Re: [PyMOL] APBS error

2013-06-18 Thread Troels Emtekær Linnet
Do you have linux or windows?

Do you have PDB2PQR on your system?
http://pymolwiki.org/index.php/Apbsplugin
http://www.poissonboltzmann.org/pdb2pqr


Troels Emtekær Linnet


2013/6/18 Chen Zhao chenzhaoh...@gmail.com

 Thank you so much Troels,

 This solves my problem. But based on this, it seems that APBS In pymol
 failed to find PDB2PQR.

 Chen


 On Tue, Jun 18, 2013 at 1:40 AM, Troels Emtekær Linnet 
 tlin...@gmail.comwrote:

 Have a look on the earlier message on this.


 http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg11148.html



 Troels Emtekær Linnet


 2013/6/18 Chen Zhao chenzhaoh...@gmail.com

  Dear Pymol Users,

 I have been trying to configure APBS-1.4 plugin of pymol 1.6 on a Debian
 Wheezy machine. The initialization is successful, but when I hit set
 grid, I got the error message below:

 *error: 1
 type 'exceptions.UnboundLocalError' Exception in Tk callback
   Function: function lambda at 0x33a6938 (type: type 'function')
   Args: ()
 Traceback (innermost last):
   File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py,
 line 1747, in __call__
 return apply(self.func, args)
   File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py,
 line 153, in lambda
 command=lambda self=self, name=name: self._doCommand(name))
   File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py,
 line 132, in _doCommand
 return command(name)
   File
 /usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line
 1075, in execute
 self.runPsize()
   File
 /usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line
 1096, in runPsize
 good = self.generatePqrFile()
   File
 /usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line
 1007, in generatePqrFile
 good = self._generatePdb2pqrPqrFile()
   File
 /usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line
 1615, in _generatePdb2pqrPqrFile
 if retval != 0:
 type 'exceptions.UnboundLocalError': local variable 'retval'
 referenced before assignment*

 Also, although I specified the PATH of APBS and PDB2PQR in apbs_tools.py
 file, the APBS GUI in pymol is still unable to show the correct path of
 APBS and PDB2PQR.

 Thank you so much!

 Sincerely,
 Chen


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Re: [PyMOL] APBS error

2013-06-18 Thread Troels Emtekær Linnet
Hi Chen.

If you are up for it, pdb2pqr exist in the Pymol-script repo.
http://pymolwiki.org/index.php/Git

I have made a automatic compile script.
See here:
http://pymolwiki.org/index.php/User:Tlinnet/Linux_Install#Install_script

That should fix it for you.
Try to look it through, and just write if you have problems.




Troels Emtekær Linnet


2013/6/18 Chen Zhao chenzhaoh...@gmail.com

 I am using Debian linux and I installed PDB2PQR with path specified in
 pymol APBS GUI. However, it seems that there are some problems in python,
 although I don't understand because I am not a programmer. I will try to
 run from command line instead.

 Thank you!

 Chen


 On Tue, Jun 18, 2013 at 11:08 AM, Troels Emtekær Linnet tlin...@gmail.com
  wrote:

 Do you have linux or windows?

 Do you have PDB2PQR on your system?
 http://pymolwiki.org/index.php/Apbsplugin
 http://www.poissonboltzmann.org/pdb2pqr


 Troels Emtekær Linnet


 2013/6/18 Chen Zhao chenzhaoh...@gmail.com

 Thank you so much Troels,

 This solves my problem. But based on this, it seems that APBS In pymol
 failed to find PDB2PQR.

 Chen


 On Tue, Jun 18, 2013 at 1:40 AM, Troels Emtekær Linnet 
 tlin...@gmail.com wrote:

 Have a look on the earlier message on this.


 http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg11148.html



 Troels Emtekær Linnet


 2013/6/18 Chen Zhao chenzhaoh...@gmail.com

  Dear Pymol Users,

 I have been trying to configure APBS-1.4 plugin of pymol 1.6 on a
 Debian Wheezy machine. The initialization is successful, but when I hit
 set grid, I got the error message below:

 *error: 1
 type 'exceptions.UnboundLocalError' Exception in Tk callback
   Function: function lambda at 0x33a6938 (type: type 'function')
   Args: ()
 Traceback (innermost last):
   File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py,
 line 1747, in __call__
 return apply(self.func, args)
   File
 /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py, line 153,
 in lambda
 command=lambda self=self, name=name: self._doCommand(name))
   File
 /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py, line 132,
 in _doCommand
 return command(name)
   File
 /usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, 
 line
 1075, in execute
 self.runPsize()
   File
 /usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, 
 line
 1096, in runPsize
 good = self.generatePqrFile()
   File
 /usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, 
 line
 1007, in generatePqrFile
 good = self._generatePdb2pqrPqrFile()
   File
 /usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, 
 line
 1615, in _generatePdb2pqrPqrFile
 if retval != 0:
 type 'exceptions.UnboundLocalError': local variable 'retval'
 referenced before assignment*

 Also, although I specified the PATH of APBS and PDB2PQR in
 apbs_tools.py file, the APBS GUI in pymol is still unable to show the
 correct path of APBS and PDB2PQR.

 Thank you so much!

 Sincerely,
 Chen


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Re: [PyMOL] Leapmotion ?

2013-06-18 Thread Troels Emtekær Linnet
That looks so cool.

Please make a video/blog of the outcome!

/Troels

Troels Emtekær Linnet


2013/6/19 Aurélien Grosdidier aurelien.grosdid...@gmail.com:
 Hi all,

 We're planning to try PyMol with the leap motion device
 (https://www.leapmotion.com/). Has anyone already succeeded to do so ?

 Best,

 Aurélien.

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Re: [PyMOL] how to draw lines between residue pairs

2013-06-17 Thread Troels Emtekær Linnet
I would make a distance between them,
and then modify the distance line look.

http://pymolwiki.org/index.php/Distance

Between arbitrary points, I would make
2 pseudoatoms.



Troels Emtekær Linnet


2013/6/17 Li Xue me.li...@gmail.com

 Hello all,

 Given a residue pair, is there anyway to draw a straight line between
 their C-alpha atoms in pymol?

 Many thanks.

 Li

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 Bioinformatics and Computational Biology program
 Computer Science
 Iowa State University
 Ames, IA 50011 - USA
 Email: me.li...@gmail.com
 Web site: http://www.cs.iastate.edu/~lixue/


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Re: [PyMOL] APBS error

2013-06-17 Thread Troels Emtekær Linnet
Have a look on the earlier message on this.

http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg11148.html



Troels Emtekær Linnet


2013/6/18 Chen Zhao chenzhaoh...@gmail.com

 Dear Pymol Users,

 I have been trying to configure APBS-1.4 plugin of pymol 1.6 on a Debian
 Wheezy machine. The initialization is successful, but when I hit set
 grid, I got the error message below:

 *error: 1
 type 'exceptions.UnboundLocalError' Exception in Tk callback
   Function: function lambda at 0x33a6938 (type: type 'function')
   Args: ()
 Traceback (innermost last):
   File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py, line
 1747, in __call__
 return apply(self.func, args)
   File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py,
 line 153, in lambda
 command=lambda self=self, name=name: self._doCommand(name))
   File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py,
 line 132, in _doCommand
 return command(name)
   File
 /usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line
 1075, in execute
 self.runPsize()
   File
 /usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line
 1096, in runPsize
 good = self.generatePqrFile()
   File
 /usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line
 1007, in generatePqrFile
 good = self._generatePdb2pqrPqrFile()
   File
 /usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line
 1615, in _generatePdb2pqrPqrFile
 if retval != 0:
 type 'exceptions.UnboundLocalError': local variable 'retval' referenced
 before assignment*

 Also, although I specified the PATH of APBS and PDB2PQR in apbs_tools.py
 file, the APBS GUI in pymol is still unable to show the correct path of
 APBS and PDB2PQR.

 Thank you so much!

 Sincerely,
 Chen


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Re: [PyMOL] PyMOL APBS plugin on Ubuntu 12.10 - error after 'run APBS'

2013-06-03 Thread Troels Emtekær Linnet
Hej Tobias.

Some time ago, a year+?, I played around fixing some small things in APBS,
to make it easier to work. (Most fixing small path things)

Orginal version:
http://pymolwiki.org/index.php/APBS

Small modified version:
http://pymolwiki.org/index.php/Apbsplugin

The modified version, is packed into the Pymol-script-repo
http://pymolwiki.org/index.php/Git

I made this installation script some time ago,
http://www.pymolwiki.org/index.php/User:Tlinnet/Linux_Install#Install_script

which download the Pymol-script-repo, and sets the path right.

at the moment I can't test it? since:
svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol
svn: E210002: Unable to connect to a repository at URL 'svn://
svn.code.sf.net/p/pymol/code/trunk/pymol'
svn: E210002: Network connection closed unexpectedly

But maybe you can see from the script, what you have to do.

Best


Troels Emtekær Linnet


2013/5/31 Tobias Beck tobiasb...@gmail.com:
 Dear all,

 I am trying to run the ABPS plugin with PyMOL Version 1.6.0.0 on Ubuntu
 12.10. I have compiled pymol from source
 (http://www.pymolwiki.org/index.php/Linux_Install).

 When running the plugin, I can set the grid, but after clicking on Run
APBS,
 I get the following error:

 Unexpected error: (type 'exceptions.ImportError', ImportError('No module
 named pdb2pqr.pdb2pqr',), traceback object at 0x7fd130771200)
 type 'exceptions.UnboundLocalError' Exception in Tk callback
   Function: function lambda at 0x7fd13078e398 (type: type
'function')
   Args: ()
 Traceback (innermost last):
   File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py, line
 1747, in __call__
 return apply(self.func, args)
   File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py,
line
 153, in lambda
 command=lambda self=self, name=name: self._doCommand(name))
   File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py,
line
 132, in _doCommand
 return command(name)
   File /home/pymol-svn/modules/pmg_tk/startup/apbs_tools.py, line 1036,
in
 execute
 good = self.generatePqrFile()
   File /home/pymol-svn/modules/pmg_tk/startup/apbs_tools.py, line 1007,
in
 generatePqrFile
 good = self._generatePdb2pqrPqrFile()
   File /home/pymol-svn/modules/pmg_tk/startup/apbs_tools.py, line 1615,
in
 _generatePdb2pqrPqrFile
 if retval != 0:
 type 'exceptions.UnboundLocalError': local variable 'retval' referenced
 before assignment

 The first line suggests that the pdb2pqr module cannot be loaded. However,
 the grid seems to be set okay. Has anybody encountered this error before
and
 knows how to solve it?

 I have also tried the pymol version that can be installed with apt-get,
but
 same error.

 Thanks for any advice!

 Best wishes, Tobias.



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[PyMOL] Labels not showing in 1.6

2013-04-30 Thread Troels Emtekær Linnet
Hi pymolers.

I have this strange problem, that labels
are not showing, unless I use the ray command.

Anyone experience the same?

image1: http://snag.gy/fhk3J.jpg
image2: http://snag.gy/0143z.jpg



fetch 1lev, async=0
preset.publication(selection='all')
remove chain F
select substrates, organic
select f6p, resn F6P
zoom f6p
util.cbac('f6p')

select act_site, byres f6p around 3.5
show sticks, act_site

distance pol_cont, f6p, act_site, mode=2

select cli, /1lev//A/CLI # OR: select cli, resn CLI
select mn, name MN # OR: select mn, symbol Mn # OR: select mn, inorganic
show spheres, mn

label act_site and name CB, resn+resi

zoom pol_cont
viewport 1024,768
bg_color white




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test.pml
Description: Binary data
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Re: [PyMOL] Error while running a python script

2013-03-20 Thread Troels Emtekær Linnet
Is that a space in your command?

cmd.load (1A73.pdb)



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2013/3/20 bharat gupta bharat.85.m...@gmail.com

 Hi,

 I am a newbie in python scripting from pymol. I am getting the following
 error while using the command cmd.load :-


 from pymol import cmd

 print Current PyMoL Directory:, cmd.pwd()
 cmd.load (1A73.pdb)

 Error:-
 --
 Traceback (most recent call last):
   File test.py, line 5, in module
 cmd.load (1A73.pdb)
   File /usr/lib/python2.7/site-packages/pymol/importing.py, line 872, in
 load
 _self.unlock(r,_self)
   File /usr/lib/python2.7/site-packages/pymol/locking.py, line 79, in
 unlock
 if (thread.get_ident() == pymol.glutThread):
 AttributeError: 'module' object has no attribute 'glutThread'



 
 Bharat



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Re: [PyMOL] PyMOL to 3D PDF

2013-03-13 Thread Troels Emtekær Linnet
Yeah.

That is a cool feature, and is kind of the future of publishing. :-)
Or at least, a very powerful tool for teaching.

*But it is sad that it only have cartoon export.*
I wish that it could include other representations.

For now I use Jmol, which can export the *whole representation in the window
*.
I can import small molecules through. Files-Get MOL- And then CAS number
or smiles.
For proteins I scoop into rcsb.org, and find the protein in the Jmol online
viewer. (Just changing to white back ground).

Right click in Jmol window-Export file-Export IDTF 3D model.

That saves a .idtf file, and a .tex file ready for LaTeX.
Rename the .idtf file, so it only ends on .idtf and not: filename.xyz.idtf

Simpy converting the .idtf to .u3d as instructed in,
http://www.pymolwiki.org/index.php/3d_pdf)
and you are ready to go from the given .tex file. (Removing the last looong
comment section.)

With a little practice, it only takes 3 min, to have 3d implementation of
your molecule
in teaching material / beamer presentation.

I wish that could be implemented in PyMOL, and I have been looking for a
wish list,
but I don't know where that exists?

Best

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2013/3/12 Mooers, Blaine H.M. (HSC) blaine-moo...@ouhsc.edu

 I saw Jason Vertrees update of http://www.pymolwiki.org/index.php/3d_pdf.
 It has the address to the source code for u3d-1.4.3. I could not compile
 earlier
 versions of this program on a Mac running Snow Leopard, but I had
 success with this version. I followed Jason's directions for compiling on
 Linux through  chmod g+wx. I had installed cmake earlier.

 The program compiles fine on Ubuntu 12.04 too.

 I used pdflatex from fink with beamer and the movies15 package.


 Blaine Mooers
 Assistant Professor
 Director Macromolecular Crystallography Lab
 Member Stephenson Cancer Center
 Department of Biochemistry and Molecular Biology
 University of Oklahoma Health Sciences Center
 S.L. Young Biomedical Research Center Rm. 466

 Letter address:
 P.O. Box 26901, BRC 466
 Oklahoma City, OK 73190

  Shipping address:
  975 NE 10th Street, BRC 466
 Oklahoma City, OK 73104-5419

 office: (405) 271-8300   lab: (405) 271-8313  fax:  (405) 271-3910

 e-mail:  blaine-moo...@ouhsc.edu

 Faculty webpage:
 http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/faculty/blaine-mooers-ph-d-
 X-ray lab webpage:
 http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/department-facilities/macromolecular-crystallography-laboratory
 SAXS Links webpage:
 http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/small-angle-x-ray-scattering-links.html?sfvrsn=0


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Re: [PyMOL] PyMOL to 3D PDF

2013-03-13 Thread Troels Emtekær Linnet
Hi Mike.

Try the example pdfs at:
http://pymolwiki.org/index.php/3d_pdf

1zqa PDF http://www.fys.ku.dk/~tlinnet/1zqa.pdf
beamer 1zqa PDF http://www.fys.ku.dk/~tlinnet/beamer_1zqa.pdf


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2013/3/13 Mike Marchywka marchy...@hotmail.com




 
  From: blaine-moo...@ouhsc.edu
  To: tlin...@gmail.com
  Date: Wed, 13 Mar 2013 04:45:59 -0500
  CC: pymol-users@lists.sourceforge.net
  Subject: Re: [PyMOL] PyMOL to 3D PDF
 
  PyMOL will also save surfaces in addition to cartoons to vwrl and idtf.
  Any representation composed of triangular surfaces should work.
 
  Thus, PuMOL fails to save labels to vmrl or idtf. This is another major
 advantage of
  JMOL over PyMOL at present.


 When you make 3D PDF how well do they display and manipulate? I thought
 this would be a nice
 feature for even 3D plots and IIRC tried it with an example from CRAN's R
 a while back , I can't remember how it
 came out in detail but seem to recall the pages took a while to load etc
 and at the time it
 was easier to load the data in an app rather than try to publish it that
 way.  for many actual
 pubs, they provide links in supplementary information section and it may
 be just as easy to publish
 a viewer script along with static images for illustration. A plugin would
 be nice, I always liked CHIME
 and that worked well on Internet Explorer about 10 years ago.


