From: DeLano S. <de...@de...> - 2007-05-24 04:36:31
|
Folks, Several parties recently reported problems computing local / in-vacuo electrostatic potentials in PyMOL 0.99rev9. The fix was trivial, so I've pushed out a 0.99rev10 release. If you haven't upgraded to 0.99rev9 yet, just skip forward to 0.99rev10. As usual, Mac/Win/Linux binaries for subscribers at http://delsci.com/ip and open-sourcers grab SVN branch b099 revision 2974. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:de...@de... "Not yet a PyMOL Subscriber, but want to support the project? Email sa...@de... to quote your lab, school, or employer. Thank you for sponsoring this open-source endeavor!" -WLD |
From: Oganesyan, V. <OganesyanV@MedImmune.com> - 2007-05-24 17:48:01
|
I'll appreciate some help with APBS plugin. =20 In both Win or Lin the same error appears: =20 ObjectMapLoadDXFile-Error: Unable to open file! =20 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,=20 the *.pqr file is created using pdb2pqr server with and without chain identifier. =20 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. =20 Vaheh Oganesyan =20 |
From: Michael L. <mgl...@gm...> - 2007-05-24 18:16:20
|
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 <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 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 > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > > |
From: Todd M. L. <tod...@gm...> - 2007-05-29 19:45:00
|
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=92ve 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 =96 I don=92t 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 >> >> >> ---------------------------------------------------------------------=20= >> ---- >> 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 >> PyM...@li... >> https://lists.sourceforge.net/lists/listinfo/pymol-users >> >> > > ----------------------------------------------------------------------=20= > --- > 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 > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users |
From: Oganesyan, V. <OganesyanV@MedImmune.com> - 2007-05-30 13:50:21
|
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 >> >> >> --------------------------------------------------------------------- = >> ---- >> 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 >> PyM...@li... >> 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 > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users |
From: D. E. D. <d.e...@gm...> - 2007-05-30 14:01:13
|
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 <Oga...@me...> 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:tod...@gm...] > Sent: Tue 5/29/2007 3:44 PM > To: Michael Lerner > Cc: Oganesyan, Vaheh; pym...@li... > 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 <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 > >> 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 > >> PyM...@li... > >> 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 > > PyM...@li... > > 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 > PyM...@li... > 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 |
From: Robert C. <rob...@qu...> - 2007-05-30 15:06:49
|
Hi Vaheh, * Oganesyan, Vaheh <OganesyanV@MedImmune.com> [2007-05-30 09:45] 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 ^^^^^^^^^^^^^^^^^^ This error would seem to indicate that you are running PyMOL on one kind of computer but the apbs executable was compiled for a different one. Are you perhaps mixing i686 and x86_64 Linuxes, for example? Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 Fax: 613-533-2497 <rob...@qu...> http://pldserver1.biochem.queensu.ca/~rlc |
From: Oganesyan, V. <OganesyanV@MedImmune.com> - 2007-05-31 14:43:36
|
Dear Robert, Thank you for your note. You were right. I downloaded i386 for my Linux computer and it runs. The funny part is that my computer has 64 bit Xeon processor. Go figure ... Vaheh Oganesyan -----Original Message----- From: pym...@li... [mailto:pym...@li...]On Behalf Of Robert Campbell Sent: Wednesday, May 30, 2007 11:06 AM To: pym...@li... Subject: Re: [PyMOL] APBS Hi Vaheh, * Oganesyan, Vaheh <OganesyanV@MedImmune.com> [2007-05-30 09:45] 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: > =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. 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/PmwDialo g.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/PmwDialo g.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= DOU T) > 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 ^^^^^^^^^^^^^^^^^^ This error would seem to indicate that you are running PyMOL on one kind of computer but the apbs executable was compiled for a different one. Are you perhaps mixing i686 and x86_64 Linuxes, for example? Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 Fax: 613-533-2497 <rob...@qu...> http://pldserver1.biochem.queensu.ca/~rlc ------------------------------------------------------------------------ - 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 PyM...@li... https://lists.sourceforge.net/lists/listinfo/pymol-users |
From: Soisson, S. M. <ste...@me...> - 2007-05-31 14:49:33
|
64-bit machines can still run 32-bit executables, and you may actually be running a 32-bit version of PyMOL, hence the mismatch. Steve=20 -----Original Message----- =46rom: pym...@li... [mailto:pym...@li...] On Behalf Of Oganesyan, Vaheh Sent: Thursday, May 31, 2007 10:43 AM To: Robert Campbell Cc: pym...@li... Subject: Re: [PyMOL] APBS Dear Robert, Thank you for your note. You were right. I downloaded i386 for my Linux computer and it runs. The funny part is that my computer has 64 bit Xeon processor. Go figure ... Vaheh Oganesyan -----Original Message----- =46rom: pym...@li... [mailto:pym...@li...]On Behalf Of Robert Campbell Sent: Wednesday, May 30, 2007 11:06 AM To: pym...@li... Subject: Re: [PyMOL] APBS Hi Vaheh, * Oganesyan, Vaheh <OganesyanV@MedImmune.com> [2007-05-30 09:45] 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: > =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. 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/PmwDialo g.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/PmwDialo g.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.STDOU T) > 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 ^^^^^^^^^^^^^^^^^^ This error would seem to indicate that you are running PyMOL on one kind of computer but the apbs executable was compiled for a different one. Are you perhaps mixing i686 and x86_64 Linuxes, for example=3F Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 Fax: 613-533-2497 <rob...@qu...> http://pldserver1.biochem.queensu.ca/~rlc ------------------------------------------------------------------------ - 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 PyM...@li... 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 PyM...@li... https://lists.sourceforge.net/lists/listinfo/pymol-users ---------------------------------------------------------------------------= --- Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp & Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is=20 available at http://www.merck.com/contact/contacts.html) that may be=20 confidential, proprietary copyrighted and/or legally privileged. It is=20 intended solely for the use of the individual or entity named on this=20 message. 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From: Robert C. <rob...@qu...> - 2007-05-31 15:01:36
|
Vaheh, * Soisson, Stephen Michael <ste...@me...> [2007-05-31 10:49] wrote: > 64-bit machines can still run 32-bit executables, and you may actually > be running a 32-bit version of PyMOL, hence the mismatch. In fact you may even be running a 32-bit version of Linux. Check with uname -m and see if it reports "i686" or "x86_64" Rob > > Steve > > -----Original Message----- > From: pym...@li... > [mailto:pym...@li...] On Behalf Of > Oganesyan, Vaheh > Sent: Thursday, May 31, 2007 10:43 AM > To: Robert Campbell > Cc: pym...@li... > Subject: Re: [PyMOL] APBS > > Dear Robert, > > Thank you for your note. You were right. I downloaded i386 for my Linux > computer and it runs. The funny part is that my computer has 64 bit > Xeon processor. > Go figure ... > > Vaheh Oganesyan -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 Fax: 613-533-2497 <rob...@qu...> http://pldserver1.biochem.queensu.ca/~rlc |