414cfbc4> (type: <type 'function'>) Args: () Traceback (innermost last): File "/Xsoftware/pymol/ext/lib/python2.3/Pmw/Pmw_1_2/lib/ PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/Xsoftware/pymol/ext/lib/python2.3/Pmw/Pmw_1_2/lib/ PmwDialog.py", line 153, in <lambda> command=lambda self=self, name=name: self._doCommand(name)) File "/Xsoftware/pymol/ext/lib/python2.3/Pmw/Pmw_1_2/lib/ PmwDialog.py", line 132, in _doCommand return command(name) File "/Xsoftware/pymol/modules/pmg_tk/startup/apbs_tools.py", line 1055, in execute self.runPsize() File "/Xsoftware/pymol/modules/pmg_tk/startup/apbs_tools.py", line 1096, in runPsize size.runPsize(pdb_filename) File "/usr/local/apbs-0.4.0/tools/manip/psize.py", line 267, in runPsize self.parseInput(filename) File "/usr/local/apbs-0.4.0/tools/manip/psize.py", line 102, in 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 ? A. |
From: Peter A. M. <pa...@co...> - 2006-11-26 22:03:54
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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 |
From: Andreas H. <ah...@bi...> - 2006-11-29 19:40:47
Attachments:
psize.py
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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 > > > > > >------------------------------------------------------------------------- >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 >PyM...@li... >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: ah...@bi... |