 
 
 
  Blaine Mooers
  Assistant Professor
  Director Macromolecular Crystallography Lab
  Member Stephenson Cancer Center
  Department of Biochemistry and Molecular Biology
  University of Oklahoma Health Sciences Center
  S.L. Young Biomedical Research Center Rm. 466
 
  Letter address:
  P.O. Box 26901, BRC 466
  Oklahoma City, OK 73190
 
  Shipping address:
  975 NE 10th Street, BRC 466
  Oklahoma City, OK 73104-5419
 
  office: (405) 271-8300 lab: (405) 271-8313 fax: (405) 271-3910
 
  e-mail: blaine-moo...@ouhsc.edu
 
  Faculty webpage:
 http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/faculty/blaine-mooers-ph-d-
  X-ray lab webpage:
 http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/department-facilities/macromolecular-crystallography-laboratory
  SAXS Links webpage:
 http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/small-angle-x-ray-scattering-links.html?sfvrsn=0
 
  
  From: Troels Emtekær Linnet [tlin...@gmail.com]
  Sent: Wednesday, March 13, 2013 4:19 AM
  To: Mooers, Blaine H.M. (HSC)
  Cc: pymol-users@lists.sourceforge.net
  Subject: Re: [PyMOL] PyMOL to 3D PDF
 
  Yeah.
 
  That is a cool feature, and is kind of the future of publishing. :-)
  Or at least, a very powerful tool for teaching.
 
  But it is sad that it only have cartoon export.
  I wish that it could include other representations.
 
  For now I use Jmol, which can export the whole representation in the
 window.
  I can import small molecules through. Files-Get MOL- And then CAS
 number or smiles.
  For proteins I scoop into rcsb.org
 https://urldefense.proofpoint.com/v1/url?u=http://rcsb.orgk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0As=13813dfb4e17158190791d134f870a433ff7cc614007ae72c21c5a5810c10091,
 and find the protein in the Jmol online viewer. (Just changing to white
 back ground).
 
  Right click in Jmol window-Export file-Export IDTF 3D model.
 
  That saves a .idtf file, and a .tex file ready for LaTeX.
  Rename the .idtf file, so it only ends on .idtf and not:
 filename.xyz.idtf
 
  Simpy converting the .idtf to .u3d as instructed in,
 http://www.pymolwiki.org/index.php/3d_pdf
 https://urldefense.proofpoint.com/v1/url?u=http://www.pymolwiki.org/index.php/3d_pdfk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0As=25a32bf64cd6f0227c7a8a73361f42721f9a6a377010deef4b50acdb49f29ccd
 )
  and you are ready to go from the given .tex file. (Removing the last
 looong comment section.)
 
  With a little practice, it only takes 3 min, to have 3d implementation
 of your molecule
  in teaching material / beamer presentation.
 
  I wish that could be implemented in PyMOL, and I have been looking for a
 wish list,
  but I don't know where that exists?
 
  Best
 
  Troels Emtekær Linnet
  Ved kløvermarken 9, 1.th
 https://urldefense.proofpoint.com/v1/url?u=http://1.thk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0As=5edb01bafbd605fcdadfe489b90dfe0d526e9a96b0ba86b04791e8d92bc46a63
 
  2300 København S
  Mobil: +45 60210234
 
 
  2013/3/12 Mooers, Blaine H.M. (HSC) blaine-moo...@ouhsc.edumailto:
 blaine-moo...@ouhsc.edu
  I saw Jason Vertrees update of http://www.pymolwiki.org/index.php/3d_pdf
 
 https

Re: [PyMOL] PyMOL to 3D PDF

2013-03-13 Thread Troels Emtekær Linnet
Hi Gianluigi.

The line goes into LaTeX.
I guess it tells something about the center of the molecule,
or some light settings.

Have you tried:
save pymol.idtf, all
(or some other selection)

The line should come out in the command window, like the
get_view
command.

Jmol automatically write this line in the .tex file it exports.

Best
Troels

2013/3/13, Gianluigi Caltabiano chimic...@yahoo.it:


 Very interesting features!

 I have never tried and was trying to do it, following the tutorial in
 pymolwiki but at :

   * Save your molecule to an IDTF file in PyMOL:
 save pymol.idtf, *
 PyMOL will print a line that looks like:
 3Daac=20.0, 3Droll=0, 3Dc2c=0 0 1, 3Droo=62.45, 3Dcoo=0 0 -62.45
 I did not have any line like this, not in the window panel neither in the
 idtf file. Where should I take this line?

 I used Hybrid PyMOL 1.5.0.3 on an iMAC.

 Thanks,

 Gianluigi




 
  Da: Troels Emtekær Linnet tlin...@gmail.com
 A: Mike Marchywka marchy...@hotmail.com
 Cc: pymol-users@lists.sourceforge.net
 Inviato: Mercoledì 13 Marzo 2013 13:01
 Oggetto: Re: [PyMOL] PyMOL to 3D PDF


 Hi Mike.

 Try the example pdfs at:
 http://pymolwiki.org/index.php/3d_pdf


 1zqa PDF
 beamer 1zqa PDF


 Troels Emtekær Linnet

 Ved kløvermarken 9, 1.th
 2300 København S
 Mobil: +45 60210234


 2013/3/13 Mike Marchywka marchy...@hotmail.com





 From: blaine-moo...@ouhsc.edu
 To: tlin...@gmail.com
 Date: Wed, 13 Mar 2013 04:45:59 -0500
 CC: pymol-users@lists.sourceforge.net

 Subject: Re: [PyMOL] PyMOL to 3D PDF


 PyMOL will also save surfaces in addition to cartoons to vwrl and idtf.
 Any representation composed of triangular surfaces should work.

 Thus, PuMOL fails to save labels to vmrl or idtf. This is another major
 advantage of
 JMOL over PyMOL at present.


When you make 3D PDF how well do they display and manipulate? I thought
 this would be a nice
feature for even 3D plots and IIRC tried it with an example from CRAN's R a
 while back , I can't remember how it
came out in detail but seem to recall the pages took a while to load etc
 and at the time it
was easier to load the data in an app rather than try to publish it that
 way.  for many actual
pubs, they provide links in supplementary information section and it may be
 just as easy to publish
a viewer script along with static images for illustration. A plugin would
 be nice, I always liked CHIME
and that worked well on Internet Explorer about 10 years ago.






 Blaine Mooers
 Assistant Professor
 Director Macromolecular Crystallography Lab
 Member Stephenson Cancer Center
 Department of Biochemistry and Molecular Biology
 University of Oklahoma Health Sciences Center
 S.L. Young Biomedical Research Center Rm. 466

 Letter address:
 P.O. Box 26901, BRC 466
 Oklahoma City, OK 73190

 Shipping address:
 975 NE 10th Street, BRC 466
 Oklahoma City, OK 73104-5419

 office: (405) 271-8300 lab: (405) 271-8313 fax: (405) 271-3910

 e-mail: blaine-moo...@ouhsc.edu

 Faculty webpage:
 http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/faculty/blaine-mooers-ph-d-
 X-ray lab webpage:
 http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/department-facilities/macromolecular-crystallography-laboratory
 SAXS Links webpage:
 http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/small-angle-x-ray-scattering-links.html?sfvrsn=0

 
 From: Troels Emtekær Linnet [tlin...@gmail.com]
 Sent: Wednesday, March 13, 2013 4:19 AM
 To: Mooers, Blaine H.M. (HSC)
 Cc: pymol-users@lists.sourceforge.net
 Subject: Re: [PyMOL] PyMOL to 3D PDF

 Yeah.

 That is a cool feature, and is kind of the future of publishing. :-)
 Or at least, a very powerful tool for teaching.

 But it is sad that it only have cartoon export.
 I wish that it could include other representations.

 For now I use Jmol, which can export the whole representation in the
 window.
 I can import small molecules through. Files-Get MOL- And then CAS
 number or smiles.
 For proteins I scoop into
 rcsb.orghttps://urldefense.proofpoint.com/v1/url?u=http://rcsb.orgk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0As=13813dfb4e17158190791d134f870a433ff7cc614007ae72c21c5a5810c10091,
 and find the protein in the Jmol online viewer. (Just changing to white
 back ground).

 Right click in Jmol window-Export file-Export IDTF 3D model.

 That saves a .idtf file, and a .tex file ready for LaTeX.
 Rename the .idtf file, so it only ends on .idtf and not:
 filename.xyz.idtf

 Simpy converting the .idtf to .u3d as instructed in,
 http://www.pymolwiki.org/index.php/3d_pdfhttps://urldefense.proofpoint.com/v1/url?u=http://www.pymolwiki.org/index.php/3d_pdfk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=9qhiQpTD7yw1v1CYn82swYWLHkc%2FkmViU2tMT7DUu9c%3D%0As

[PyMOL] Help to compile u3d converter - IDTF to U3D on linux 64

2013-03-04 Thread Troels Emtekær Linnet
Dear Pymolers.

I am playing around with creating a pdf file with 3 D graphics.
I am saving in *idtf* format, which I convert to *u3d, *and then include in
pdf through latex.

I can do this on windows, but I can't compile IDTFConverter *on linux 64.*

I have made this progress

http://pymolwiki.org/index.php/3d_pdf#Linux_install

But when I compile, I get.


### ERROR ###
Building Core
 Build started: Project: Base, Configuration: release Lin32 -
In file included from IFXVectorHasher.cpp:32:
IFXVectorHasher.h: In member function ‘BOOL
IFXVectorHasherNodeIterator::Next()’:
IFXVectorHasher.h:215: error: cast from ‘IFXVectorHasherVectorNode*’
to ‘BOOL’ loses precision
IFXVectorHasher.h: In member function ‘BOOL IFXVectorHasherBinIterator::Next()’:
IFXVectorHasher.h:279: error: cast from ‘IFXVectorHasherBinNode*’ to
‘BOOL’ loses precision
make: *** [all] Error 1
Base - 2 error(s), 0 warning(s)
*** BUILD Core ERROR  *
--- Build done ---
Base - 2 error(s), 0 warning(s) : failed
--
Entire build: 0 succeeded, 1 failed
=
ERROR, build process is not complete
=
#


I think it it because that I try to compile 32 bit, with a gcc 64 bit
version.

*Does anyone know how-to compile this on a linux machine?*
I would be happy if we could get IDTFConverter on out linux machines in the
lab.

Best
Troels


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[PyMOL] Making 3D-pdf's and keeping selections/colors

2013-03-03 Thread Troels Emtekær Linnet
Hi Pymolers.

I tried today the directions on http://pymolwiki.org/index.php/3d_pdf
It works fine, and I have pdf with my pymol figure.

But the colors and selections are not as when I save as .idtf.
I just get a plain blue cartoon representation.

Does anyone know where I should change something?
 - When saving as .idtf.
 - When converting to .u3d
 - Or when using movie15 package?


Best

Troels Emtekær Linnet
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2300 København S
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Re: [PyMOL] freeglut error

2013-02-12 Thread Troels Emtekær Linnet
There should be No asterixs.

I tried to mark the part in bold via email.

best



2013/2/12 mark m.r...@5-cent.us

 On 02/11/13 09:30, Troels Emtekær Linnet wrote:

 Hi.

 Well, I don't know really what you wan't, but I remember pain with
 graphics and computers. :-)

 I see the same error (X Error of failed request) when I get a
 kernel update to my CentOS comp. That screws up my NVIDIA driver
 installation, pymol fails, and I have to reinstall the driver
 package.


 Nope, not needed. I had not updated the system before the pymol package
 was installed - it did come as a package from a standard repository.


 The term LIBGL_ALWAYS_INDIRECT=1, is controlling something with
 which method draws the window. By OpenGL or by the mesa driver.
 (Something like that). The OpenGL is super fast, and mesa driver is
 slow.

  Yeah, it appears to definitely be freeglut. In googling, I found several
 references to a variable or function name change.
 snip


 If this can help, our execution script for pymol is:

 --**--**
 --


  [tlinnet@tomat pymolsvn]$ cat pymolMPEG.sh

 #!/bin/bash if [ ! -f
 $HOME/.local/share/**applications/pymolsvn.desktop ]; then ln -s
 /ourlab/software/pymolsvn/**pymolsvn.desktop
 $HOME/.local/share/**applications/pymolsvn.desktop fi

 export FREEMOL=/ourlab/software/**pymolsvn/svnfreemol/freemol export
 PYMOL_GIT_MOD=/ourlab/**software/pymolsvn/Pymol-**script-repo/modules
 export
 PYTHONPATH=$PYTHONPATH:/**ourlab/software/x64/lib64/**
 python2.6/site-packages/PIL


  export

 PYTHONPATH=$PYTHONPATH:/**ourlab/software/x64/lib64/**
 python2.6/site-packages/lib-tk


  export

 PYTHONPATH=$PYTHONPATH:/**ourlab/software/x64/lib64/**
 python2.6/site-packages/lib-**dynload


  export

 PYTHONPATH=/ourlab/software/**pymolsvn/Pymol-script-repo/**
 modules:$PYTHONPATH


  export PYTHONPATH=/ourlab/software/**pymolsvn/Pymol-script-repo:$**
 PYTHONPATH

 export
 LD_LIBRARY_PATH=$LD_LIBRARY_**PATH:/ourlab/software/x64/lib/**pymollib
 *export LIBGL_ALWAYS_INDIRECT=no*

 /usr/bin/python /ourlab/software/pymolsvn/**modules/pymol/__init__.py
 $@


 snip
 I'll look at that tomorrow. One thing I question: why are there asterisks
 around the export LIBGL_ALWAYS_INDIRECT?

 mark


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Re: [PyMOL] representing ferrocene in pymol

2013-02-11 Thread Troels Emtekær Linnet
How about.

import select_sites
sites 1a3l
set_bond stick_radius, 0.1, resi 213
extract Fe_atom, resi 213 and name Fe

Wiki
http://www.pymolwiki.org/index.php/Select_sites
http://www.pymolwiki.org/index.php/Set_bond


Best
Troels

Troels Emtekær Linnet
Ved kløvermarken 9, 1.th
2300 København S
Mobil: +45 60210234

2013/2/11 Edward Deira edward.de...@gmail.com

 Dear all,

 How can I accurately represent ferrocene in pymol, without using CONECT
 lines in the pdb file ?
 By accurately I mean at least including the C-C bonds; I'd rather not
 have any Fe-C bonds, but if they are present I can live.

 I've been trying to figure out how to do this using atom selections, or
 trying to get gonds between the nonbonded...

 Any hints are welcome,

 all the best
  Ed.


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Re: [PyMOL] freeglut error

2013-02-11 Thread Troels Emtekær Linnet
Hi.

Well, I don't know really what you wan't, but I remember pain with graphics
and computers. :-)

I see the same error (X Error of failed request) when I get a kernel
update to my CentOS comp.
That screws up my NVIDIA driver installation, pymol fails, and I have to
reinstall the driver package.

The term LIBGL_ALWAYS_INDIRECT=1, is controlling something with which
method draws the window.
By OpenGL or by the mesa driver. (Something like that).
The OpenGL is super fast, and mesa driver is slow.

Our shared installation of pymol, means that computers with the NVIDIA
driver works super fast, while
the computers which havent an updated NVIDIA driver is just running slow.
(Pain slow).

If this can help, our execution script for pymol is:

--
[tlinnet@tomat pymolsvn]$ cat pymolMPEG.sh
#!/bin/bash
if [ ! -f $HOME/.local/share/applications/pymolsvn.desktop ];
then
ln -s /ourlab/software/pymolsvn/pymolsvn.desktop
$HOME/.local/share/applications/pymolsvn.desktop
fi

export FREEMOL=/ourlab/software/pymolsvn/svnfreemol/freemol
export PYMOL_GIT_MOD=/ourlab/software/pymolsvn/Pymol-script-repo/modules
export
PYTHONPATH=$PYTHONPATH:/ourlab/software/x64/lib64/python2.6/site-packages/PIL
export
PYTHONPATH=$PYTHONPATH:/ourlab/software/x64/lib64/python2.6/site-packages/lib-tk
export
PYTHONPATH=$PYTHONPATH:/ourlab/software/x64/lib64/python2.6/site-packages/lib-dynload
export
PYTHONPATH=/ourlab/software/pymolsvn/Pymol-script-repo/modules:$PYTHONPATH
export PYTHONPATH=/ourlab/software/pymolsvn/Pymol-script-repo:$PYTHONPATH
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/ourlab/software/x64/lib/pymollib
*export LIBGL_ALWAYS_INDIRECT=no*

/usr/bin/python /ourlab/software/pymolsvn/modules/pymol/__init__.py $@




Best
Troels Emtekær Linnet
Ved kløvermarken 9, 1.th
2300 København S
Mobil: +45 60210234


2013/2/7 m.r...@5-cent.us

 Hi, folks,

 If there's a howto or FAQ on this, please give me a pointer.

 We've recently install pymol on several systems. We're running CentOS 6.3,
 and the yum installed pymos is 1.3.3.20100705svn3911

 ssh -Y into other workstations lets me run it with no problem. However, if
 I do the same to a headless server, on which X is *not* running (if that
 makes any difference - it is installed), results in
 freeglut (pymol):  ERROR:  Internal error FBConfig with necessary
 capabilities not found in function fgOpenWindow
 X Error of failed request:  BadWindow (invalid Window parameter)
   Major opcode of failed request:  4 (X_DestroyWindow)
   Resource id in failed request:  0x0
   Serial number of failed request:  33
   Current serial number in output stream:  36
  PyMOL: abrupt program termination.

