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Re: [PyMOL] APBS
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From: Oganesyan, V. <Oga...@Me...> - 2007-05-30 13:50:21
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I did not get much luck with those recommendations either. I was doing =
exactly the same. Something is phishy with my pymol and/or APBS =
installation. I did check for different pdb files, so it is not pdb =
related. The roor message is below:
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Running ('/usr/bin/APBS/apbs-0.5.0/bin/apbs', =
'/home/Vaheh/Work/Fc3M/pymol-generated.in')
OSError Exception in Tk callback
Function: <function <lambda> at 0xf608448c> (type: <type 'function'>)
Args: ()
Traceback (innermost last):
File =
"/usr/bin/pymol/ext/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.p=
y", line 1747, in __call__
return apply(self.func, args)
File =
"/usr/bin/pymol/ext/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwDialog=
.py", line 153, in <lambda>
command=3Dlambda self=3Dself, name=3Dname: self._doCommand(name))
File =
"/usr/bin/pymol/ext/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwDialog=
.py", line 132, in _doCommand
return command(name)
File "/usr/bin/pymol/modules/pmg_tk/startup/apbs_tools.py", line 1101, =
in execute
(retval,progout) =3D =
run(self.binary.getvalue(),(self.pymol_generated_in_filename.getvalue(),)=
)
File "/usr/bin/pymol/modules/pmg_tk/startup/apbs_tools.py", line 317, =
in run
retcode =3D =
subprocess.call(args,stdout=3Doutput_file.fileno(),stderr=3Dsubprocess.ST=
DOUT)
File "/usr/bin/pymol/ext/lib/python2.4/subprocess.py", line 412, in =
call
return Popen(*args, **kwargs).wait()
File "/usr/bin/pymol/ext/lib/python2.4/subprocess.py", line 542, in =
__init__
errread, errwrite)
File "/usr/bin/pymol/ext/lib/python2.4/subprocess.py", line 975, in =
_execute_child
raise child_exception
OSError: [Errno 8] Exec format error
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Comments and solutions are appreciated.
VO
-----Original Message-----
From: Todd M. Link [mailto:tod...@gm...]
Sent: Tue 5/29/2007 3:44 PM
To: Michael Lerner
Cc: Oganesyan, Vaheh; pym...@li...
Subject: Re: [PyMOL] APBS
=20
I also continually had this problem unless I got pqr coordinates =20
(with hydrogens)
below is the instructions I wrote for myself and group so that I =20
would be able to do it again next time (getting old and the memory =20
isn't what it used to be)
pqr corrdinates - Can do it on the web at
http://pdb2pqr.sourceforge.net/
http://agave.wustl.edu/pdb2pqr/server.html
I just used the defaults
Under plugins go to APBS tools
Choose use another PQR. (maybe if you select Use PDB2PQR it might do =20
this automatically without first going on line to do it?)
default configuration
Each time I've always had to set the APBS binary location. The other =20
sections leave blank
default Temporary File Locations
To start APBS 1st select Set Grid, then do Run APBS - I don't know =20
why the buttons are placed in that order. Also, it seems you must =20
click on Run APBS twice before it launches. Run Top in unix window =20
to make sure it runs
For Hfq, ~400 residues, APBS took about a minute.
Go to Visualization and click on Update
For most reasonable looking Molecular Surfaces I turn off Solvent =20
Accessible Surface and turn on Color by potential on sol. acc. surf. =20
Select Show. If you change the range you must also click on Update
When I tried to do this with another loaded structure, it actually =20
looked like it mapped the first EPS onto the surface of the second =20
structure.
Make sure to remove waters (and probably everyother non-protein =20
residue). EP on the left was done with waters in structure. Notice =20
red surface where ever water molecules appeare
non-linear Bolzman
Linear Bolzman
On May 24, 2007, at 1:16 PM, Michael Lerner wrote:
> Hi,
>
> Can you try installing the most recent version of my plugin from
> http://www-personal.umich.edu/~mlerner/Pymol/index.html (you can use
> the normal Install Plugin menu option .. there's no need to do things
> by hand anymore)? It fixes some problems and gives better error
> messages on others.
>
> Thanks,
>
> -Michael
>
> --=20
> Biophysics Graduate Student
> Carlson Lab, University of Michigan
> http://www.umich.edu/~mlerner
>
>
> On 5/24/07, Oganesyan, Vaheh <Oga...@me...> wrote:
>>
>>
>>
>>
>> I'll appreciate some help with APBS plugin.
>>
>>
>>
>> In both Win or Lin the same error appears:
>>
>>
>>
>> ObjectMapLoadDXFile-Error: Unable to open file!
>>
>>
>>
>> After googling with this error message I've checked all of the
>> possibilities:
>>
>> Map file is loaded OK, folders with apbs.exe and psize.py files do =20
>> not
>> contain blanks,
>>
>> the *.pqr file is created using pdb2pqr server with and without chain
>> identifier.
>>
>>
>>
>> At this point I do not know what else to try. Before (about 1 year =20
>> ago) I've
>> used it with no problems.
>>
>> Could someone point me to the problem?
>>
>> Windows version is 0_99rc6 installed using binaries.
>>
>> Thanks in advance.
>>
>>
>>
>> Vaheh Oganesyan
>>
>>
>> --------------------------------------------------------------------- =
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>
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