[PyMOL] export the mesh or surface

2008-01-15 Thread Lu Lin 

Hi all,
Anyone can tell me whether I can export the mesh or surface into a file 
(e.g. .wrl/.obj etc.)?

Thanks!!

Linda

[PyMOL] two objects with synchronous rotation about their axes

2008-01-15 Thread Oganesyan, Vaheh 
Is there a way in pymol to create such two objects that will rotate with
mouse each around its own axis?
I hope I'm clear.

Oganesyan Vaheh
Antibody Discovery
MedImmune, Inc.
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Re: [PyMOL] CCP4 workshop in US, 2nd announcement

2008-01-15 Thread Sanishvili, Ruslan 
The workshop will be held from May 23 through 28, 2008.
 

Ruslan Sanishvili (Nukri), Ph.D. 

GM/CA-CAT, Bld. 436, D007 
Biosciences Division, ANL 
9700 S. Cass Ave. 
Argonne, IL 60439 

Tel: (630)252-0665 
Fax: (630)252-0667 
rsanishv...@anl.gov   



 



From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of
Sanishvili, Ruslan
Sent: Tuesday, January 15, 2008 3:11 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] CCP4 workshop in US, 2nd announcement


Dear Colleagues,

 

This is second announcement of the CCP4 workshop.

 

WHAT "CCP4 school: From data processing to structure refinement and
beyond".

WHERE Advanced Photon Source, Argonne National Laboratory, near Chicago,
USA.

ORGANIZERS CCP4, University of York, GM/CA-CAT Argonne

PROGRAM Lectures in the morning, tutorials in the afternoon, hands-on
trouble shooting in the evening. Registered student are encouraged to
bring their own "problem" data.

COVERED SOFTWARE INCLUDES Mosflm, Scala, HKL2000, Refmac, ArpWarp,
PHENIX, Phaser, Coot, SHELXC/D/E, Balbes, Mrbump, Buccaneer, more

PARTICIPANTS Young scientists with basic knowledge of CCP4. Up to 20
registered students will be provided with computers and will participate
in hands-on session. Others are welcome to listen to lectures

FEES There are no registration fees. Meals and hotel will be covered by
the organizers.  Students will pay only for their transportation

DEADLINE Applications will be accepted until March 31. Selection of
students will be made and notifications sent within two weeks after
that.

APPLICATIONS together with the letter of support from the supervisor
should be sent to Nukri (rsanishv...@anl.gov
 ) or Garib (ga...@ysbl.york.ac.uk) or Ronan
(r.m.kee...@dl.ac.uk  )

 

 

 

Ruslan Sanishvili (Nukri), Ph.D. 

GM/CA-CAT, Bld. 436, D007 
Biosciences Division, ANL 
9700 S. Cass Ave. 
Argonne, IL 60439 

Tel: (630)252-0665 
Fax: (630)252-0667 
rsanishv...@anl.gov

[PyMOL] CCP4 workshop in US, 2nd announcement

2008-01-15 Thread Sanishvili, Ruslan 
Dear Colleagues,

 

This is second announcement of the CCP4 workshop.

 

WHAT "CCP4 school: From data processing to structure refinement and
beyond".

WHERE Advanced Photon Source, Argonne National Laboratory, near Chicago,
USA.

ORGANIZERS CCP4, University of York, GM/CA-CAT Argonne

PROGRAM Lectures in the morning, tutorials in the afternoon, hands-on
trouble shooting in the evening. Registered student are encouraged to
bring their own "problem" data.

COVERED SOFTWARE INCLUDES Mosflm, Scala, HKL2000, Refmac, ArpWarp,
PHENIX, Phaser, Coot, SHELXC/D/E, Balbes, Mrbump, Buccaneer, more

PARTICIPANTS Young scientists with basic knowledge of CCP4. Up to 20
registered students will be provided with computers and will participate
in hands-on session. Others are welcome to listen to lectures

FEES There are no registration fees. Meals and hotel will be covered by
the organizers.  Students will pay only for their transportation

DEADLINE Applications will be accepted until March 31. Selection of
students will be made and notifications sent within two weeks after
that.

APPLICATIONS together with the letter of support from the supervisor
should be sent to Nukri (rsanishv...@anl.gov
 ) or Garib (ga...@ysbl.york.ac.uk) or Ronan
(r.m.kee...@dl.ac.uk  )

 

 

 

Ruslan Sanishvili (Nukri), Ph.D. 

GM/CA-CAT, Bld. 436, D007 
Biosciences Division, ANL 
9700 S. Cass Ave. 
Argonne, IL 60439 

Tel: (630)252-0665 
Fax: (630)252-0667 
rsanishv...@anl.gov

Re: [PyMOL] Problems with space group recognition

2008-01-15 Thread DeLano Scientific 
Mark,

Thank you for attempting to troubleshoot the problem.  Although I am still
not certain as to what the underlying problem is, it appears to be specific
to Python 2.5.1 and 64-bit.  However, since sglite & ExtensionClass are no
longer maintained in their present form and are thus liabilities, I have
just replaced them with something simpler and more maintainable.