 When I first log in, glxgears also doesn't run. Having done a lot of
 googling, once I execute
 export LIBGL_ALWAYS_INDIRECT=1
 glxgears runs, albeit slowly and irregularly (faster, slower, etc).
 However, pymol still gives me the same errors (and I have read that there
 are two of them, the freeglut and the X error.

 Any solutions? workarounds?

 Thanks in advance.

 mark, sysadmin, not researcher



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Re: [PyMOL] fetch biounits or NMR model

2013-02-11 Thread Troels Emtekær Linnet
Hi Michael.

Something similar has been made to show the SITES labels of a pdb file,
for quick referencing of a crystal structure.
http://pymolwiki.org/index.php/Select_sites

You could look into how that is written, and provide something similar for
an NMR structure?

Best
Troels


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2013/2/8 Zimmermann, Michael T., Ph.D. zimmermann.mich...@mayo.edu

  Dear PyMOL Users,

 ** **

 I’ve been using fetch and fetchlocal (from the wiki) for working with
 multiple datasets of structures, but have a nagging issue that I have not
 found an efficient way to solve. I typically download the first biological
 unit, which works for X-ray structures. The trouble is (for good reason),
 NMR structures don’t have a .pdb1 file. Does anyone have a script to do, or
 have a good idea about how to implement, the following? (It’s really my
 lack of familiarity with catching the value from functions like
 cmd.get_names (rather than it just being printed) in python that’s my
 barrier…)

 ** **

 Attempt to fetch 2yrq.pdb1

 If fetch fails, try fetching 2yrq.pdb

 If successful and we have 1 state, save the first state

 ** **

 Thanks!

 ** **

 *Michael T. Zimmermann*

 Ph. D. in Bioinformatics | Health Sciences Research | Division of
 Biomedical Statistics and Informatics

 *Mayo Clinic* | 200 First Street SW | Rochester, MN 55905 | 
 mayoclinic.orghttp://www.mayoclinic.org
 

 ** **


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Re: [PyMOL] apbs2 plugin failure

2013-01-10 Thread Troels Emtekær Linnet
Hi Andreas.

The line:
/usr/lib64/python2.6/site-packages/pmg_tk/startup/apbs_tools.py

shows that you are using the apbs tools from Michael G. Lerner.
http://pymolwiki.org/index.php/APBS

You might want to try out a little modified version of that.
http://pymolwiki.org/index.php/Apbsplugin

You might also want to try this.
That is the repository with all scripts from Pymolwiki, to work out of the
box.
http://pymolwiki.org/index.php/Git_intro



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2013/1/3 Andreas Förster docandr...@gmail.com

 Dear all,

 on our RHEL computers (6.2, 64-bit) with PyMOL compiled from CVS, the
 APBS2 plugin isn't functioning anymore.  The plugin window opens just
 fine and the executables are found.

 When I select Use PDB2PQR in the Main tab, clicking on Set grid
 produces the following error:

 Error: 1
 type 'exceptions.UnboundLocalError' Exception in Tk callback
Function: function lambda at 0x7fc2b0705410 (type: type
 'function')
Args: ()
 Traceback (innermost last):
File /usr/lib/python2.6/site-packages/Pmw/Pmw_1_3_3/lib/PmwBase.py,
 line 1747, in __call__
  return apply(self.func, args)
File
 /usr/lib/python2.6/site-packages/Pmw/Pmw_1_3_3/lib/PmwDialog.py, line
 153, in lambda
  command=lambda self=self, name=name: self._doCommand(name))
File
 /usr/lib/python2.6/site-packages/Pmw/Pmw_1_3_3/lib/PmwDialog.py, line
 132, in _doCommand
  return command(name)
File
 /usr/lib64/python2.6/site-packages/pmg_tk/startup/apbs_tools.py, line
 1075, in execute
  self.runPsize()
File
 /usr/lib64/python2.6/site-packages/pmg_tk/startup/apbs_tools.py, line
 1096, in runPsize
  good = self.generatePqrFile()
File
 /usr/lib64/python2.6/site-packages/pmg_tk/startup/apbs_tools.py, line
 1007, in generatePqrFile
  good = self._generatePdb2pqrPqrFile()
File
 /usr/lib64/python2.6/site-packages/pmg_tk/startup/apbs_tools.py, line
 1615, in _generatePdb2pqrPqrFile
  if retval != 0:
 type 'exceptions.UnboundLocalError': local variable 'retval'
 referenced before assignment

 When I chose User PyMOL generated PQR and PyMOL generated Hydrogens and
 termini or User PyMOL generated PQR and existing hydrogens and
 termini, I can set the grid, run APBS and visualize the result just fine.

 I'm happy with that, but maybe someone has an idea of why the first
 approach fails.


 Thanks.


 Andreas




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Re: [PyMOL] electron density map

2012-11-01 Thread Troels Emtekær Linnet
Hi mehdi.

Look for inspiration here.
http://www.pymolwiki.org/index.php/Dynamic_mesh

fetch 1HWK, async=1
fetch 1HWK, 1hwk_map, type=2fofc, async=1

Best
Den 01/11/2012 18.09 skrev Mehdi Talebzadeh Farooji mahdi...@yahoo.com:

 Dear All,

 I am trying to create a electron density map for the pdb file which is not
 deposited in RCSB bank, however I do not find any option on
 http://eds.bmc.uu.se/eds/. Is there any way to get density map for the
 pdb files which are not deposited in pdb data bank?

 All the best,

 Mehdi


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[PyMOL] Getting surface residues

2012-10-31 Thread Troels Emtekær Linnet
Hi Pymolers.

How would you get a list of surface residues the fastest way?

Like:
 [3-10], [14-18]

I have a rough structure from crystallography, and have made
a trypsin digest and mass spec analysis.

And I see fragments which have been post-trans modified.

Now I am interested in matching if those fragments are surface exposed or
internal.

What tools does pymol have to find out if the residues are surface exposed?
Or is there another easy tool?

Best
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Re: [PyMOL] Getting surface residues

2012-10-31 Thread Troels Emtekær Linnet
Thanks!

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2012/10/31 Abdullah Kahraman abdul...@imsb.biol.ethz.ch

 Dear Troels,

 Personally I don't use PyMol for this problem. Rather I use the
 application NACCESS (http://www.bioinf.manchester.ac.uk/naccess/) and
 choose a total relative solvent accessibility of at least 5% (Miller, S.
 et al, 1987, *J Mol Biol* 196, 641–656) to assess whether a residue is at
 the protein surface or not. The relative solvent accessibilities are listed
 in 5th column of the NACCESS .rsa output file.

 Best
 Abdullah


 On 31 Oct 2012, at 07:11, Troels Emtekær Linnet tlin...@gmail.com wrote:

 Hi Pymolers.

 How would you get a list of surface residues the fastest way?

 Like:
  [3-10], [14-18]

 I have a rough structure from crystallography, and have made
 a trypsin digest and mass spec analysis.

 And I see fragments which have been post-trans modified.

 Now I am interested in matching if those fragments are surface exposed or
 internal.

 What tools does pymol have to find out if the residues are surface exposed?
 Or is there another easy tool?

 Best
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Re: [PyMOL] Help with autodock plugin for PyMOL

2012-10-27 Thread Troels Emtekær Linnet
What is the atom name of EFP.ligand:A:EFP999?
Can you check your pdb file? Do you rename them before running the plugin?
Den 26/10/2012 23.26 skrev Ragnar Thomsen rthoms...@gmail.com:

 I have a problem when running the autodock plugin for PyMOL. I followed the
 tutorial at http://www.pymolwiki.org/index.php/Autodock_plugin.
 When I prepare the ligand I get the following error output:

 Batch: /usr/lib/python2.7/site-
 packages/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py -l
 /home/ragnar/pymol/EFP.ligand.pdb -o /home/ragnar/pymol/EFP.pdbqt -A
 checkhydrogens
 swig/python detected a memory leak of type 'BHtree *', no destructor found.
 Traceback (most recent call last):
   File /usr/lib/python2.7/site-
 packages/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py, line
 207, in module
 if a.coords!=coord_dict[a]: bad_list.append(a)
 KeyError: Atom instance EFP.ligand:A:EFP999:HN

 Software versions:
 PyMOL 1.5.0.1
 mgltools 1.5.4
 autodock/autogrid 4.2.3
 audodock vina 1.1.2

 Any help appreciated...

 Regards,
 Rthomsen


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[PyMOL] Make sure zoom is viewed from surface

2012-10-07 Thread Troels Emtekær Linnet
Hi pymolers.

I am generating a list of residue ID's from some calculations.
Now I want to make a little script that select the residue and sticks it
and then zoom and make .png file.

How do I make sure that the zoom, is viewed from outside the protein for
each residue/.png file?

Best

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Re: [PyMOL] Introducing hydrogen bonds between ligand and target in pymol that runs on linux ubuntu operating system

2012-10-01 Thread Troels Emtekær Linnet
# See http://www.pymolwiki.org/index.php/Displaying_Biochemical_Properties
reinitialize

cd /sbinlab2/tlinnet/Desktop
fetch 2xml, async=0
show_as cartoon, 2xml

select OGA, OGA
select EDO, EDO
select ZN, ZN
select NI, NI
select CL, CL

show sticks, OGA or EDO
show spheres, ZN or NI or CL
dist hydbonds_OGA, OGA, 2xml, mode=2
dist hydbonds_EDO, EDO, 2xml, mode=2

print cmd.get_setting_text('h_bond_cutoff_center')
print cmd.get_setting_text('h_bond_cutoff_edge')

select OGA_A_near_resi, byres 2xml within 3.6 of OGA and chain A
select OGA_B_near_resi, byres 2xml within 3.6 of OGA and chain B

show sticks, OGA_*

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2012/9/29 Mona Kab Omir kzq...@alumni.ku.dk

  Hei
 I have  a question about how to introduce hydrogen bonds between ligands
 and target molecule in pymol that runs on linux ubuntu 12.04 operative
 system.
 I have searched and tried to type following command:
 set h_bond_cutoff_center, 3.6
 set h_bond_cutoff_edge, 3.2
  and I tried to choose [A]- [find]- polar contacts- different options,
 but it also don't helped at all.
 Do any of you have a suggestion to what might have been gone wrong?

 Many big thanks!

 regards

 Mona



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Re: [PyMOL] Define Variables in pml scripts

2012-10-01 Thread Troels Emtekær Linnet
Dear James.

Switch to use the python command syntax and string printing in input
arguments.

*reinitialize*
*cd C:\Users\tlinnet\Desktop*
*
*
*prot=1dwq*
*
*
*#fetch 1dw1*
*cmd.fetch(prot,async=0)*
*
*
*select visible*
*#load 1dw1.map.ccp4*
*cmd.fetch(prot,async=0,type=2fofc)*
*
*
*#isomesh map, 1dw1.map, 3.0, sele, carve=1.6*
*cmd.isomesh(%s_map%prot, %s_2fofc%prot, 3.0, sele, carve=1.6)*
*
*
*#color br2, map*
*cmd.color(br2, %s_map%prot)*
*#cmd.color(yellow, %s_map%prot)*
*
*
*#set mesh_width, 0.5*
*print cmd.get_setting_text('mesh_width')*
*cmd.set(mesh_width, 0.5)*
*print cmd.get_setting_text('mesh_width')*
*
*
*#bg_color black*
*cmd.bg_color(white)*
*
*
*#set ray_trace_fog, 0*
*print cmd.get_setting_text('ray_trace_fog')*
*cmd.set(ray_trace_fog, 0)*
*print cmd.get_setting_text('ray_trace_fog')*
*
*
*#set depth_cue, 0*
*print cmd.get_setting_text('depth_cue')*
*cmd.set(depth_cue, 0)*
*print cmd.get_setting_text('depth_cue')*
*
*
*#set ray_shadows, off*
*print cmd.get_setting_text('ray_shadows')*
*cmd.set(ray_shadows, off)*
*print cmd.get_setting_text('ray_shadows')*
*
*
*#ray 1280,1024*
*#cmd.ray(1280,1024)*
*
*
*#png 1dw1.png*
*#cmd.png(1dw1.png)*


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2012/10/1 James Starlight jmsstarli...@gmail.com

 Dear PyMol users!

 I wounder to know how to define variables in pml scripts.

 E.g in below command sets for processing of ccp4 maps the PDB ID
 (1dw1) of the processed pdb file is mentioned several times. How I
 could define variable for that pdb id only once in the start of that
 simple script to allow me edit pdb id only once  at that defined
 variable each time when I change pdb file ?

 fetch 1dw1

 select visible
 load 1dw1.map.ccp4


 isomesh map, 1dw1.map, 3.0, sele, carve=1.6

 color br2, map
 set mesh_width, 0.5
 bg_color black
 set ray_trace_fog, 0
 set depth_cue, 0
 set ray_shadows, off
 ray 1280,1024
 png 1dw1.png


 Thanks for help

 James


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Re: [PyMOL] APBS Tools library error

2012-10-01 Thread Troels Emtekær Linnet
Hi Christian.

I had a similar problem on my windows machine, but with .
Try to set the temp path.

*reinitialize*
*fetch 4ins, async=0*
*
*
*import os*
*print os.environ['temp']*
*print os.getcwd()*
*os.environ['temp']=os.getcwd()*
and then run the apbs plugin.

My own problem on my windows computer, was that I default had set .py files
to be opened with
notepad++. When I in apbs plugin then executed the Set grid, the pdb2pqr
would be opened in Notepad++
instead of executing the script.
I had to default opening of .py files to python before it worked.

I dont know if these problems would be meaning full on CentOS ?

Please report how it goes :-)

Best
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2012/9/27 Christian Roth christian.r...@bbz.uni-leipzig.de

 Dear all,

 we have with our system Ubuntu a problem with APBS in the new pymol 1.5.
 We use exactyl this version:
 This Executable Build integrates and extends Open-Source PyMOL 1.5.0.4.
  The following error occurs:
 PDB2PQR - a Python-based structural conversion utility
 --
 Please cite your use of PDB2PQR as:
   Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA.
   PDB2PQR: an automated pipeline for the setup, execution,
   and analysis of Poisson-Boltzmann electrostatics calculations.
   Nucleic Acids Research 32 W665-W667 (2004).

 ran main.mainCommand
 Erasing contents of pymol-generated.pqr in order to clean it up
 I WILL RETURN TRUE from pdb2pqr
 GENERATED
 Running:
 prog=/software/linuxsoft/pymol/freemol/bin/apbs.exe
 args=('/software/linuxsoft/pymol/freemol/bin/apbs.exe', '
 pymol-generated.in')
 Results were:
 Return value: 127
 Output:
 /software/linuxsoft/pymol/freemol/bin/apbs.exe: symbol lookup error:
 /software/linuxsoft/ifc/compiler60/ia32/lib/libimf.so: undefined symbol:
 __aullshr

 Could not find pymol-generated.dx so searching for pymol-generated-PE0.dx
 ObjectMapLoadDXFile-Error: Unable to open file!
 ObjectMapLoadDXFile: Does 'pymol-generated-PE0.dx' exist?

 It seems to be a very strange error within the intelfortan compiler
 library.
 However we cannot find so far  solution.
 So far we did not find a usable new library version to overcome the
 problem.
 Interestingly the APBS version within pymol build 1.2r3pre using APBS
 It works. This was a centos45 version of pymol.

 Does anyone has encountered a similar error and found a more elegant
 solution
 than just using an old pymol for such calculations?

 Thank you very much in advance for your help an suggestions.

 Best Regards

 Christian
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Re: [PyMOL] Create NMR-like trajectory from initial X-ray set

2012-09-23 Thread Troels Emtekær Linnet
Hrellow James.

You could do it like this:

-
reinitialize

fetch 2yh2, async=0
fetch 3zwq, async=0

super 3zwq, 2yh2

print cmd.get_names(objects)
print cmd.get_names(public_objects)

my_objects = cmd.get_names(public_objects)

python
for i in range(len(my_objects)):
   cmd.create(my_protein, my_objects[i], 1, (i+1))
   cmd.remove(my_objects[i])
   cmd.delete(my_objects[i])
python end

show_as cartoon, my_protein
save my_protein.pdb, my_protein, state=0
set movie_fps, 1
mplay
-


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2012/9/23 James Starlight jmsstarli...@gmail.com

 Dear PyMol users!

 I've already created such topic and found sollution to it but now I
 forgot how exactly I did it :)

 The main task is the creation of the trajectory in NMR-like format
 from initial X-ray structures ( each of them is the indivixual
 snapshot for suture trajectory).
 E.g in Pymol I have opened 15 x-ray structures aligned against one
 reference. All of that structures also consist of different numbers of
 states (models). As the result I want to chose only first state from
 each of that structures and create new common pdb file consisted of
 each structure (total 15 snapshots). Its important that In that new
 NMR-like file order of the models must be corresponded to the order of
 structures in the PyMol window. How I could do that?


