You can try this:
Give your pdb to the PDB2PQR server:
http://agave.wustl.edu/pdb2pqr/server.html
Strip the waters/ligands and load in your pdb. Choose that you want to
create an APBS input file. You get 2 files: *.pqr and *.in. Rename
without .txt extension (if the output has them. My mac put them on).
You can load input pdb (the one with waters/ligands stripped). Change
the temp file locations (temp.pqr, *.pdb, and APBS input file). Don't
change the "pymol generated dx". Under main, choose "use another
pqr". Choose "externally generated" pqr and browse for your x.pqr.
Click "set grid". Click "run APBS". That will spit out a
"pymol-generated.dx". In pymol type load_dx [file].dx. In APBS window,
go to the visualization tab and choose "show mol. surface". Change
levels and update.
Perhaps not the best way to get this to work, but it will give you a
surface to look at. Good luck,
Eric
On 5/30/07, Oganesyan, Vaheh <oganesy...@medimmune.com> wrote:
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:
==============================================================================================================
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.py",
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=lambda self=self, name=name: 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) =
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 =
subprocess.call(args,stdout=output_file.fileno(),stderr=subprocess.STDOUT)
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
==============================================================================================
Comments and solutions are appreciated.
VO
-----Original Message-----
From: Todd M. Link [mailto:toddml...@gmail.com]
Sent: Tue 5/29/2007 3:44 PM
To: Michael Lerner
Cc: Oganesyan, Vaheh; pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] APBS
I also continually had this problem unless I got pqr coordinates
(with hydrogens)
below is the instructions I wrote for myself and group so that I
would be able to do it again next time (getting old and the memory
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
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
sections leave blank
default Temporary File Locations
To start APBS 1st select Set Grid, then do Run APBS - I don't know
why the buttons are placed in that order. Also, it seems you must
click on Run APBS twice before it launches. Run Top in unix window
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
Accessible Surface and turn on Color by potential on sol. acc. surf.
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
looked like it mapped the first EPS onto the surface of the second
structure.
Make sure to remove waters (and probably everyother non-protein
residue). EP on the left was done with waters in structure. Notice
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
>
> --
> Biophysics Graduate Student
> Carlson Lab, University of Michigan
> http://www.umich.edu/~mlerner
>
>
> On 5/24/07, Oganesyan, Vaheh <oganesy...@medimmune.com> 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
>> 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
>> 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
>>
>>
>> ---------------------------------------------------------------------
>> ----
>> This SF.net email is sponsored by DB2 Express
>> Download DB2 Express C - the FREE version of DB2 express and take
>> control of your XML. No limits. Just data. Click to get it now.
>> http://sourceforge.net/powerbar/db2/
>> _______________________________________________
>> PyMOL-users mailing list
>> PyMOL-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>>
>
> ----------------------------------------------------------------------
> ---
> This SF.net email is sponsored by DB2 Express
> Download DB2 Express C - the FREE version of DB2 express and take
> control of your XML. No limits. Just data. Click to get it now.
> http://sourceforge.net/powerbar/db2/
> _______________________________________________
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
-------------------------------------------------------------------------
This SF.net email is sponsored by DB2 Express
Download DB2 Express C - the FREE version of DB2 express and take
control of your XML. No limits. Just data. Click to get it now.
http://sourceforge.net/powerbar/db2/
_______________________________________________
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users
--
D. Eric Dollins
C266 LSRC, Box 3813
Duke University Medical Center
Durham, NC 27710
(919)681-1668
