pymol-users Mailing List for PyMOL Molecular Graphics System

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

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 <Oga...@Me...> [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

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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 <Oga...@Me...> [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

Hi Vaheh,

* Oganesyan, Vaheh <Oga...@Me...> [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

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.
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>
>
>
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-- 
D. Eric Dollins
C266 LSRC, Box 3813
Duke University Medical Center
Durham, NC 27710
(919)681-1668

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

This email is directed towards users of Chemical Computing Group's
"Molecular Operating Environment" (MOE) as well as other molecular modeling
suites (e.g. Maestro, Sybyl, Discovery Studio, GROMACS, etc.).
 
As announced previously, our precompiled beta builds of PyMOL 1.0 (now beta
25 http://delsci.com/ip/beta ) have native support for reading ".MOE"
(dot-MOE) files, making it much easier for you to share MOE molecular
modeling results using PyMOL. 
 
Together with CCG, we would like as much feedback as possible on this new
feature.  Also, we would also like to know where it is being tested and/or
used, so that we can appropriately prioritize joint effort supporting this
capability in the future.
 
Thus, if you are currently making use of the PyMOL ".MOE" reader, or if you
think someone in your company or lab will likely make use of it, please drop
us an email (assuming you haven't done so already).  To the extent that this
feature matters to you, we need to know it.
 
On the other hard, if you mainly use another another molecular modeling
suite and would like to see PyMOL support its file format natively as well,
please drop us an email to that effect.  
 
Thank you for your feedback! 
 
Cheers,
Warren
 
wa...@de...
DeLano Scientific LLC
 
 
 

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

	On behalf of the 3DSig organising committee,

	I would like to bring to your attention the approaching deadline to  
submit an abstract to the forthcoming 3DSig 2007: Structural  
bioinformatics and computational biophysics ISMB satellite meeting to  
be held on July 19-20 in Vienna, Austria.

	http://structure.bu.edu/3DSig/

	The deadline for abstract submissions is June 1st. Authors can  
choose to present their contribution as a laptop presentation and/or  
a poster (which may be the same as that to be presented in the main  
ISMB event). Furthermore, contributions can be selected for oral  
presentations.

	Registration for 3DSig does not require registration for the main  
ISMB event.

	The third 3Dsig meeting will consist of two full days with a balance  
of invited talks, short oral presentations, two laptop/poster- 
sessions, critical, topic-focused discussions and a dinner session. A  
truly unique event bringing together in one place the structural  
computational biology community.

Relevant topics include among others:

	Structure representation, structure prediction, structural genomics
	Structural databases and 3D data mining
	Structure-based function prediction
	Evolution studied through structure
	Protein-protein, protein-ligand, and protein-RNA/DNA interactions  
(docking, analysis & prediction)
	Prediction and analysis of domains
	Membrane protein structure prediction and analysis
	The role of geometry and energetics in protein and RNA structure and  
function
	Protein and RNA dynamics and simulation: folding, stability,  
interactions, conformational gating
	Computer-aided protein and RNA design
	Structure-based drug design and pharmacophore analysis
	Chemoinformatics

	3Dsig 2007 is continuing the tradition established through the  
successful 3Dsig 2006 and 3Dsig 2004. To better appreciate the wealth  
of leading topics and presenters, please explore the programs and  
proceedings from past 3Dsig 2004 and 2006 meetings. The program will  
be built around talks from accepted abstracts and invited speakers.

	The scientific committee is looking for fresh, effective voices with  
new, high impact ideas. Accepted abstracts will fall into two  
categories: oral presentation and laptop/poster presentation.  
Participants with accepted abstracts for the latter type will have  
the choice of presenting their work as either a regular poster, a  
laptop presentation, or a combination thereof. Those choosing to use  
a laptop to substitute or augment their poster presentation will have  
a stand or table and electric socket for a personal laptop  
(presenters must bring their own laptops). The aim of the poster/ 
laptop session is to facilitate interactions between the presenter  
and the viewers.

	http://structure.bu.edu/3DSig/

	Looking forward to seeing you in Vienna!