 Thanks for help

 James


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Re: [PyMOL] Question about mutagenesis wizard

2012-09-19 Thread Troels Emtekær Linnet
Hi.

I tried a little:

*test1.pml*
# See http://www.pymolwiki.org/index.php/Peptide_Sequence
# See http://www.pymolwiki.org/index.php/propka

reinitialize
cd C:\Users\tlinnet\Desktop

python
for aa in CVGLTSW:
cmd._alt(string.lower(aa))
python end
create pdb1, cys
remove cys
delete cys
save pdb1.fasta, pdb1

###First time
#python
#for aa in ALTWSIK:
#cmd._alt(string.lower(aa))
#python end
#create pdb2, ala
#remove ala
#delete ala
#translate [-6,-15,0], pdb2
#save pdb2.pdb, pdb2
### Second time
load pdb2.pdb

alter pdb1, chain='A'
alter pdb2, chain='A'
rebuild
create pdb3, pdb1

chainresnresi3 = []
chainresnresi2 = []
iterate pdb3 and name CA, chainresnresi3.append([pdb3,chain,resn,resi])
iterate pdb2 and name CA, chainresnresi2.append([pdb2,chain,resn,resi])
#print chainresnresi3
#print chainresnresi2

python
cmd.wizard(mutagenesis)
for i in range(len(chainresnresi2)):
cmd.do(refresh_wizard)
cmd.get_wizard().set_mode(%s%chainresnresi2[i][2])
#print %s%chainresnresi2[i][2]

selection=/%s//%s/%s%(chainresnresi3[i][0],chainresnresi3[i][1],chainresnresi3[i][3])
#print
/%s//%s/%s%(chainresnresi3[i][0],chainresnresi3[i][1],chainresnresi3[i][3])
cmd.get_wizard().do_select(selection)
cmd.frame(1)
cmd.get_wizard().apply()
python end
cmd.set_wizard(done)

translate [10,-25,0], pdb3

*test2.pml*
reinitialize
cd C:\Users\tlinnet\Desktop

fab CVGLTSW, pdb1, resi=1, chain=A
save pdb1.fasta, pdb1

fab ALTWSIK, pdb2, resi=1, chain=A
translate [0,-15,0], pdb2

create pdb3, pdb1
translate [0,-30,0], pdb3

chainresnresi3 = []
chainresnresi2 = []
iterate pdb3 and name CA, chainresnresi3.append([pdb3,chain,resn,resi])
iterate pdb2 and name CA, chainresnresi2.append([pdb2,chain,resn,resi])
print chainresnresi3
print chainresnresi2

python
cmd.wizard(mutagenesis)
for i in range(len(chainresnresi2)):
cmd.do(refresh_wizard)
cmd.get_wizard().set_mode(%s%chainresnresi2[i][2])
#print %s%chainresnresi2[i][2]

selection=/%s//%s/%s%(chainresnresi3[i][0],chainresnresi3[i][1],chainresnresi3[i][3])
#print
/%s//%s/%s%(chainresnresi3[i][0],chainresnresi3[i][1],chainresnresi3[i][3])
cmd.get_wizard().do_select(selection)
cmd.frame(1)
cmd.get_wizard().apply()
python end
cmd.set_wizard(done)

*test3.pml*
reinitialize
cd C:\Users\tlinnet\Desktop

load pdb1.fasta
load pdb2.fasta
translate [0,-15,0], pdb2

create pdb3, pdb1
translate [0,-30,0], pdb3

chainresnresi3 = []
chainresnresi2 = []
iterate pdb3 and name CA, chainresnresi3.append([pdb3,chain,resn,resi])
iterate pdb2 and name CA, chainresnresi2.append([pdb2,chain,resn,resi])
print chainresnresi3
print chainresnresi2

python
cmd.wizard(mutagenesis)
for i in range(len(chainresnresi2)):
cmd.do(refresh_wizard)
cmd.get_wizard().set_mode(%s%chainresnresi2[i][2])
#print %s%chainresnresi2[i][2]

selection=/%s//%s/%s%(chainresnresi3[i][0],chainresnresi3[i][1],chainresnresi3[i][3])
#print
/%s//%s/%s%(chainresnresi3[i][0],chainresnresi3[i][1],chainresnresi3[i][3])
cmd.get_wizard().do_select(selection)
cmd.frame(1)
cmd.get_wizard().apply()
python end
cmd.set_wizard(done)

*pdb1.fasta*
pdb1
CVGLTSW

*pdb2.fasta*
pdb2
ALTWSIK

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2012/9/14 Maurício Menegatti Rigo mauriciomr1...@gmail.com

 Hi Thomas,

 thank you for your response. Actually,  the  modeling part comes later in
 the process. First, I need  to perform  this step  in pymol. In fact, it
 would facilitate the modeling process.

 Sincerely,
 --
 Maurício M Rigo


 2012/9/14 Thomas Holder spel...@users.sourceforge.net

 Hi Maurício,

 what you describe here is called homology modeling. Although PyMOL has
 some modeling capabilities, I'd strongly recommend to use a real homology
 modeling tool such as MODELLER to do this.

 http://salilab.org/modeller/

 Hope that helps.

 Cheers,
   Thomas

 Maurício Menegatti Rigo wrote, On 09/14/12 19:44:

 Dear Pymol users,

 I'm  a begginer  with command lines in Pymol.  I'm trying to
 complete  the following task through a pymol  script:

 1) Write a file named file1.txt with an aminoacid sequence (e.g.
 CVGLTUW)

 2) Open  a .pdb molecule (file2.pdb) with the same number of
 residues, but with a different sequence (e.g. ALTWSIK)

 3) Write a code where the pymol will pick each residue of the
 file2.pdb (I believe that this could be made by the mutagenesis
 wizard command) and mutate for the respective aminoacid written in
 my file1.txt

 4) Save the new filein .pdb format (file3.pdb)

 I'll be very greatful for any help!

 Thanks  in advance,
 -- M.Sc. Maurício Menegatti Rigo
 Núcleo de Bioinformática do Laboratório de Imunogenética
 Departamento de Genética
 Instituto de Biociências
 Universidade Federal do Rio Grande do Sul - Campus do Vale
 Av. Bento Gonçalves, 9500 - Bairro Agronomia - Prédio 43323 M
 CEP:91501-970 Caixa Postal 15053

Re: [PyMOL] Importing simplejson in pymol on OSX

2012-07-25 Thread Troels Emtekær Linnet
Hi.

You probably want to make sure your file is somewhere in your system path.
write in pymol

import sys
print sys.path

Then locate a directory where you can store your file.
You can also make some kung-fu, and add to the PYTHONPATH:

You could have a start script something like this

#!/bin/bash
export FREEMOL=/xxx/software/pymolsvn/svnfreemol/freemol
export PYMOL_GIT_MOD=/xxx/software/pymolsvn/Pymol-script-repo/modules
export
PYTHONPATH=$PYTHONPATH:/xxx/software/x64/lib64/python2.6/site-packages/PIL
export
PYTHONPATH=$PYTHONPATH:/xxx/software/x64/lib64/python2.6/site-packages/lib-tk
export
PYTHONPATH=$PYTHONPATH:/xxx/software/x64/lib64/python2.6/site-packages/lib-dynload
export
PYTHONPATH=/xxx/software/pymolsvn/Pymol-script-repo/modules:$PYTHONPATH
export PYTHONPATH=/xxx/software/pymolsvn/Pymol-script-repo:$PYTHONPATH
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/xxx/software/x64/lib/pymollib
export LIBGL_ALWAYS_INDIRECT=no

/usr/bin/python /xxx/software/pymolsvn/modules/pymol/__init__.py $@

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2012/7/24 Matthew Baumgartner mp...@pitt.edu

 Hi,
 I wrote a short script that I am going to use in pymol.  I need to parse
 a json file and then display the contents in some manner. It works just
 fine in Ubuntu 12.04, but when I try it on OSX, it doesn't work. The
 problem that I am having is that when I try `import simplejson` or
 `import json` it throws an ImportError.

 I assume that this is related to the PYTHON_PATH variable, but thus far
 my google-fu has come up short.
 I've tried it in both pymol version 1.3 and 1.5.0.3.

 Any help would be appreciated.

 Thanks,
 Matt Baumgartner


 Technical Details:
 pymol 1.5.0.3 and 1.3
 OSX 10.6.8



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Re: [PyMOL] Pymol-MOLE error

2012-07-16 Thread Troels Emtekær Linnet
Hi Srinivasan.

It seems you need the package:
*whrandom *
*
*
Try starting pymol and write in console:
*from whrandom import random
help(random)*

*PyMOLfrom whrandom import random *
*PyMOLhelp(random)*
*Help on module whrandom.random in whrandom:*
* *
*NAME*
*whrandom.random*
* *
*FILE*
*c:\python27\pymol\pymol-script-repo\modules\mole\whrandom\random.py*


The package is included in the project Pymol-script-repo project.
http://www.pymolwiki.org/index.php/Git
http://www.pymolwiki.org/index.php/Git_install


Best
Troels

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2012/7/16 Srinivasan Rengacahri srinivasan.rengach...@yahoo.com

 Dear Pymol Users,

  I tried to run the program MOLE for computing tunnels on my
 protein and i got the following error message. I can be considered a
 beginner when it comes to these problems coz I am not sure if its a
 problem of the plugin or with pymol; it would be kind to get some help
 to sort this out. And yes, windows is the operating system.

 Many thanks for your help,
 Vasan

 Error: 1
 type 'exceptions.ImportError' Exception in Tk callback
Function: function lambda at 0x0C400438 (type: type
 'function')
Args: ()
 Traceback (innermost last):
File C:\Program
 Files\PyMOL\PyMOL/modules\Pmw\Pmw_1_2\lib\PmwBase.py, line 1747, in
 __call__
  return apply(self.func, args)
File C:\Program
 Files\PyMOL\PyMOL/modules\Pmw\Pmw_1_2\lib\PmwDialog.py, line 153, in
 lambda
  command=lambda self=self, name=name: self._doCommand(name))
File C:\Program
 Files\PyMOL\PyMOL/modules\Pmw\Pmw_1_2\lib\PmwDialog.py, line 132, in
 _doCommand
  return command(name)
File C:\Program Files\PyMOL\PyMOL/modules\pmg_tk\startup\mole.py,
 line 586, in execute
  execfile(pathpy)
File C:\Mole\tmp\found_001_001.py, line 10, in module
  from whrandom import random
 type 'exceptions.ImportError': No module named whrandom


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Re: [PyMOL] Is there or should there be a pymol annotation server?

2012-07-14 Thread Troels Emtekær Linnet
Dear Pymolers.

Thanks for all the suggestions. :-)

I definitely think that http://jolecule.appspot.com can become handy for a
teaching situation
or sending a colleague a question to a protein. Thanks!

And I am all in for interactive publications, which I hope could use one
day.

The Uniprot_features http://pymolwiki.org/index.php/Uniprot_features is
probably what I am looking for.
So I will try that out.

Best

Troels Emtekær Linnet


2012/7/14 Thomas Holder spel...@users.sourceforge.net

 indeed, the SITE records could easily be parsed and made available as
 named selections.

 Similar: http://pymolwiki.org/index.php/Uniprot_features
   - makes named selections from uniprot annotations

 Cheers,
Thomas

 Nat Echols wrote, On 07/13/12 23:24:
  On Fri, Jul 13, 2012 at 2:12 PM, Jason Vertrees
  jason.vertr...@schrodinger.com wrote:
  It would be nice if publishers required a common CSV format for
  specifying contacts and annotations. Then we could easily pull the
  data from reliable resources. But, alas, this doesn't exist.
 
  One possible (albeit incomplete) way to do this is with the SITE
  records in PDB files:
 
  http://www.wwpdb.org/procedure.html#toc_10
 
  For instance, trypsin (
 http://www.rcsb.org/pdb/files/1SGT.pdb?headerOnly=YES):
 
  SITE 1 CAT  3 HIS A  57  ASP A 102  SER A 195
  SITE 1 AC1  6 ASP A 165  ALA A 177A GLU A 180  GLU A 230
  SITE 2 AC1  6 HOH A 259  HOH A 261
 
  Obviously this still requires that the authors actually perform the
  annotation.  It's a poor substitute for having (for instance) entire
  PyMOL sessions accompanying a PDB deposition, but I've learned to keep
  my expectations low.
 
  -Nat

 --
 Thomas Holder
 MPI for Developmental Biology
 Spemannstr. 35
 D-72076 Tübingen


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Re: [PyMOL] Is there or should there be a pymol annotation server?

2012-07-14 Thread Troels Emtekær Linnet
Once again Thomas Holder have done a very nice work, and made a solution.


Check it out here:
http://www.pymolwiki.org/index.php/Select_sites


fetch 1sgt, async=0import select_sites
select_sites



It works really brilliant.

Best
Troels Emtekær Linnet



2012/7/14 Troels Emtekær Linnet tlin...@gmail.com

 Dear Pymolers.

 Thanks for all the suggestions. :-)

 I definitely think that http://jolecule.appspot.com can become handy for
 a teaching situation
 or sending a colleague a question to a protein. Thanks!

 And I am all in for interactive publications, which I hope could use one
 day.

 The Uniprot_features http://pymolwiki.org/index.php/Uniprot_features is
 probably what I am looking for.
 So I will try that out.

 Best

 Troels Emtekær Linnet



 2012/7/14 Thomas Holder spel...@users.sourceforge.net

 indeed, the SITE records could easily be parsed and made available as
 named selections.

 Similar: http://pymolwiki.org/index.php/Uniprot_features
   - makes named selections from uniprot annotations

 Cheers,
Thomas

 Nat Echols wrote, On 07/13/12 23:24:
  On Fri, Jul 13, 2012 at 2:12 PM, Jason Vertrees
  jason.vertr...@schrodinger.com wrote:
  It would be nice if publishers required a common CSV format for
  specifying contacts and annotations. Then we could easily pull the
  data from reliable resources. But, alas, this doesn't exist.
 
  One possible (albeit incomplete) way to do this is with the SITE
  records in PDB files:
 
  http://www.wwpdb.org/procedure.html#toc_10
 
  For instance, trypsin (
 http://www.rcsb.org/pdb/files/1SGT.pdb?headerOnly=YES):
 
  SITE 1 CAT  3 HIS A  57  ASP A 102  SER A 195
  SITE 1 AC1  6 ASP A 165  ALA A 177A GLU A 180  GLU A 230
  SITE 2 AC1  6 HOH A 259  HOH A 261
 
  Obviously this still requires that the authors actually perform the
  annotation.  It's a poor substitute for having (for instance) entire
  PyMOL sessions accompanying a PDB deposition, but I've learned to keep
  my expectations low.
 
  -Nat

 --
 Thomas Holder
 MPI for Developmental Biology
 Spemannstr. 35
 D-72076 Tübingen


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[PyMOL] Is there or should there be a pymol annotation server?

2012-07-13 Thread Troels Emtekær Linnet
Dear PyMolers.

Reading crystallographic papers, and feeling the
need for seing a papers annotation and explanation of important residues,
I often have pymol at my hand.

fetching the protein, and typing in commands to see the mentioned residues.
That is time-consuming, but okay.

Inspired by John Amraph's need for a preset.lig​and_cartoo​n, when
loadning
a paper, I would wish there were a: preset.as_article or a fetch 1SVN,
as_article.

Simply a pymol script file that fetch the protein, shows it as cartoon, and
selecting/labelling/showing the
mentioned important residues in the article. Or the catalytic triad, the
substrate channels... etc.
You get the point. :-)

So, does anyone know there already exist such a databank/annotation server?
If it exist, could one make a script that can fetch and convert these
annotations to a pymol script?
Or if doesnt exist, would it be a interesting project to pursue?

Best
Troels Emtekær Linnet
PhD student
SBiNLab, Copenhagen University
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Re: [PyMOL] Is there a simple way to script in pymol?

2012-06-18 Thread Troels Emtekær Linnet
How about using python blocks:


python
resis = [[1DSB,*,30,red],[1ERT,*,32,green]]
 for p,c,r,col in resis:
cmd.fetch(p,async=0)
cmd.refresh()
cmd.show(cartoon,p)   cmd.color(col,p)python end





2012/6/18 Yotam Avital yota...@gmail.com

 I may have asked this question before but I can't find the solution
 anywhere.

 I have several (30) files of the same type I want to examine. On each file
 I need to run about ten commands. Is there a way to do this automatically?

 The commands I want to run are:
 show spheres
 color (red/blue/green)
 hide
 zoom
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[PyMOL] Combine the Improved plugin manager and the Pymol-script-repo

2012-06-08 Thread Troels Emtekær Linnet
Dear PyMOL users.

Since 1/5-2012 (revision 3997) pymol has an improved plugin manager due to
Thomas Holder's effort.
I personally believe that it is a wonderful tool to extend the capabilities
of PyMOL, making it easy and fast to acquire new scripts.