Please try attempting to compile from the subversion trunk 

via distutils:

python setup.py build install 
python setup2.py install

Cheers,
Warren


> -Original Message-
> From: pymol-users-boun...@lists.sourceforge.net 
> [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf 
> Of Mark Wehner
> Sent: Sunday, January 13, 2008 9:13 AM
> To: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] Problems with space group recognition
> 
> Hi Warren,
> 
> I used a small python script to reenact the steps of xray.py.
> And the first problem occuring is:
> 
> SgOps = sglite.SgOps(Symbols_Inp['Hall'])
> TypeError: 'ExtensionClass' object is not callable
> 
> Before that:
> 
> Symbols_Inp = sglite.SgSymbolLookup(sgsymbol) print Symbols_Inp
> 
> gives a reasonable output.
> 
> Any idea what I'm doing wrong here?
> 
> Regards,
> Mark
> 
> PS: The compiler isn't throwing any errors at compile time. I 
> downgraded one gcc version to test if it's my gcc version, 
> but still no sucess... Do you see any problematic flags here?
> x86_64-pc-linux-gnu-gcc -pthread -fno-strict-aliasing 
> -march=nocona -Os -pipe -fPIC -DPythonTypes -Icontrib/sglite 
> -Icontrib/modules -I/usr/include/python2.5 -c 
> contrib/sglite/runtests.c -o 
> build/temp.linux-x86_64-2.5/contrib/sglite/runtests.o
> 
> 
> On Saturday 12 January 2008, you wrote:
> > Mark,
> >
> > It sounds like the sglite module may not have compiled correctly.
> >
> > Cheers,
> > Warren
> >
> > --
> > DeLano Scientific LLC
> > Subscriber Support Services
> > mailto:del...@delsci.info
> >
> > > -Original Message-
> > > From: pymol-users-boun...@lists.sourceforge.net
> > > [mailto:pymol-users-boun...@lists.sourceforge.net] On 
> Behalf Of Mark 
> > > Wehner
> > > Sent: Saturday, January 12, 2008 4:07 AM
> > > To: pymol-users@lists.sourceforge.net
> > > Subject: [PyMOL] Problems with space group recognition
> > >
> > > Dear Pymol users & staff,
> > >
> > > I'm facing a problem with the recognition of space groups 
> from (once 
> > > working) valid pdb files with the last three or maybe 4 
> versions of 
> > > Pymol. If I load any (all space groups I tested failed!) pdb file 
> > > I'm able to use all features except those that are 
> symmetry-related; 
> > > especially I need to generate symmetry mates for certain 
> proteins. 
> > > The output is already pointing to an error, but I can't find the 
> > > error in the source code...
> > >
> > > Output:
> > > 'ObjectMolecule: Read crystal symmetry information.
> > > Symmetry-Error: Urecognized space group symbol 'C 1 2 1'.
> > > Symmetry-Error: Unable to get matrices from sglite.
> > > CmdLoad: "pdb/1f5n.pdb" loaded as "1f5n".'
> > >
> > > I'm using Gentoo Linux and compiled against Python 2.5 using
> > > gcc-4.1.2 on a 64-bit architecture (not using too much 
> optimization 
> > > [-Os]).
> > >
> > > Any help on this would be greatly appreciated. Thanks in advance.
> > > Mark Wehner
> > >
> > > --
> > > ---
> > > Check out the new SourceForge.net Marketplace.
> > > It's the best place to buy or sell services for just 
> about anything 
> > > Open Source.
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> > et/marketplace
> >
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> 
> 
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[PyMOL] electrostatics

2008-01-15 Thread Mark Wehner 
Hi,

1. Use 'util.protein_vacuum_esp("object")' to generate the electrostatic 
surface.
2. Use 'show surface, object' to show the surface or if you only need the 
surface representation use 'as surface, object'

Regards,
Mark

[PyMOL] electrostatics

2008-01-15 Thread Robert Fenwick 


Hi,

I would like to add simple representation of electrostatics to a  
movie and wanted to execute the generation of the surface using a  
script.


The action that I want to execute is equivalent to clicking on the  
action button for a selection and then > generate > vacuum  
electrostatics > protein contact potential


I would also like to be able to add a van der Waals surface via some  
scripting.


Cheers,

Bryn



==
R. Bryn FenwickDepartment of Biochemistry,
rb...@cam.ac.ukUniversity of Cambridge,
bryn.fenw...@cantab.net80 Tennis Court Road,
Tel: +44 1223 766018   Old Addenbrookes Site,
Fax: +44 1223 766002   Cambridge, CB2 1GA, UK.
==