Dr. Rafael Najmanovich
European Bioinformatics Institute
Wellcome Trust Genome Campus
Cambridge CB10 1SD
United Kingdom

rafael.najmanovich [at] ebi.ac.uk - www.ebi.ac.uk/~rafi
+44-1223-492599 (voice) +44-7951-394145 (mobile) +44-1223-494468 (fax)

Hi pymol users,
I want to create a pdb file that contains two polypeptide molecules. And 
create a distance between them, i.e move one relative to the other. Can i do 
this in Pymol?
Please i'll appreciate any help with this.
Regards
John

_________________________________________________________________
Make every IM count. Download Messenger and join the i’m Initiative now. 
It’s free. http://im.live.com/messenger/im/home/?source=TAGHM_MAY07

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
>
>

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

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
 

Hi Thomas,

Just a as a note. A focal blur is not like a fog, but results from
sort of averaging a series of images, with the in-focus plane being
well-defined and the planes in front and in the back blurred according
to the distance from the in-focus plane (and the aperture). Not
completely trivial to implement... And PovRay usually does an
excellent job for me :)

Cheers,

Tsjerk

On 5/23/07, Thomas Blicher <bl...@cb...> wrote:
>
>
>
>
> Dear PyMOL users,
>
>
>
> I was wondering if it is possible to implement focus depth (also known as
> depth of field or DOF) in PyMOL. I have come across several links to DOF =
and
> it appears to be a common feature of ray-tracing programs. I imagine that=
 it
> could work like the fog function =96 possibly in combination with this =
=96 to
> give an even more realistic feeling of depth/perspective, especially in
> close-ups. It is probably most useful for making artistic molecular
> graphics, i.e. for ray-traced images, so it wouldn't have to work real-ti=
me.
>
>
>
> Does anyone have ideas on how to implement this in PyMOL (other than
> exporting files and rendering them in POVRay)?
>
>
>
> Best regards,
>
> Thomas Blicher
> -------------------------------------------------------------------------
> 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
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

Implementing DOF  in PyMol wouldn't be trivial and I'm not sure it's a =
priority/necessity. There are excellent open-source (and proprietary) =
rendering engines out there that can render better and faster than =
PyMol.  Why re-invent the wheel... my 2 cents' worth :)
=20
However, aside from exporting to PovRay, you can do DOF from PyMol =
ray-traced PNG's (32-bit, i.e. w/ alpha channel) in post-production =
using the alpha channel as a Z-depth channel.  If there is interest, I =
don't mind writing up a tutorial, but note that it does involve other =
software aside from PyMol, such as Photoshop.
=20
Best,
=20
JP
=20
________________________________

From: pym...@li... on behalf of Thomas =
Blicher
Sent: Wed 5/23/2007 5:32 AM
To: pym...@li...
Subject: [PyMOL] Focus depth



Dear PyMOL users,

=20

I was wondering if it is possible to implement focus depth (also known =
as depth of field or DOF) in PyMOL. I have come across several links to =
DOF and it appears to be a common feature of ray-tracing programs. I =
imagine that it could work like the fog function - possibly in =
combination with this - to give an even more realistic feeling of =
depth/perspective, especially in close-ups. It is probably most useful =
for making artistic molecular graphics, i.e. for ray-traced images, so =
it wouldn't have to work real-time.

=20

Does anyone have ideas on how to implement this in PyMOL (other than =
exporting files and rendering them in POVRay)?

=20

Best regards,

Thomas Blicher

Dear PyMOL users,

 

I was wondering if it is possible to implement focus depth (also known as
depth of field or DOF) in PyMOL. I have come across several links to DOF and
it appears to be a common feature of ray-tracing programs. I imagine that it
could work like the fog function - possibly in combination with this - to
give an even more realistic feeling of depth/perspective, especially in
close-ups. It is probably most useful for making artistic molecular
graphics, i.e. for ray-traced images, so it wouldn't have to work real-time.

 

Does anyone have ideas on how to implement this in PyMOL (other than
exporting files and rendering them in POVRay)?

 

Best regards,

Thomas Blicher

Hi Nick,

Unfortunately, there's nothing you can do about it. mpng just writes
out the frames one after the other, with raytrace_frames set
raytraycing each of them. cache_frames just puts each (rendered) frame
in memory, so Pymol can cycle through them sort of smoothly after all
frames are rendered. It has nothing to do with your problem. The only
solution is to script the duplication or to write some python script
to handle the moviemaking/ raytracing/ framewriting.
It would of course be nice to have Pymol recognize that from one frame
to the other the scene did not change and hence the same image could
be written to disk again...

Cheers,

Tsjerk

On 5/23/07, nick hatch <nic...@gm...> wrote:
> I'm rendering some longer movies that have long sequences of duplicate
> frames, eg:
>
> Molecule side view (5 seconds)
> Rotate/Zoom (3 seconds)
> Another view (5 seconds)
>
> I've noticed that when using the mpng command, these duplicate frames are
> rendered, one after another...
>
> Is there a setting I'm missing? cache_frames doesn't seem to prevent the
> behavior, and is unusable for longer movies. If not, may I humbly suggest
> this as a feature request? It could reduce rendering times significantly.
> I've debated scripting the duplication of a single frame post rendering, but
> I'm not sure it's worth the extra work.
>
> Thanks,
>
> -Nick
>
>
> -------------------------------------------------------------------------
> 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
>
>


-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

I'm rendering some longer movies that have long sequences of duplicate
frames, eg:

Molecule side view (5 seconds)
Rotate/Zoom (3 seconds)
Another view (5 seconds)

I've noticed that when using the mpng command, these duplicate frames are
rendered, one after another...