Since November 2011, a group of pymol users has been involved in moving a
kind-of-large fraction of the scripts in pymolwiki under revision control
via git and hosted at

https://github.com/Pymol-**Scripts/Pymol-script-repohttps://github.com/Pymol-Scripts/Pymol-script-repo

This makes it easy to download all the scripts at one time, and also make
it possible to the authors to push changes and corrections out to the users.

*The combination of the improved plugin manager and the repository is
powerful, and I would be interested to hear if this is useful for others.*

I have tried to make an easy guide to use the combination.
 So, if you are a little experienced in pymol+python and know a little
about paths and if have a PyMOL version with the new plugin manager, then I
would be interested in any comments.

The project is described here:
http://pymolwiki.org/index.**php/Githttp://pymolwiki.org/index.php/Git
The guide is here:
http://pymolwiki.org/index.**php/Git_installhttp://pymolwiki.org/index.php/Git_install

1) Get the repository
 - One can either download a zip file of the git repository, and  unpack it.
http://pymolwiki.org/index.**php/Git_install#Manual_**download_of_scriptshttp://pymolwiki.org/index.php/Git_install#Manual_download_of_scripts
 - Or install a git repository manager, and directly pull changes from the
repository.
http://pymolwiki.org/index.**php/Git_install#Git_install_**instructionshttp://pymolwiki.org/index.php/Git_install#Git_install_instructions

2) Combine with plugin manager :

Then open PyMOL. Go to top menu: Plugin-Plugin Manager

   1. Installed plugins: Unclick apbs_tools as load on startup. (The
   Pymol-script-repo has a fine-tuned version, apbsplugin)
   2. Settings-Add new directory: Point to:
   /custom/path/Pymol-script-repo/plugins
   3. Restart PyMOL


--

If there is any script or plugin from the pymolwiki, which you think would
be good to have in the repository, don't hesitate to write me
with the suggestion, and I will put it in.
http://www.pymolwiki.org/index.php/Category:Script_Library
http://www.pymolwiki.org/index.php/Category:Plugins



Best
Troels Emtekær Linnet
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Re: [PyMOL] problem compiling latest svn on RHEL system

2012-05-18 Thread Troels Emtekær Linnet
So, i took the solution to install CentOS 6.2 on one machine.

Together with the EPEL repository, I could install all the necessary
libraries.
And then compile on CentOS.

It now works fine for all our RHEL 6.2 computers in the group.

Thanks!


2012/5/18 Jason Vertrees jason.vertr...@schrodinger.com

 Hi Troels,

 Sorry for these delayed responses. For the last two weeks, I've been
 in training our PyMOL users across the pond in Europe.

 This seems like an RHEL problem. Have you checked their lists for
 answers? libpng-devel is important enough to be used by lots of
 people.

 Cheers,

 -- Jason

 On Wed, May 16, 2012 at 12:00 PM, Troels Emtekær Linnet
 tlin...@gmail.com wrote:
  Hi.
 
  I tried to compile the latest svn -rev 3998.
 
  I think I have problem with the MyPNG.c file?
  ($HOME/pymolsvn2/svnpymol/layer0/MyPNG.c)
  It is referring to png.h which I believe is in the package: libpng-devel
 
  I have a RHEL 6.2 system.
 
  I cant find it in the RHEL repositories, epel and rpmforge.
 
  Does anyone with a RHEL system know how to get access to this package?
  When I activate the centos repo, I can find the libpng-devel, but it the
  starts to complain about dependencies and version.
 
  So, how to get centos packages, without to many dependencies problems.
 
  [tlinnet@tomat ~]$ sudo yum repolist all
  Loaded plugins: product-id, refresh-packagekit, rhnplugin, security,
  subscription-manager
  Updating certificate-based repositories.
  repo id   repo name
 
  status
  adobe-linux-i386  Adobe
 Systems
  Incorporated
 enabled:   17
  adobe-linux-x86_64Adobe
 Systems
  Incorporated
 enabled:2
  centosCentos for
  RHEL/ CentOS 6Client - x86_64
 disabled
  epel  Extra
 Packages
  for Enterprise Linux 6 - x86_64
 enabled: 7301
  epel-debuginfoExtra
 Packages
  for Enterprise Linux 6 - x86_64 - Debug
 disabled
  epel-source   Extra
 Packages
  for Enterprise Linux 6 - x86_64 - Source
disabled
  epel-testing  Extra
 Packages
  for Enterprise Linux 6 - Testing - x86_64
 disabled
  epel-testing-debuginfoExtra
 Packages
  for Enterprise Linux 6 - Testing - x86_64 - Debug
 disabled
  epel-testing-source   Extra
 Packages
  for Enterprise Linux 6 - Testing - x86_64 - Source
disabled
  google-chrome
 google-chrome
 
  enabled:3
  rhel-source   Red Hat
  Enterprise Linux 6Client - x86_64 - Source
   disabled
  rhel-source-beta  Red Hat
  Enterprise Linux 6Client Beta - x86_64 - Source
disabled
  rhel-x86_64-client-6  Red Hat
  Enterprise Linux Client (v. 6 for 64-bit x86_64)
   enabled: 5710
  rpmforge  RHEL
 6Client -
  RPMforge.net - dag
enabled: 4327
  rpmforge-extras   RHEL
 6Client -
  RPMforge.net - extras
 disabled
  rpmforge-testing  RHEL
 6Client -
  RPMforge.net - testing
disabled
  repolist: 17360
 
 
 
 
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 PyMOL Product Manager
 Schrödinger, LLC

 (e) jason.vertr...@schrodinger.com
 (o) +1 (603) 374-7120

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[PyMOL] problem compiling latest svn on RHEL system

2012-05-16 Thread Troels Emtekær Linnet
Hi.

I tried to compile the latest svn -rev 3998.

I think I have problem with the MyPNG.c file?
($HOME/pymolsvn2/svnpymol/layer0/MyPNG.c)
It is referring to *png.h* which I believe is in the package: *libpng-devel*

I have a RHEL 6.2 system.

I cant find it in the RHEL repositories, epel and rpmforge.

Does anyone with a RHEL system know how to get access to this package?
When I activate the centos repo, I can find the libpng-devel, but it the
starts to complain about dependencies and version.

So, how to get centos packages, without to many dependencies problems.

[tlinnet@tomat ~]$ sudo yum repolist all
Loaded plugins: product-id, refresh-packagekit, rhnplugin, security,
subscription-manager
Updating certificate-based repositories.
repo id   repo name

status
adobe-linux-i386  Adobe Systems
Incorporated
 enabled:   17
adobe-linux-x86_64Adobe Systems
Incorporated
 enabled:2
centosCentos for
RHEL/ CentOS 6Client - x86_64
   disabled
epel  Extra
Packages for Enterprise Linux 6 - x86_64
 enabled: 7301
epel-debuginfoExtra
Packages for Enterprise Linux 6 - x86_64 - Debug
 disabled
epel-source   Extra
Packages for Enterprise Linux 6 - x86_64 - Source
disabled
epel-testing  Extra
Packages for Enterprise Linux 6 - Testing - x86_64
 disabled
epel-testing-debuginfoExtra
Packages for Enterprise Linux 6 - Testing - x86_64 - Debug
 disabled
epel-testing-source   Extra
Packages for Enterprise Linux 6 - Testing - x86_64 - Source
disabled
google-chrome google-chrome

enabled:3
rhel-source   Red Hat
Enterprise Linux 6Client - x86_64 - Source
   disabled
rhel-source-beta  Red Hat
Enterprise Linux 6Client Beta - x86_64 - Source
  disabled
rhel-x86_64-client-6  Red Hat
Enterprise Linux Client (v. 6 for 64-bit x86_64)
   enabled: 5710
rpmforge  RHEL 6Client
- RPMforge.net - dag
  enabled: 4327
rpmforge-extras   RHEL 6Client
- RPMforge.net - extras
 disabled
rpmforge-testing  RHEL 6Client
- RPMforge.net - testing
  disabled
repolist: 17360
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Re: [PyMOL] My first script?

2012-05-09 Thread Troels Emtekær Linnet
If you have some name scheme for your molecules, you could figure it out
from this:

You want to make a python block:

python
 do python code here
python end


Then define a loop, and figure out to call your naming scheme.
Do a calculation, and add the result to an array or something.


reinitializeimport propkacmd.bg_color(white)cmd.set(auto_zoom,off)

results = []
python
resis = [[1DSB,*,30],[1ERT,*,32]]
 for p,c,r in resis:
cmd.fetch(p,async=0)
cmd.refresh()
pkavalues = 
propka.propka(molecule=p,chain=c,resi=r,logtime=,makebonds=no)
results.append(pkavalues)
cmd.refresh()
python end





2012/5/9 Joel Tyndall joel.tynd...@otago.ac.nz

  Hi folks,

 ** **

 So I have no scripting skills in python but I can use pymol reasonably
 well. 

 ** **

 I want to superimpose (pair_fit) 4 atoms (all the same) from a library of
 conformers onto a template molecule (similar to clustering after
 conformational searching). I could probably nut out how to do the
 pairfitting actually I could do this easily by command line but I have 
 100 molecules so I’m not sure how to script this.

 ** **

 Any help would be welcome

 ** **

 Cheers


 Joel

 ** **

 _

 Joel Tyndall, PhD

 Senior Lecturer in Medicinal Chemistry
 National School of Pharmacy
 University of Otago
 PO Box 56 Dunedin 9054
 New Zealand   

 Skype: jtyndall

 ** **

 Ph: +64 3 479 7293

 ** **


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Re: [PyMOL] hide tube / show only filled nucleic acid rings

2012-04-03 Thread Troels Emtekær Linnet
Have you tried this:

http://www.pymolwiki.org/index.php/Examples_of_nucleic_acid_cartoons

Best
Troels Emtekær Linnet

2012/4/2 Francis E Reyes francis.re...@colorado.edu


 Tricky one I tried hide cartoon, name P but no go..

 instead cartoon skip will do it.



 On Apr 2, 2012, at 2:50 PM, Eike Schulz wrote:

  Hello everybody,
 
  I am looking for a way to display nucleic acids in cartoon mode but
  without showing the backbone trace. Unfortunately set
  cartoon_tube_radius=0 leaves a thin line behind.
 
  Thanks a lot in advance
 
Best
 
Eike
 
 
 
 
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Re: [PyMOL] GUI to improve interaction between user and PyMOL

2012-03-23 Thread Troels Emtekær Linnet
Sorry for being rude, it was not meant in that way.

I was just puzzled by the fact, that you would be graded higher if you
don't use the command line.
That is just weird.

Back to the question.
Suhaila, you should try to explore the action button.

First get a protein, which is good to illustrate.
Go to the menu: Plugin-PDB Loader Service. Enter: 1hpu
(Or write in command: fetch 1hpu )  :-)

Then go to the A (Action) button in the right menu.
Press: preset - ligand sites - cartoon

Try some of the presets. They are very good!

If you want to find some polar contacts.
Select your residue by clicking it:
Action - find - polar contacts - Then something from the menu

I hope that helps!

Best
Troels

2012/3/23 Suhaila Haji Mohd Hussin bell_beaut...@hotmail.com

  OK. It does sound pretty weird prolly because the way I asked isn't
 precise.

 We plot predicted contacts that can be viewed in various ways. So it'd be
 better to create a GUI select menu or something like that for user's ease
 of interacting with our project.

 Suhaila.

 --
 From: tlin...@gmail.com
 Date: Thu, 22 Mar 2012 22:14:39 +0100
 CC: pymol-users@lists.sourceforge.net
 Subject: Re: [PyMOL] GUI to improve interaction between user and PyMOL


 That is seriously the strangest thing I ever heard about...

 The GUI is for the small fast thing to do.
 Why just don't press all button and see?
 It can only take a little time.

 Or google: pymol + name of button
 That should give you an answer...

 The command line is where the power is.
 Use that.

 /Troels



 2012/3/22 Suhaila Haji Mohd Hussin bell_beaut...@hotmail.com

  Hello everyone.

 Is there any useful online reference that can be shared for me to learn
 how to add GUI executed by Python script?

 I know PyMOL can visualize the protein just by typing in on PyMOL command
 but my supervisor will  grade my group project higher if we can make it
 more interactive where the user can just use a mouse to click button or
 something and less typing on command.

 Best regards,
 *Suhaila*


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Re: [PyMOL] pymol 1.4.1 (incentive), segfault upon help-about

2012-02-27 Thread Troels Emtekær Linnet
Try install tkinter

Tkinter uses tcl 8.4 (something...)



Troels Emtekær Linnet
Lyongade 24. 4.mf, 2300 København S
Mobil: +45 60210234



2012/2/27 greipel.joac...@mh-hannover.de

 Hi Jason,

 I just installed pymol 1.5.0.3 on our linux machines and the segfault in
 libtcl8.5.so upon help-about is still present. Do you have any hint when
 this will be fixed?

 Best regards,
 Joachim
 --
 Dr. rer. nat. Joachim Greipel
 Med. Hochschule Hannover
 Biophys. Chem. OE 4350
 Carl-Neuberg-Str. 1
 30625 Hannover
 Germany

 Fon: +49-511-532-3718
 Fax: +49-511-532-16-3718



  -Ursprüngliche Nachricht-
  Von: Jason Vertrees [mailto:jason.vertr...@schrodinger.com]
  Gesendet: Donnerstag, 19. Mai 2011 17:53
  An: Greipel, Joachim Dr.
  Cc: pymol-users@lists.sourceforge.net; h...@schrodinger.com
  Betreff: Re: [PyMOL] pymol 1.4.1 (incentive), segfault upon
  help-about
 
  Hi Joachim,
 
   I always get a segmentation fault, when I click
  help-about to see the
   version details of pymol. The respective entry in
  /var/log/messages is:
  
   pymol.exe[4991]: segfault at 3e0019b ip f74857a0 sp
  f3bab9a8
   error 4 in libtcl8.5.so[f741+ed0
   00]
 
  Indeed on a few Linux distros, there is a crash when selecting Help 
  About.  We're trying to track down the cause.  The error happens in
  our pure Python code and the segfault happens in the libtcl8.5 shared
  library.
 
  If you're checking for the PyMOL version number, please use
  get_version in the meantime.
 
  Cheers,
 
  -- Jason
 
  --
  Jason Vertrees, PhD
  PyMOL Product Manager
  Schrodinger, LLC
 
  (e) jason.vertr...@schrodinger.com
  (o) +1 (603) 374-7120
 


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[PyMOL] Running pymol over SSH and setting LIBGL_ALWAYS_INDIRECT

2012-02-26 Thread Troels Emtekær Linnet
Hi pymolers.

I was trying to test our lab pymol installation from home.
But i ran into an error in freeglut, when executing over SSH.
I have found a solution, but is unsure what it does, and if means something
for
speed and 3D rendering.

*When I ran:*
*[software@elvis ~]$ pymol*
*freeglut (pymol):  ERROR:  Internal error FBConfig with necessary
capabilities not found in function fgOpenWindow*
*X Error of failed request:  BadWindow (invalid Window parameter)*
*  Major opcode of failed request:  4 (X_DestroyWindow)*
*  Resource id in failed request:  0x0*
*  Serial number of failed request:  33*
*  Current serial number in output stream:  36*
* PyMOL: abrupt program termination.*

I found a solution here:
http://superuser.com/questions/203587/remotely-connecting-to-ubuntu-server-from-a-macbook-cant-run-pymol
http://unix.stackexchange.com/questions/1437/what-does-libgl-always-indirect-1-actually-do
http://ubuntuforums.org/showthread.php?t=1682020

*I then changed the pymol exexution script.*
*
*
*[software@elvis ~/pymolsvn]$ ls*
*modules  pymol  pymolMPEG.sh  pymolplugins  Pymol-script-repo
 pymolsvn.desktop  svnfreemol  svnpymol  updatepymol.sh*
*[software@elvis ~/pymolsvn]$ cat pymolMPEG.sh *
*#!/bin/bash*
*if [ ! -f $HOME/.local/share/applications/pymolsvn.desktop ];*
*then*
*ln -s /sbinlab2/software/pymolsvn/pymolsvn.desktop
$HOME/.local/share/applications/pymolsvn.desktop*
*fi*
*
*
*export FREEMOL=/sbinlab2/software/pymolsvn/svnfreemol/freemol*
*export PYMOL_GIT_MOD=/sbinlab2/software/pymolsvn/Pymol-script-repo/modules*
*export
PYTHONPATH=$PYTHONPATH:/sbinlab2/software/x64/lib64/python2.6/site-packages/PIL
*
*export
PYTHONPATH=$PYTHONPATH:/sbinlab2/software/x64/lib64/python2.6/site-packages/lib-tk
*
*export
PYTHONPATH=$PYTHONPATH:/sbinlab2/software/x64/lib64/python2.6/site-packages/lib-dynload
*
*export PYTHONPATH=/sbinlab2/software/pymolsvn:$PYTHONPATH*
*export
PYTHONPATH=/sbinlab2/software/pymolsvn/Pymol-script-repo/modules:$PYTHONPATH
*
*export PYTHONPATH=/sbinlab2/software/pymolsvn/Pymol-script-repo:$PYTHONPATH
*
*export PYMOL_PATH=/sbinlab2/software/pymolsvn/modules/pymol/pymol_path*
*export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/sbinlab2/software/x64/lib/pymollib
*
*export LIBGL_ALWAYS_INDIRECT=no*
*
*
*/usr/bin/python /sbinlab2/software/pymolsvn/modules/pymol/__init__.py $@*


It now works fine when running pymol.
And it also works when i set: *export LIBGL_ALWAYS_INDIRECT=yes*
*
*
But what is the fastest solution, so pymol can use Direct rendering?
Locally, when sitting at the computer and over SSH.

