Hi Evan:
I ran pdb2pqr by hand and I think the Zn and CTP is problematic:
REMARK 5 WARNING: PDB2PQR was unable to assign charges
REMARK 5 to the following atoms (omitted below):
REMARK 5 7220 ZN in ZN 154
REMARK 5 7221 ZN in ZN 154
REMARK 5 7222 N1 in CTP 901
REMARK 5 7223 C2 in CTP 901
REMARK 5 7224 N3 in CTP 901
REMARK 5 7225 C4 in CTP 901
REMARK 5 7226 C5 in CTP 901
REMARK 5 7227 C6 in CTP 901
REMARK 5 7228 O2 in CTP 901
REMARK 5 7229 N4 in CTP 901
REMARK 5 7230 C1' in CTP 901
REMARK 5 7231 C2' in CTP 901
REMARK 5 7232 O2' in CTP 901
REMARK 5 7233 C3' in CTP 901
REMARK 5 7234 C4' in CTP 901
REMARK 5 7235 O4' in CTP 901
REMARK 5 7236 O3' in CTP 901
REMARK 5 7237 C5' in CTP 901
REMARK 5 7238 O5' in CTP 901
REMARK 5 7239 PA in CTP 901
REMARK 5 7240 O1A in CTP 901
REMARK 5 7241 O2A in CTP 901
REMARK 5 7242 O3A in CTP 901
REMARK 5 7243 PB in CTP 901
REMARK 5 7244 O1B in CTP 901
REMARK 5 7245 O2B in CTP 901
REMARK 5 7246 O3B in CTP 901
REMARK 5 7247 PG in CTP 901
REMARK 5 7248 O1G in CTP 901
REMARK 5 7249 O2G in CTP 901
REMARK 5 7250 O3G in CTP 901
REMARK 5 7251 N1 in CTP 902
REMARK 5 7252 C2 in CTP 902
REMARK 5 7253 N3 in CTP 902
REMARK 5 7254 C4 in CTP 902
REMARK 5 7255 C5 in CTP 902
REMARK 5 7256 C6 in CTP 902
REMARK 5 7257 O2 in CTP 902
REMARK 5 7258 N4 in CTP 902
REMARK 5 7259 C1' in CTP 902
REMARK 5 7260 C2' in CTP 902
REMARK 5 7261 O2' in CTP 902
REMARK 5 7262 C3' in CTP 902
REMARK 5 7263 C4' in CTP 902
REMARK 5 7264 O4' in CTP 902
REMARK 5 7265 O3' in CTP 902
REMARK 5 7266 C5' in CTP 902
REMARK 5 7267 O5' in CTP 902
REMARK 5 7268 PA in CTP 902
REMARK 5 7269 O1A in CTP 902
REMARK 5 7270 O2A in CTP 902
REMARK 5 7271 O3A in CTP 902
REMARK 5 7272 PB in CTP 902
REMARK 5 7273 O1B in CTP 902
REMARK 5 7274 O2B in CTP 902
REMARK 5 7275 O3B in CTP 902
REMARK 5 7276 PG in CTP 902
REMARK 5 7277 O1G in CTP 902
REMARK 5 7278 O2G in CTP 902
REMARK 5 7279 O3G in CTP 902
REMARK 5
REMARK 6 Total charge on this protein: -10.0000 e
REMARK 6
Bill
On Fri, 21 Sep 2007 08:46:43 -0700
"DeLano Scientific" <del...@delsci.info> wrote:
Evan,
This appears to be a problem with file format incompatibility between PyMOL
and the psize.py script. I suspect that rounding off the atom coordinates
will eliminate it:
alter_state 1, all, (x,y,z)=(int(x*1000)/1000.0, int(y*1000)/1000.0,
int(z*1000)/1000.0)
Cheers,
Warren
_____
From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Evan
Kantrowitz
Sent: Friday, September 21, 2007 7:28 AM
To: PyMOL-users@lists.sourceforge.net
Subject: [PyMOL] Pymol apbs problem
With a certain file 1za1 from pdb when I try to run apbs I get the errors
below. Other files are OK. Any suggestions?
error: 1
ValueError Exception in Tk callback
Function: <function <lambda> at 0x182892b0> (type: <type 'function'>)
Args: ()
Traceback (innermost last):
File
"/Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/Pmw/Pmw_1_2/lib/Pmw
Base.py", line 1747, in __call__
return apply(self.func, args)
File
"/Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/Pmw/Pmw_1_2/lib/Pmw
Dialog.py", line 153, in <lambda>
command=lambda self=self, name=name: self._doCommand(name))
File
"/Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/Pmw/Pmw_1_2/lib/Pmw
Dialog.py", line 132, in _doCommand
return command(name)
File
"/Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/pmg_tk/startup/apbs
_tools.py", line 1111, in execute
self.runPsize()
File
"/Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/pmg_tk/startup/apbs
_tools.py", line 1155, in runPsize
size.runPsize(pdb_filename)
File "/sw/share/xtal/bin/psize.py", line 267, in runPsize
self.parseInput(filename)
File "/sw/share/xtal/bin/psize.py", line 102, in parseInput
self.parseLines(file.readlines())
File "/sw/share/xtal/bin/psize.py", line 116, in parseLines
self.q = self.q + float(words[3])
ValueError: invalid literal for float(): 1.00101.59
-------------------------------------------------------------------
Evan R. Kantrowitz, Ph.D evan.kantrow...@bc.edu
Boston College Tel. 617-552-4558
Department of Chemistry FAX 617-552-2705
Merkert Chemistry Center, Rm 239 www2.bc.edu/~kantrow
Chestnut Hill, MA 02467
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