Is there a setting I'm missing? cache_frames doesn't seem to prevent the
behavior, and is unusable for longer movies. If not, may I humbly suggest
this as a feature request? It could reduce rendering times significantly.
I've debated scripting the duplication of a single frame post rendering, but
I'm not sure it's worth the extra work.

Thanks,

-Nick

Thanks! That works.

In the past I had actually wanted to set solvent radius fairly large,  
but had poor luck getting the results I wanted. Now it seems to solve  
this particular problem. Go figure.

Richard


On May 22, 2007, at 10:53 AM, Tsjerk Wassenaar wrote:

> Hi Richard,
>
> What about
>
> set solvent_radius,3
>
> That seems to do the trick for me.
>
> Cheers,
>
> Tsjerk
>
> On 5/22/07, Richard Gillilan <re...@co...> wrote:
>>
>> In the past I have used PyMol pretty successfully to visualize low-
>> resolution x-ray solution scattering results in which each "atom" in
>> a pdb file is actually a large sphere (say 4-6 Angstroms)
>> representing some density.  I would use
>>
>>  >alter <molecule name>, vdw = 6.0
>>
>> to set the sphere sizes appropriately, then compute a surface using
>> the "surface" option in the "Show" pulldown of the appropriate  
>> object.
>>
>> Strangely, this seems to have quit working for me. When I select
>> surface, nothing happens, not even an error message.
>> It still works fine for older files I have, so it must be something
>> particular about the geometry of the object I have (it is a rather
>> sparse extended object). Anyone seen this kind of problem?
>>
>> File is included below:
>>
>>
>>
>>
>> --------------------------------------------------------------------- 
>> ----
>> 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
>>
>>
>>
>
>
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623

Hi Richard,

What about

set solvent_radius,3

That seems to do the trick for me.

Cheers,

Tsjerk

On 5/22/07, Richard Gillilan <re...@co...> wrote:
>
> In the past I have used PyMol pretty successfully to visualize low-
> resolution x-ray solution scattering results in which each "atom" in
> a pdb file is actually a large sphere (say 4-6 Angstroms)
> representing some density.  I would use
>
>  >alter <molecule name>, vdw = 6.0
>
> to set the sphere sizes appropriately, then compute a surface using
> the "surface" option in the "Show" pulldown of the appropriate object.
>
> Strangely, this seems to have quit working for me. When I select
> surface, nothing happens, not even an error message.
> It still works fine for older files I have, so it must be something
> particular about the geometry of the object I have (it is a rather
> sparse extended object). Anyone seen this kind of problem?
>
> File is included below:
>
>
>
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by DB2 Express
> Download DB2 Express C - the FREE version of DB2 express and take
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>


-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

In the past I have used PyMol pretty successfully to visualize low- 
resolution x-ray solution scattering results in which each "atom" in  
a pdb file is actually a large sphere (say 4-6 Angstroms)  
representing some density.  I would use

 >alter <molecule name>, vdw = 6.0

to set the sphere sizes appropriately, then compute a surface using  
the "surface" option in the "Show" pulldown of the appropriate object.

Strangely, this seems to have quit working for me. When I select  
surface, nothing happens, not even an error message.
It still works fine for older files I have, so it must be something  
particular about the geometry of the object I have (it is a rather  
sparse extended object). Anyone seen this kind of problem?

File is included below:

	On behalf of the 3DSig organising committee,

	I would like to bring to your attention the approaching deadline to  
submit an abstract to the forthcoming 3DSig 2007: Structural  
bioinformatics and computational biophysics ISMB satellite meeting to  
be held on July 19-20 in Vienna, Austria.

	http://structure.bu.edu/3DSig/

	The deadline for abstract submissions is June 1st. Authors can  
choose to present their contribution as a laptop presentation and/or  
a poster (which may be the same as that to be presented in the main  
ISMB event). Furthermore, contributions can be selected for oral  
presentations.

	Registration for 3DSig does not require registration for the main  
ISMB event.

	The third 3Dsig meeting will consist of two full days with a balance  
of invited talks, short oral presentations, two laptop/poster- 
sessions, critical, topic-focused discussions and a dinner session. A  
truly unique event bringing together in one place the structural  
computational biology community.