Best
Troels
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Re: [PyMOL] Isstall on CentOS 6

2012-02-24 Thread Troels Emtekær Linnet
You can see the requirements here:

http://www.pymolwiki.org/index.php/Linux_Install#Red_Hat_Enterprise_Linux_RHEL_6_compile_and_install_with_MPEG_support_for_x86_64_bit

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2012/2/24 Andreas Förster docandr...@gmail.com

 Hi Yuri,

 I'd say yes.  It runs under RHEL 6.2.  In contrast to what was
 officially said, there is no requirement for python 2.7.  Version 2.6.6
 works fine.


 Andreas



 On 24/02/2012 4:12, Yuri wrote:
  Hello everyone,
  Does the latest free Pymolv1.5.0.1 from sourceforge run on CentOS 6?
  Thanks

 --
  Andreas Förster, Research Associate
 Paul Freemont  Xiaodong Zhang Labs
 Department of Biochemistry, Imperial College London
 http://www.msf.bio.ic.ac.uk


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Re: [PyMOL] compiling Open Source PyMOL v1.5.0.1

2012-02-15 Thread Troels Emtekær Linnet
Hi Thomas.

I succeded with the last version of Pymol 1.4.x compilation, and have
written it here.
http://www.pymolwiki.org/index.php/Linux_Install#Red_Hat_Enterprise_Linux_RHEL_6_compile_and_install_with_MPEG_support_for_x86_64_bit

sudo yum install subversion gitsudo yum install python-imaging pygame
apbssudo yum install gcc-c++ python-devel python-pmw glew-devel
freeglut-devel libpng-devel freetype-devel


It was for RHEL 6, and so it should be the same for centos.

I have not yet tried for 1.5, since Jason said that it need python 2.7, and
our system comes with
python 2.6.6

Best
Troels

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Lyongade 24. 4.mf, 2300 København S
Mobil: +45 60210234



2012/2/14 Thomas Stout tst...@exelixis.com

  Hi All -

 I am trying to compile the open-source code for PyMOL for the first time
 (on CentOS) and running into all sorts of issues.  Is there a listing
 somewhere of *all* the dependencies (and their versions) that I could use
 as a guide to get everything I need all at once, rather than continuing to
 fix compile failures one-at-a-time (which is confusing and frustrating)

 Conversely, is there a distro that more-or-less just works?  I can
 create a virtual machine in which I compile, but I'm only allowed to have
 RHEL or CentOS on my physical machine...

 Thanks!
 -Tom



 --
 *From:* Jason Vertrees [mailto:jason.vertr...@schrodinger.com]
 *Sent:* Mon 2/13/2012 11:27 AM
 *To:* pymol-users@lists.sourceforge.net
 *Subject:* [PyMOL] Open Source PyMOL v1.5.0.1

  Greetings,

 It is my pleasure to announce the release of open source PyMOL
 v1.5.0.1. The source code has been committed to the open-source
 repository. It is revision 3976. An svn tag and downloadable bz2
 source file were also created. All of this is accessible form the
 PyMOL project page on SourceForge
 (http://sourceforge.net/projects/pymol/).

 Before upgrading PyMOL -- please -- upgrade your video drivers! NVidia
 and AMD/ATI cards are known to work well. But, Intel Mobile and other
 low-end cards might have issues with the new rendering. The majority
 of rendering anomalies are fixed by simply upgrading your video
 drivers.

 You should be able to pull and build just like normal. You will need
 Python 2.7.

 Some simple testing on my Linux machine shows the following
 improvements in real-time rendering performance for a large protein
 (58,000 atom Gro-EL, PDB 1AON) with the new open-source PyMOL code:

 Lines:
240% increase (81 FPS to 270 FPS)
 Spheres:
864% increase (28 FPS to 270 FPS)
 Sticks:
2100% increase (8 FPS to 180 FPS)
 Cartoon:
3757% increase (27 to 270 FPS)
 Surface:
2600% increase (10 to 270 FPS)
 Mesh:
33% (180 FPS to 270 FPS)

 Your numbers will be different. This Linux machine has a powerful card
 used for development
 (
 http://www.amd.com/us/products/workstation/graphics/ati-firepro-3d/v8800/Pages/v8800.aspx
 ).
 It was generously donated by AMD. If you use an AMD/ATI card and PyMOL
 works for you it's because AMD/ATI helped out. You may want to thank
 them. What I've seen is that the more powerful your card the greater
 the _difference_ in speed. That is, low-end cards should see
 improvements in the range of tens to hundreds of percent while more
 powerful cards should register improvements like mine, in the
 thousands of percent for some representations.

 To quickly test performance of the new code on your machine just load
 a large structure (eg. 1AON; 3R8O and 3R8T) and quickly
 rotate/translate it. To see the refresh rate, type set
 show_frame_rate. The refresh rate shows up in the lower right hand
 corner. Compare the frame rate, smoothness, and rendering quality when
 the setting use_shaders is turned off and when it's turned on.
 Compare different representations, each time turning on and off the
 use_shaders setting.

 You can quickly update old PyMOL session files to the new rendering by
 clicking, Settings  Rendering  Modernize after loading the old
 session file. PyMOL will flip all the right settings to update
 rendering. If the new code doesn't render properly, you can revert to
 the old style rendering by typing:

  set use_shaders, 0

  set sphere_mode, 0


 Please let us know how it goes.

 Cheers,

 -- Jason, Blaine  the PyMOL Team

 --
 Jason Vertrees, PhD
 PyMOL Product Manager
 Schrödinger, LLC

 (e) jason.vertr...@schrodinger.com
 (o) +1 (603) 374-7120


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Re: [PyMOL] PyMOL-users Digest, Vol 69, Issue 12

2012-02-15 Thread Troels Emtekær Linnet
If you need publication citation, I would go for the
Cealign   ww.pymolwiki.org/index.php/Cealign

There is references you can read and understand. :-)

See a list of alignment methods and tools
http://www.pymolwiki.org/index.php/Align#SEE_ALSO


Best
T


Troels Emtekær Linnet
Lyongade 24. 4.mf, 2300 København S
Mobil: +45 60210234



2012/2/15 Bachar Cheaib cheaib.bac...@gmail.com

 Dear All,

 I am a Pymol's user

 I would like to know how could I find the algorithm publication of three
 functions for superimposition of multi-structures?

 1- fit
 2- align
 3- super

 I would thanks in advance for your reply

 Sincerely



 BaCh

 On Wed, Feb 15, 2012 at 11:31 AM, 
 pymol-users-requ...@lists.sourceforge.net wrote:

 Send PyMOL-users mailing list submissions to
pymol-users@lists.sourceforge.net

 To subscribe or unsubscribe via the World Wide Web, visit
https://lists.sourceforge.net/lists/listinfo/pymol-users
 or, via email, send a message with subject or body 'help' to
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 You can reach the person managing the list at
pymol-users-ow...@lists.sourceforge.net

 When replying, please edit your Subject line so it is more specific
 than Re: Contents of PyMOL-users digest...


 Today's Topics:

   1. Re: Open Source PyMOL v1.5.0.1 (David Hall)
   2. Re: solid objects (Jason Vertrees)
   3. compiling Open Source PyMOL v1.5.0.1 (Thomas Stout)
   4. 1.5 version runs slow with large objects (Vitali Stanevich)
   5. Re: Open Source PyMOL v1.5.0.1 (?? ??)


 --

 Message: 1
 Date: Tue, 14 Feb 2012 12:03:33 -0500
 From: David Hall li...@cowsandmilk.net
 Subject: Re: [PyMOL] Open Source PyMOL v1.5.0.1
 To: Jason Vertrees jason.vertr...@schrodinger.com
 Cc: pymol-users@lists.sourceforge.net
 Message-ID:

 capuwn_9wwuwpcaa6htud3vsmbxmwguynqnj-kzdwowdt7b_...@mail.gmail.com
 Content-Type: text/plain; charset=ISO-8859-1

 On Mon, Feb 13, 2012 at 2:27 PM, Jason Vertrees
 jason.vertr...@schrodinger.com wrote:
  Greetings,
 
  It is my pleasure to announce the release of open source PyMOL
  v1.5.0.1. The source code has been committed to the open-source
  repository. It is revision 3976. An svn tag and downloadable bz2
  source file were also created. All of this is accessible form the
  PyMOL project page on SourceForge
  (http://sourceforge.net/projects/pymol/).

 For those of you on openSUSE, I've updated the pymol packages in the
 openSUSE Build Service to this release. You can test this new version
 by visiting
 http://software.opensuse.org/download.html?project=devel:languages:pythonpackage=pymol
 and choosing the appropriate openSUSE release and architecture.

 -David



 --

 Message: 2
 Date: Tue, 14 Feb 2012 12:40:02 -0500
 From: Jason Vertrees jason.vertr...@schrodinger.com
 Subject: Re: [PyMOL] solid objects
 To: Daniel Larsson lars...@xray.bmc.uu.se
 Cc: pymol-users@lists.sourceforge.net
 Message-ID:

 caax+4zfqqdafwyiqmmdm3hkuiyrtvhoin70bc5eof4hbeae...@mail.gmail.com
 Content-Type: text/plain; charset=ISO-8859-1

 Daniel,

 Filling clipped spheres is not yet available. We'll look at adding it.

 Cheers,

 -- Jason

 On Tue, Feb 14, 2012 at 12:00 PM, Daniel Larsson lars...@xray.bmc.uu.se
 wrote:
  Thanks for the quick reply.
 
  A closely related issue is that clipped spheres are rendered very
 strangely. It seems they only consists of a half-sphere and if the clipping
 plane intersects the sphere in the front-most half, then you can see
 straight through it.
 
  Daniel
 
 
  On Feb 14, 2012, at 17:50 , Jason Vertrees wrote:
 
  Daniel,
 
  # reset the setting
 
  set ray_interior_color, default
 
  # set the setting for each object
 
  set ray_interior_color, marine, protA
 
  set ray_interior_color, magenta, protB
 
 
  PyMOL does not support this via the 'draw' command (unless you set
  draw_mode, 3, but that's just ray tracing). Please file an RFE and
  we'll look into it.
 
  Cheers,
 
  -- Jason
 
  On Tue, Feb 14, 2012 at 11:17 AM, Daniel Larsson 
 lars...@xray.bmc.uu.se wrote:
  Hi,
 
  Is there a way to render truncated/clipped objects as dense. I.e. a
 lid on clipped objects, such as surfaces or spheres.
 
  Want I want is something similar to the A sliced image example in
 the wiki gallery (http://www.pymolwiki.org/index.php/Gallery), but with
 that technique I can only pick one color for all molecules. I would like to
 set ray_interior_color different for different molecules or objects.
 Basically, I want the color to be the same on the inside as on the outside.
 It would be great if it would work with the draw command as well.
 
  Is it possible with version 1.5? Or is there a chances of having this
 implemented anytime soon?
 
  Daniel
 
 
 
 --
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  The most comprehensive online

Re: [PyMOL] Open Source PyMOL v1.5.0.1

2012-02-15 Thread Troels Emtekær Linnet
Hi.

I can confirm that you can compile pymol 1.5.0.1 on RHEL 6, with python
2.6.6 from the RHEL repositories.
http://www.pymolwiki.org/index.php/Linux_Install#Red_Hat_Enterprise_Linux_RHEL_6_compile_and_install_with_MPEG_support_for_x86_64_bit

Still splash screen 1.3.x  ... Funny bug.

Best
Troels
--
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Re: [PyMOL] Open Source PyMOL v1.5.0.1

2012-02-13 Thread Troels Emtekær Linnet
Thanks!

It worked. :-)

Troels Emtekær Linnet


2012/2/13 Justin Lecher j.lec...@fz-juelich.de

 On 13.02.2012 20:27, Jason Vertrees wrote:
  Greetings,
 
  It is my pleasure to announce the release of open source PyMOL
  v1.5.0.1. The source code has been committed to the open-source
  repository. It is revision 3976. An svn tag and downloadable bz2
  source file were also created. All of this is accessible form the
  PyMOL project page on SourceForge
  (http://sourceforge.net/projects/pymol/).
 
  Before upgrading PyMOL -- please -- upgrade your video drivers! NVidia
  and AMD/ATI cards are known to work well. But, Intel Mobile and other
  low-end cards might have issues with the new rendering. The majority
  of rendering anomalies are fixed by simply upgrading your video
  drivers.
 
  You should be able to pull and build just like normal. You will need
 Python 2.7.
 
  Some simple testing on my Linux machine shows the following
  improvements in real-time rendering performance for a large protein
  (58,000 atom Gro-EL, PDB 1AON) with the new open-source PyMOL code:
 
  Lines:
 240% increase (81 FPS to 270 FPS)
  Spheres:
 864% increase (28 FPS to 270 FPS)
  Sticks:
 2100% increase (8 FPS to 180 FPS)
  Cartoon:
 3757% increase (27 to 270 FPS)
  Surface:
 2600% increase (10 to 270 FPS)
  Mesh:
 33% (180 FPS to 270 FPS)
 
  Your numbers will be different. This Linux machine has a powerful card
  used for development
  (
 http://www.amd.com/us/products/workstation/graphics/ati-firepro-3d/v8800/Pages/v8800.aspx
 ).
  It was generously donated by AMD. If you use an AMD/ATI card and PyMOL
  works for you it's because AMD/ATI helped out. You may want to thank
  them. What I've seen is that the more powerful your card the greater
  the _difference_ in speed. That is, low-end cards should see
  improvements in the range of tens to hundreds of percent while more
  powerful cards should register improvements like mine, in the
  thousands of percent for some representations.
 
  To quickly test performance of the new code on your machine just load
  a large structure (eg. 1AON; 3R8O and 3R8T) and quickly
  rotate/translate it. To see the refresh rate, type set
  show_frame_rate. The refresh rate shows up in the lower right hand
  corner. Compare the frame rate, smoothness, and rendering quality when
  the setting use_shaders is turned off and when it's turned on.
  Compare different representations, each time turning on and off the
  use_shaders setting.
 
  You can quickly update old PyMOL session files to the new rendering by
  clicking, Settings  Rendering  Modernize after loading the old
  session file. PyMOL will flip all the right settings to update
  rendering. If the new code doesn't render properly, you can revert to
  the old style rendering by typing:
 
   set use_shaders, 0
 
   set sphere_mode, 0
 
 
  Please let us know how it goes.
 
  Cheers,
 
  -- Jason, Blaine  the PyMOL Team
 


 Hi Jason,

 thanks for the work.

 I cannot compile the molfile support:

 x86_64-pc-linux-gnu-gcc -pthread -Ofast -pipe -ftracer -march=corei7-avx
 -mtune=corei7-avx -mcx16 -msahf -mno-movbe -maes -mpclmul -mpopcnt
 -mno-abm -mno-lwp -mno-fma -mno-fma4 -mno-xop -mno-bmi -mno-tbm -mavx
 -msse4.2 -msse4.1 --param l1-cache-size=32 --param l1-cache-line-size=64
 --param l2-cache-size=8192 -frecord-gcc-switches -g -funroll-loops
 -Wimplicit-function-declaration -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE
 -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS
 -D_PYMOL_VMD_PLUGINS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS
 -D_CGO_DRAWARRAYS -D_PYMOL_GL_CALLLISTS -DOPENGL_ES_2 -Iov/src -Ilayer0
 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2
 -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src
 -Imodules/cealign/src -Imodules/cealign/src/tnt -Igenerated/include
 -Igenerated/src -I/usr/include/python2.7 -c
 contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c -o

 build-2.7/temp.linux-x86_64-2.7/contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.o
 contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c: In function
 ‘read_basis_metadata’:
 contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:208:11: error:
 ‘molfile_qm_metadata_t’ has no member named ‘have_esp’
 contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:209:11: error:
 ‘molfile_qm_metadata_t’ has no member named ‘have_npa’
 contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:211:11: error:
 ‘molfile_qm_metadata_t’ has no member named ‘have_internals’
 error: command 'x86_64-pc-linux-gnu-gcc' failed with exit status 1


 Thanks,

 justin



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[PyMOL] One liner for getting amino acid sequence from pdb file

2012-02-08 Thread Troels Emtekær Linnet
Hi.

I have a pdb file, which is a modelled structure from another sequence.

I want to check the amino acid sequence in the structure.
Does anyone know a one-liner in pymol which will extract the sequence
in one-letter code?

best
Troels
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Re: [PyMOL] One liner for getting amino acid sequence from pdb file

2012-02-08 Thread Troels Emtekær Linnet
Thanks!

I put it on the wiki:
http://pymolwiki.org/index.php/Get_fastastr

Cheers


2012/2/8 Thomas Holder spel...@users.sourceforge.net

 print cmd.get_fastastr('all')

 Cheers,
  Thomas


 On 02/08/2012 03:24 PM, Troels Emtekær Linnet wrote:

 Hi.

 I have a pdb file, which is a modelled structure from another sequence.

 I want to check the amino acid sequence in the structure.
 Does anyone know a one-liner in pymol which will extract the sequence
 in one-letter code?

 best
 Troels


 --
 Thomas Holder
 MPI for Developmental Biology
 Spemannstr. 35
 D-72076 Tübingen

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[PyMOL] Change default read position of .pymolrc and .pymolrc.py

2012-02-08 Thread Troels Emtekær Linnet
Hi.

We have builded svn pymol at our unilabs linux computers.

Is there a way to tell pymol it should look for .pymolrc and .pymolrc.py
other places than the users home library?

Or can you run the commands in these files in another way?

Best
Troels
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Re: [PyMOL] Display electrostatic potential at different pH

2012-02-04 Thread Troels Emtekær Linnet
How about using the APBS plugin?
http://www.poissonboltzmann.org/apbs/examples/visualization/apbs-electrostatics-in-pymol

The plugin that is shipped with Pymol as standard
http://www.pymolwiki.org/index.php/APBS

The same plugin, but in the
Pymol-script-repohttp://www.pymolwiki.org/index.php/Git_intro
.
Here the plugin is setup to find the included (psize.py) and (pdb2pqr.py)
http://www.pymolwiki.org/index.php/Apbsplugin

And calculate the PQR at different pH?
http://www.poissonboltzmann.org/pdb2pqr/user-guide/using-pdb2pqr
Server
http://kryptonite.nbcr.net/pdb2pqr/

In the Main tab, in the APBS pymol plugin.
Select: Choose Externally generated PQR.

Or use this:


python pdb2pqr.py --ff=AMBER --with-ph=5


As far as I know, pdb2pqr, uses PROPKA 1.0 to get the pKa.
There has been a large development to PROPKA since then.
Version 3.1 is available at homepage: http://propka.ki.ku.dk/

If you want to visualize the pKa, try this Pymol script.
http://www.pymolwiki.org/index.php/Propka


Troels Emtekær Linnet
Lyongade 24. 4.mf, 2300 København S
Mobil: +45 60210234



2012/2/3 Xiaoshan Min xs...@yahoo.com

 Hi Pymoler,

 I want to present a structure to non-structural biologist. They want to
 visualize the change of surface charge at different pH.  For example,
 Histidine will have different protonation state at pH 7.5 and 5.  What
 would be the best way to visualize this?  I know an accurate calculation
 probably is too hard, but would like to know if there is a clever way of
 approximation.

 Thanks a lot.

 Xiaoshan



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[PyMOL] Open .pdb / .pml files in ubuntu/mint

2012-01-29 Thread Troels Emtekær Linnet
Hi guys.

Ehh. I have a newly installed Mint 12 box with gnome 3.

I have that annoying thing, that when I click a text .pdb files, it opens
with gedit.
Then I can right click and select .pdb files to open with pymol.
But when I then click a .txt file, it opens it with pymol.

Grrr...
I know its something with mimetypes, and I got it to work on my mint 11.
But now I am a little lost, and can't find it on the web...

So, anyone did this?

Best
Troels
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[PyMOL] Access to pymolwiki

2012-01-26 Thread Troels Emtekær Linnet
I am not able to reach the site?

Is it down?

Troels Emtekær Linnet
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Re: [PyMOL] Access to pymolwiki

2012-01-26 Thread Troels Emtekær Linnet
No. :-)

Works as a charm now.

It was a temporary thing for 10 minutes.
Maybe my internet solution from the uni was a little strange.

/T



2012/1/27 Jason Vertrees jason.vertr...@schrodinger.com

 Hi Troels,

 I can get to it. Still having problems?

 Cheers,

 -- Jason

 2012/1/26 Troels Emtekær Linnet tlin...@gmail.com:
  I am not able to reach the site?
 
  Is it down?
 
  Troels Emtekær Linnet
 
 
 
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 --
 Jason Vertrees, PhD
 PyMOL Product Manager
 Schrodinger, LLC

 (e) jason.vertr...@schrodinger.com
 (o) +1 (603) 374-7120

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Re: [PyMOL] Problems with FindSeq.py script

2012-01-16 Thread Troels Emtekær Linnet
Dear James.

That is because there are different ways, how to get functions available in
Python.
Either you can import a script.py or you can execute it.

If you execute the script.
In Python, you would do: *execfile(script.py)*
In PyMOL, a shortcut to this is: *run script.py OR execfile(script.py)*

Then the functions in the script file will be directly available with the
function names.
functionname(inp1=A, inp2=B)

If you import the script in Python/Pymol, it will be handled as a module.
*import script*
That means, that you have access to functions like this
script.functionname(inp1=A, inp2=B)

For small scripts, the name of the functions in the file is probably
similar to the filename of the script.
Thats why, you would see:
findseq.findseq(inp1=A, inp2=B)

Then comes the export feature in PyMOL. The line:
cmd.extend(findseq, findseq )

That means, that PyMOL extends the function name findseq to be directly
accessible in pymol.
So the functions can be access directly. But you have still both options.

import findseq
findseq.findseq(inp1=A, inp2=B)
findseq inp1=A, inp2=B

Notice, that the extend make it possible to call the function directly, and
making input with spaces.
This is a little more human readable.

But a problem occurs, if you want to parse a variable to the extended
method.
Say you write.

import propka
fetch 4ins, async=0
proteinname=4ins   (Your variable)
propka proteinname  (will not work)
propka 4ins(will work)
propka.propka(proteinname)  (will work)

I hope this clarify a little.

Read more about namespaces here:
http://www.pymolwiki.org/index.php/Running_Scripts
http://docs.python.org/tutorial/modules.html

Best
Troels


2012/1/16 James Starlight jmsstarli...@gmail.com

 Troels,


 Commonly I run pymol scripts by means of

 run script.py

 or

 @ script.py

 from PyMol shell!

 then I use script_command ( e.g findSeq ) and further script syntax for my
 tasks

 e.g findSeq s.g 1f88

 works perfect but
 the above command for the ensemmble of pdbs give me error.

 James


 2012/1/16 Troels Emtekær Linnet tlin...@gmail.com

 It depends on, if you run or import the script. The namespace will be
 different.

 What do you do?

 This is no error. This is basic Python knowledge.

 Troels Emtekær Linnet
 Slotsvej 2
 4300 Holbæk
 Mobil: +45 60210234



 2012/1/16 James Starlight jmsstarli...@gmail.com

 Hi Troels!

 I've tried to use

 for x in cmd.get_names(): findSeq.findSeq(QTG, x, sele_+x, firstOnly=1)





 but I obtained error

 NameError: name 'findSeq' is not defined

 At the same time just

 findSeq QTG, 3sn6

 wokrs perfect

 2012/1/14 Troels Emtekær Linnet tlin...@gmail.com

 Hi James.

 I moved the script under the git repository yesterday, and took care of
 the bug.
 The script look a little different now.

 So try the new one again from:
 http://www.pymolwiki.org/index.php/findseqhttp://www.pymolwiki.org/index.php/Findseq

 The follow the guide on the page.

 # Find the regular expression:#  ..H[TA]LVWH# in the few proteins loaded.# 
 I then showed them as sticks and colored them to highlight matched AAsfor 
 x in cmd.get_names(): findseq.findseq(..H[TA]LVWH, x, sele_+x, 
 firstOnly=1)



 2012/1/14 James Starlight jmsstarli...@gmail.com

 Jason, hello!

 Also I've found possible fix for that bug by lpacing this line in the
 47 line of the script

 if type(selName)!=(types.StringType) and
 type(selName)!=(types.NoneType):


 By the way I've found another bug when I've tried to find the same
 motifs in the several homolugues structures.

 E.g I have 5 structures wich all have motiv S.G where . is the random
 amino acid. When I've tried

 findseq S.G, all

 the script find that motifs only for last fetched structure. How I could 
 solve it?








 Thanks again,

 James



 2012/1/13 Jason Vertrees jason.vertr...@schrodinger.com

 James,

 First, there's a bug in the script. It's not dealing with selName
 correctly. To get around this just provide something to selName:

 findSeq S.G, 1a3h, selName=found_seq

 If findSeq finds the sequence, it'll return the selected atoms in
 found_seq.


 Next, SYG is not in that protein. If you search for S.G you find
 SNG. You can double check this by:

 fStr = cmd.get_fastastr(1a3h)

 print SYG in fStr

 which return false.

 Cheers,

 -- Jason


 On Fri, Jan 13, 2012 at 1:25 PM, James Starlight 
 jmsstarli...@gmail.com wrote:
  Dear PyMol Users,
 
  I need to search defined sequence motifs in my structures.
 
  For that purpose I've used
 
  http://www.pymolwiki.org/index.php/FindSeq script
 
  but when I've try to use it I've got error
 
  PyMOLfindSeq SYG, 1a3h
  Error: selName was not a string.
  There was an error with a parameter.  Please see
  the above error message for how to fix it.
 
  What I've done wrong? The seqyence Ser Tyr Gly is indeed present in
 my
  structure!
 
  By the way is there any others way to search for pre-defined
 sequence motifs
  via PyMol?
 
  Thanks for help,
 
  James

Re: [PyMOL] Scene exporter for Web

2012-01-16 Thread Troels Emtekær Linnet
That looks very interesting.

I needed to make my shortcut to chrome look like this:
/opt/google/chrome/google-chrome --enable-webgl %U

Your example page is extremely fast, and the View mode change
is working perfectly and fast.

This is the first version of PyMOL-to-webpage i have seen, which looks very
easy.
I normally have only seen Jmol application for this:
http://www.proteopedia.org/wiki/index.php/4ins

God work!


Troels Emtekær Linnet
Slotsvej 2
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Mobil: +45 60210234



2012/1/16 Takanori Nakane t.nak...@mail.mfour.med.kyoto-u.ac.jp

 Dear Pymol users,

 I wrote a Pymol script to export a scene in Pymol to GLmol,
 a molecular viewer for Web browsers written in WebGL/Javascript.
 With this script, you can publish your Pymol scene for Web page.
 Visitors can rotate, zoom the molecule on the page.

 Compared to exporting polygon coordinates (VRML or Object3D),
 published pages contain only atomic coordinates so that
 the file size is much smaller and visitors can even change
 representation.

 Examples and script can be downloaded from my web page.
 http://webglmol.sourceforge.jp/pymol_exporter/index.html

 This script uses (undocumented?) cmd.get_session to
 extract which representation is enabled on each part of the molecule.
 I think this technique is useful for many purposes, for example,
 writing exporters, copying representations between aligned
 structures, etc.

 Comments and suggestions are welcome.
 If you think this script useful, I will put it on Pymol wiki.

 Best regards,

 Takanori Nakane


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Re: [PyMOL] Scene exporter for Web

2012-01-16 Thread Troels Emtekær Linnet
There is now a description available at:

http://pymolwiki.org/index.php/Pymol2glmol

If you use a webpage for teaching, you should really try this plugin out.

/Troels Linnet



2012/1/16 Takanori Nakane t.nak...@mail.mfour.med.kyoto-u.ac.jp

 Dear Pymol users,

 I wrote a Pymol script to export a scene in Pymol to GLmol,
 a molecular viewer for Web browsers written in WebGL/Javascript.
 With this script, you can publish your Pymol scene for Web page.
 Visitors can rotate, zoom the molecule on the page.

 Compared to exporting polygon coordinates (VRML or Object3D),
 published pages contain only atomic coordinates so that
 the file size is much smaller and visitors can even change
 representation.

 Examples and script can be downloaded from my web page.
 http://webglmol.sourceforge.jp/pymol_exporter/index.html

 This script uses (undocumented?) cmd.get_session to
 extract which representation is enabled on each part of the molecule.
 I think this technique is useful for many purposes, for example,
 writing exporters, copying representations between aligned
 structures, etc.

 Comments and suggestions are welcome.
 If you think this script useful, I will put it on Pymol wiki.

 Best regards,

 Takanori Nakane


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Re: [PyMOL] Using super correctly

2012-01-15 Thread Troels Emtekær Linnet
Maybe this could be interesting to.
http://www.pymolwiki.org/index.php/Color_by_conservation

This script reads an alignment object and colors the protein objects in the
alignment by the sequence conservation found in the alignment.

I tried to update a little list with the different methods available.
http://www.pymolwiki.org/index.php/Align#SEE_ALSO

Good luck
/T


2012/1/15 QT rdirect...@gmail.com

 Dear all,

 Thank you for all of the replies.  I compiled pymol from svn.  Current
 revision is 3975.

 I also switched to cealign.  It seems to give better rmsd without any
 argument than align does.  Also, if you mess around with align and give it
 low cutoff value, it will eventually make one of the structure you're
 trying to align disappeared completely...I don't think that is intended.

 Best,
 Quyen


 On Fri, Jan 13, 2012 at 10:09 AM, Jason Vertrees 
 jason.vertr...@schrodinger.com wrote:

 Hi,

 Cealign's the way to go here. If you have a massively powerful
 computer you can continue turning off the guide which selects
 special carbons to guide the alignment. We need to improve/extend
 for nucleic acids. Would someone mind filing a feature request on the
 open-source bug tracker? We also need to standardize the alignment
 interface as more and more alignment algorithms appear.

 Cheers,

 -- Jason

 On Fri, Jan 13, 2012 at 8:52 AM, David Hall li...@cowsandmilk.net
 wrote:
  I decided to dig in and answer my own question about what the seq
 argument does.
 
  seq:
  positive means use sequence and structure
  0 means use only structure
  negative means only use sequence
 
  For super, I assume you only want to use structure, so messing with
  that argument is silly advice.
 
  The problem is that when you use structure, SelectorGetResidueVLA gets
  an argument of true for ca_only
 
  Obviously, nucleic acids don't have any c-alphas, so when
  SelectorGetResidueVLA searches for residues using strcmp(ai1-name,
  CA) == 0 , pymol finds no residues in the selections, then complains
  to you about invalid selections because it thinks the selections are
  empty.
 
  -David
 
  On Fri, Jan 13, 2012 at 8:37 AM, David Hall li...@cowsandmilk.net
 wrote:
  I think super does not handle nucleic acid sequences well.
 
  super ec-5s, hm-5s, seq=-1
 
  works.
 
  I'll leave it to someone else to say what that does.  I just noted
  that align works, super doesn't, guessed it had to do with sequence
  and noted that for align, the default value of seq was -1 and for
  super, the default value was 0.
 
  -David
 
  On Fri, Jan 13, 2012 at 7:44 AM, QT rdirect...@gmail.com wrote:
  Dear all,
 
  I'm having a tough time using the super command correctly.  I want to
  superimpose two 5S structures.
 
  In pymol, I'll do the following
 
  load 2awb.pdb
  load 3cc2.pdb
 
  create ec-5s, 2awb and chain a
  create hm-5s, 3cc2 and chain 9
 
  If I issue super ec-5s, hm-5s then the cryptic error ExecutiveAlign:
  invalid selections for alignment. would appear.
 
  Issuing super /ec-5s//a, /hm-5s//9 does not help either.
 
  What am I missing?  align /ec-5s//a, /hm-5s//9 works just fine
 though...
 
  Any help from the community would be very appreciated.
 
  Best,
  Quyen
 
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 (e) jason.vertr...@schrodinger.com
 (o) +1 (603) 374-7120


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Re: [PyMOL] Problems with FindSeq.py script

2012-01-14 Thread Troels Emtekær Linnet
Hi James.

I moved the script under the git repository yesterday, and took care of the
bug.
The script look a little different now.

So try the new one again from:
http://www.pymolwiki.org/index.php/findseqhttp://www.pymolwiki.org/index.php/Findseq

The follow the guide on the page.

# Find the regular expression:#  ..H[TA]LVWH# in the few proteins
loaded.# I then showed them as sticks and colored them to highlight
matched AAsfor x in cmd.get_names(): findseq.findseq(..H[TA]LVWH, x,
sele_+x, firstOnly=1)



2012/1/14 James Starlight jmsstarli...@gmail.com

 Jason, hello!

 Also I've found possible fix for that bug by lpacing this line in the 47
 line of the script

 if type(selName)!=(types.StringType) and type(selName)!=(types.NoneType):


 By the way I've found another bug when I've tried to find the same motifs
 in the several homolugues structures.