Relevant topics include among others:

	Structure representation, structure prediction, structural genomics
	Structural databases and 3D data mining
	Structure-based function prediction
	Evolution studied through structure
	Protein-protein, protein-ligand, and protein-RNA/DNA interactions  
(docking, analysis & prediction)
	Prediction and analysis of domains
	Membrane protein structure prediction and analysis
	The role of geometry and energetics in protein and RNA structure and  
function
	Protein and RNA dynamics and simulation: folding, stability,  
interactions, conformational gating
	Computer-aided protein and RNA design
	Structure-based drug design and pharmacophore analysis
	Chemoinformatics

	3Dsig 2007 is continuing the tradition established through the  
successful 3Dsig 2006 and 3Dsig 2004. To better appreciate the wealth  
of leading topics and presenters, please explore the programs and  
proceedings from past 3Dsig 2004 and 2006 meetings. The program will  
be built around talks from accepted abstracts and invited speakers.

	The scientific committee is looking for fresh, effective voices with  
new, high impact ideas. Accepted abstracts will fall into two  
categories: oral presentation and laptop/poster presentation.  
Participants with accepted abstracts for the latter type will have  
the choice of presenting their work as either a regular poster, a  
laptop presentation, or a combination thereof. Those choosing to use  
a laptop to substitute or augment their poster presentation will have  
a stand or table and electric socket for a personal laptop  
(presenters must bring their own laptops). The aim of the poster/ 
laptop session is to facilitate interactions between the presenter  
and the viewers.

	http://structure.bu.edu/3DSig/

	Looking forward to seeing you in Vienna!

Dr. Rafael Najmanovich
European Bioinformatics Institute
Wellcome Trust Genome Campus
Cambridge CB10 1SD
United Kingdom

rafael.najmanovich [at] ebi.ac.uk - www.ebi.ac.uk/~rafi
+44-1223-492599 (voice) +44-7951-394145 (mobile) +44-1223-494468 (fax)

Sorry, I meant 3D pdf (Adoobie portable document format). But what you are
doing sounds pretty cool. Please announce it when you are ready

Tsjerk Wassenaar wrote:
> Hi William,
>
> In contrast to Nick, I read your question as inquiring after a 3D
> probability density function. In case I get it wrong, just ignore this
> mail.
> It is well possible to generate 3D pdfs and display them in Pymol.
> Actually, for one project I'm doing that right now. I have modified a
> program from the Gromacs package to generate xplor density maps of
> relative occupancies in space. Something similar may be of use to you.
> If you want, I can send you the program, or a script which does a
> similar thing. Alternatively, I can just send the routine to write an
> xplor map, given a 3D array (C code, though maybe I already have it in
> python too).
>
> Hope it helps,
>
> Tsjerk
>
> On 5/21/07, William Scott <wg...@ch...> wrote:
>> Is it possible to create a 3D pdf using pymol?
>>
>>
>> William G. Scott
>>
>> Contact info:
>> http://chemistry.ucsc.edu/~wgscott/
>>
>>
>>
>> -------------------------------------------------------------------------
>> 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
>>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
>

Hi William,

In contrast to Nick, I read your question as inquiring after a 3D
probability density function. In case I get it wrong, just ignore this
mail.
It is well possible to generate 3D pdfs and display them in Pymol.
Actually, for one project I'm doing that right now. I have modified a
program from the Gromacs package to generate xplor density maps of
relative occupancies in space. Something similar may be of use to you.
If you want, I can send you the program, or a script which does a
similar thing. Alternatively, I can just send the routine to write an
xplor map, given a 3D array (C code, though maybe I already have it in
python too).

Hope it helps,

Tsjerk

On 5/21/07, William Scott <wg...@ch...> wrote:
> Is it possible to create a 3D pdf using pymol?
>
>
> William G. Scott
>
> Contact info:
> http://chemistry.ucsc.edu/~wgscott/
>
>
>
> -------------------------------------------------------------------------
> 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
>


-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

On 5/21/07, William Scott <wg...@ch...> wrote:
>
> Is it possible to create a 3D pdf using pymol?


It most certainly is possible, albeit not directly.

What type of stereo image are you trying to output? The ray functionality in
pymol will output stereo pairs which are meant for either wall-eye or
cross-eye display. The default output format is PNG, you can easily output a
high-resolution png image and convert it to PDF format afterwards. Open
Office will export to PDFs natively, and is free.

Using the ghostscript package in linux, this conversion can be automated if
you're looking for more than a one-off production.

If you're trying to generate anaglyph images (red/blue glasses), it also is
possible, but requires some scripting. Feel free to contact me for more
details.

-Nick