 E.g I have 5 structures wich all have motiv S.G where . is the random
 amino acid. When I've tried

 findseq S.G, all

 the script find that motifs only for last fetched structure. How I could 
 solve it?


 Thanks again,

 James



 2012/1/13 Jason Vertrees jason.vertr...@schrodinger.com

 James,

 First, there's a bug in the script. It's not dealing with selName
 correctly. To get around this just provide something to selName:

 findSeq S.G, 1a3h, selName=found_seq

 If findSeq finds the sequence, it'll return the selected atoms in
 found_seq.


 Next, SYG is not in that protein. If you search for S.G you find
 SNG. You can double check this by:

 fStr = cmd.get_fastastr(1a3h)

 print SYG in fStr

 which return false.

 Cheers,

 -- Jason


 On Fri, Jan 13, 2012 at 1:25 PM, James Starlight jmsstarli...@gmail.com
 wrote:
  Dear PyMol Users,
 
  I need to search defined sequence motifs in my structures.
 
  For that purpose I've used
 
  http://www.pymolwiki.org/index.php/FindSeq script
 
  but when I've try to use it I've got error
 
  PyMOLfindSeq SYG, 1a3h
  Error: selName was not a string.
  There was an error with a parameter.  Please see
  the above error message for how to fix it.
 
  What I've done wrong? The seqyence Ser Tyr Gly is indeed present in my
  structure!
 
  By the way is there any others way to search for pre-defined sequence
 motifs
  via PyMol?
 
  Thanks for help,
 
  James
 
 
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 --
 Jason Vertrees, PhD
 PyMOL Product Manager
 Schrodinger, LLC

 (e) jason.vertr...@schrodinger.com
 (o) +1 (603) 374-7120




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Re: [PyMOL] Contact Maps Visualizer 1.0

2012-01-13 Thread Troels Emtekær Linnet
Venkatramanan Krishnamani.

How about posting it on http://www.pymolwiki.org/index.php/Category:Plugins
Then it will newer get lost. :-)

Best
Troels

Troels Emtekær Linnet
Slotsvej 2
4300 Holbæk
Mobil: +45 60210234



2012/1/13 Venkatramanan Krishnamani ve...@andrew.cmu.edu

 hi everyone,

 I wrote this plugin for visualizing residue locations in a pdb file
 corresponding to its contact map.
 I am posting it here as it might be of use to other pymol users.

 ##**##**
 ###
 #Contact Maps Visualizer
#
 # Required Libraries
#
 #Tkinter (installed by default)
 #
 #PIL (Python Imaging Library) http://www.pythonware.com/**
 products/pil/ http://www.pythonware.com/products/pil/ #
 #pygame http://pygame.org/
  #
 #
 #
 # Installation (Linux Ubuntu)
 #
 #1. Run pymol from command line as an administrator
 #
 #2. Navigate to plugins  install and locate
 Contact_maps_Visualizer.py   #
 #3. Once installed restart pymol (not required to be administrator
 mode)  #
 #
 #
 ##**##**
 ###

 If the attachment doesn't work download it from here.
 http://db.tt/uB3ZaTIJ

 Cheers,

 Venkatramanan Krishnamani
 Post Doctoral Scholar
 Department of Physics
 Carnegie Mellon University
 Email:ve...@andrew.cmu.edu


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Re: [PyMOL] cmd.do(png filename) error

2012-01-13 Thread Troels Emtekær Linnet
Have you checked the right path?

Write in pymol cmd.
pwd

And check if the file is there.
Could it be that easy?


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Mobil: +45 60210234



2012/1/13 tusi t...@enzim.hu

 I have got the same result: no png image has been generated.

  Can you try doing
 
  from pymol import cmd
  cmd.load('tmp.pdb', 'tmp')
  cmd.png('tmp.png')
 
 
  -David




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[PyMOL] frag command

2012-01-13 Thread Troels Emtekær Linnet
Hi you all.

I need to build a cys residue for a script, to align it to a residue.
I am looking at the command: frag cys
cmd.do(frag cys)

but by script does not wait for frag to complete, and speed on.
Is there a cmd.frag ?

Or how can i find more information on frag?

Cheers
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Re: [PyMOL] frag command

2012-01-13 Thread Troels Emtekær Linnet
Found it.

cmd.fragment

under modules/pymol/creating.py

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2012/1/13 Troels Emtekær Linnet tlin...@gmail.com

 Hi you all.

 I need to build a cys residue for a script, to align it to a residue.
 I am looking at the command: frag cys
 cmd.do(frag cys)

 but by script does not wait for frag to complete, and speed on.
 Is there a cmd.frag ?

 Or how can i find more information on frag?

 Cheers


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Re: [PyMOL] First pre-release of new plugin architecture

2012-01-11 Thread Troels Emtekær Linnet
Hi Thomas.

Great work!

That looks like a real handsome plugin.
I succeded to get some of the scripts from the git repository to work out
of the box. :-)
And I love the info box.

But I see some funny behavior, which you probably are working on hard
alreadt.

1) New click boxes open behind the other windows
When I click Settings-Add new directory, the Choose directory windows
opens behind the plugin window and is hidden.
I see the same behavior for other pop-up windows.

2) I cannot disable a installed plugin.
If i untick Load on startup, the pymol command says: Plugin settings
saved!
But when I restart pymol, it still loads the plugin.
I do have to say, that I am running the subversion version of pymol

3) Location of Plugin search path
I am running Mint 12, where I have not installed pymol from the Synaptic,
but building pymol from the subversion repository.
There is some pymol Synaptic files
at: /usr/local/lib/python2.7/dist-packages/pmg_tk/startup, which is
available, even though i did not install pymol through Synaptic.
The real location should
be: /home/tlinnet/Software/pymol/modules/pmg_tk/startup, where the
subversion folder is residing.
The pymolplugins locates
the /usr/local/lib/python2.7/dist-packages/pmg_tk/startup, which is wrong.
And the scripts i download from the git repository is placed here.

Anyway, I think you have done a great job!

Best
Troels

2012/1/11 Jason Vertrees jason.vertr...@schrodinger.com

 Greetings,

  I'm pleased to announce the first pre-release of the new plugin
  architecture, which is part of my fellowship project (Warren L. DeLano
  Memorial PyMOL Open-Source Fellowship, http://pymol.org/fellowship).
 
  Brave beta testers can fetch the code from
  https://github.com/speleo3/pymolplugins


 For those adventurous types, please check out the code and give it a
 shot. We are planning on incorporating this code directly into PyMOL
 after we get community feedback. Make sure you read the README on the
 git-hub site before installing the manager -- it makes things easier.

 Great work, Thomas!

 Cheers,

 -- Jason


  See the README file for how to install it.
 
  Important Notice: This is work in progress. Once the code is mature
  enough, it will be merged into the main PyMOL program. At that stage the
  github repository will become obsolete.
 
  Features:
 
* multiple files per plugin/module
* user plugin directory
* rarely used plugins can be disabled for better performance and
  enabled on demand
* metadata support
* install from online repositories
* persistent settings for plugins
* fully backwards compatible with existing plugins
 
  I welcome any kind of feedback. In particular if something does not work
  as expected.
 
  Incompatible with: http://pymolwiki.org/index.php/Plugindirectory
 
  See also: http://pymolwiki.org/index.php/PluginArchitecture
 
  Cheers,
Thomas
 
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  MPI for Developmental Biology
  Spemannstr. 35
  D-72076 Tübingen
 
 
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Re: [PyMOL] First pre-release of new plugin architecture

2012-01-11 Thread Troels Emtekær Linnet
Hi Thomas.

Again, GREAT work!
You were right, about order of starting.

I found that I could not have in ~.pymolrc.py
*import sys,os*
*sys.path.append('/home/tlinnet/Software/pymol')*
*os.chdir('/home/tlinnet/pymol/')*

but only this. Or pymol will choke on startup.
*import sys,os*
*sys.path.append('/home/tlinnet/Software/pymol')*

So I have in ~.pymolrc.py
*import sys,os*
*sys.path.append('/home/tlinnet/Software/pymol')*

And i then have in ~.pymolrc
*import os*
*os.chdir('/home/tlinnet/pymol/')*

And in ~.pymolrc_plugins.py
*# AUTOGENERATED FILE*
*try:*
*  import pymolplugins*
*  pymolplugins.preferences[instantsave] = False*
*  pymolplugins.autoload = {'propka': False}*
*  pymolplugins.set_startup_path(
['/usr/local/lib/python2.7/dist-packages/pmg_tk/startup'] )*
*  pymolplugins.preferences = {'instantsave': True, 'verbose': True}*
*except:*
*  import os*
*  print Error while loading  + os.path.abspath(__script__)*
*
*
To your questions:
*
PyMOLprint pymol.__path__
['/usr/local/lib/python2.7/dist-packages/pymol']
*
*
*
PyMOLimport pmg_tk
PyMOLprint pmg_tk.__path__
['/usr/local/lib/python2.7/dist-packages/pmg_tk']

PyMOLprint cmd.__name__
pymol.cmd

PyMOLimport sys
PyMOLprint sys.path
['', '/usr/local/lib/python2.7/dist-packages/pymol', '/usr/lib/python2.7',
'/usr/lib/python2.7/plat-linux2', '/usr/lib/python2.7/lib-tk',
'/usr/lib/python2.7/lib-old', '/usr/lib/python2.7/lib-dynload',
'/usr/local/lib/python2.7/dist-packages',
'/usr/lib/python2.7/dist-packages', '/usr/lib/python2.7/dist-packages/PIL',
'/usr/lib/python2.7/dist-packages/gst-0.10',
'/usr/lib/python2.7/dist-packages/gtk-2.0', '/usr/lib/pymodules/python2.7',
'/home/tlinnet/Software/pymol/svnfreemol/freemol/libpy',
'/home/tlinnet/Software/pymol']

I guess I in someway must have missed to change my paths or so.
So, in somehow the subversion home-build pymol, is using the paths from the
pre-installed librabries.
I used this recipe, when i builded pymol:
http://www.pymolwiki.org/index.php/Linux_Install#Ubuntu.2FMint_compile_and_install_with_MPEG_support

I must have good something wrong.

Troels Emtekær Linnet
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2012/1/11 Thomas Holder spel...@users.sourceforge.net

 Hi Troels,

 thanks a lot for the feedback.


  2) I cannot disable a installed plugin.
 If i untick Load on startup, the pymol command says: Plugin settings
 saved!
 But when I restart pymol, it still loads the plugin.
 I do have to say, that I am running the subversion version of pymol


 Settings are saved to ~/.pymolrc_plugins.py, this is a script that imports
 pymolplugins. Unfortunately this is loaded before your .pymolrc, where you
 have the sys.path.append() line.

 Fix like this: Create a ~/.pymolrc.py and place the sys.path.append() line
 there, it should be loaded before ~/.pymolrc_plugins.py and ~/.pymolrc


  3) Location of Plugin search path
 I am running Mint 12, where I have not installed pymol from the Synaptic,
 but building pymol from the subversion repository.
 There is some pymol Synaptic files at: 
 /usr/local/lib/python2.7/dist-**packages/pmg_tk/startup,
 which is available, even though i did not install pymol through Synaptic.
 The real location should be: 
 /home/tlinnet/Software/pymol/**modules/pmg_tk/startup,
 where the subversion folder is residing.
 The pymolplugins locates the 
 /usr/local/lib/python2.7/dist-**packages/pmg_tk/startup,
 which is wrong. And the scripts i download from the git repository is
 placed here.


 Are you sure about that? Can you please copy/paste this to the PyMOL
 command prompt and send me the output?

 import pymol
 print pymol.__path__

 import pmg_tk
 print pmg_tk.__path__

 print cmd.__name__

 Thanks,

  Thomas

 --
 Thomas Holder
 MPI for Developmental Biology
 Spemannstr. 35
 D-72076 Tübingen

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Re: [PyMOL] rotate

2011-12-29 Thread Troels Emtekær Linnet
Hi Vivek.

I will suggest looking at:
http://pymolwiki.org/index.php/Rotkit

Best
Troels Linnet

2011/12/29 Jason Vertrees jason.vertr...@schrodinger.com

 Vivek,

 Yes, it is.  Please read the web page I suggested.

 Cheers,

 Jason

 Sent from my android.
 On Dec 28, 2011 9:04 PM, Vivek Ranjan vran...@gmail.com wrote:

 Is it possible to define an arbitrary axis (say a line connecting two
 atoms).

 Thanks,

 Vivek

 On Wednesday, December 28, 2011, Jason Vertrees 
 jason.vertr...@schrodinger.com wrote:
  Hi Vivek,
 
  Check out the rotate command (http://pymolwiki.org/index.php/Rotate).
 
  Cheers,
 
  -- Jason
 
  On Wed, Dec 28, 2011 at 1:58 PM, Vivek Ranjan vran...@gmail.com
 wrote:
  Hello,
 
  I would like to rotate a group of atoms around an axis defined by line
  connecting two atoms in the group. Is it possible in Pymol ? How to do
  it ?
 
  --
  Thank you and Regards,
 
  Vivek Ranjan
 
 
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 --
 Thank you and Regards,

 Vivek Ranjan



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Re: [PyMOL] Problem with open source pymol

2011-12-19 Thread Troels Emtekær Linnet
2011-12-19 12:32:21.901 Python[243:5d03] *** Terminating app due to
uncaught exception 'NSInvalidArgumentException', reason*:
'-[GLUTApplication _setup:]:* unrecognized
--


Do you have glut installed ?

http://www.pymolwiki.org/index.php/Linux_Install#Requirements


freeglut3-dev


Best
Troels



2011/12/19 Lauren Porter lauren.pers...@gmail.com

 Hi Everyone,

I've compiled and installed pymol 1.3 on my Mac (OS 10.6 running Snow
 Leopard), but pymol keeps crashing.  The compilation looks clean, so I have
 no idea why it's giving me trouble.  I have pasted the details below.  Any
 help would be much appreciated.  Thanks!

 ~Lauren

 Python 2.5.4 (r254:67916, Aug  1 2011, 15:52:49)
 [GCC 4.2.1 (Apple Inc. build 5646)] on darwin
 Type help, copyright, credits or license for more information.
  import pymol
  pymol.finish_launching()
  2011-12-19 12:32:21.895 Python[243:5d03] -[GLUTApplication _setup:]:
 unrecognized selector sent to instance 0x1805490
 2011-12-19 12:32:21.898 Python[243:5d03] An uncaught exception was raised
 2011-12-19 12:32:21.899 Python[243:5d03] -[GLUTApplication _setup:]:
 unrecognized selector sent to instance 0x1805490
  selector sent to instance 0x1805490'
 *** Call stack at first throw:
 (
 0   CoreFoundation  0x906e36ca __raiseError + 410
 1   libobjc.A.dylib 0x990c15a9
 objc_exception_throw + 56
 2   CoreFoundation  0x9073090b
 -[NSObject(NSObject) doesNotRecognizeSelector:] + 187
 3   CoreFoundation  0x90689c06 ___forwarding___ +
 950
 4   CoreFoundation  0x906897d2
 _CF_forwarding_prep_0 + 50
 5   Tk  0x17e11ea8 TkpInit + 601
 6   Tk  0x17d7d60a
 Tk_PkgInitStubsCheck + 2489
 7   _tkinter.so 0x01d9afe8 Tcl_AppInit + 130
 8   _tkinter.so 0x01d9af09 var_perform + 2295
 9   Python  0x0007ad4d PyEval_EvalFrameEx
 + 16241
 10  Python  0x0007cac6 PyEval_EvalCodeEx +
 1734
 11  Python  0x000274ce PyClassMethod_New +
 2213
 12  Python  0xc2a8 PyObject_Call + 50
 13  Python  0x00015db7 PyClass_New + 1710
 14  Python  0xc2a8 PyObject_Call + 50
 15  Python  0x00076130
 PyEval_CallObjectWithKeywords + 211
 16  Python  0x0001566f PyInstance_New + 330
 17  Python  0xc2a8 PyObject_Call + 50
 18  Python  0x0007c332 PyEval_EvalFrameEx
 + 21846
 19  Python  0x0007cac6 PyEval_EvalCodeEx +
 1734
 20  Python  0x000274ce PyClassMethod_New +
 2213
 21  Python  0xc2a8 PyObject_Call + 50
 22  Python  0x00015db7 PyClass_New + 1710
 23  Python  0xc2a8 PyObject_Call + 50
 24  Python  0x00076130
 PyEval_CallObjectWithKeywords + 211
 25  Python  0x0001566f PyInstance_New + 330
 26  Python  0xc2a8 PyObject_Call + 50
 27  Python  0x0007c332 PyEval_EvalFrameEx
 + 21846
 28  Python  0x0007cac6 PyEval_EvalCodeEx +
 1734
 29  Python  0x00027461 PyClassMethod_New +
 2104
 30  Python  0xc2a8 PyObject_Call + 50
 31  Python  0x0007c363 PyEval_EvalFrameEx
 + 21895
 32  Python  0x0007aedc PyEval_EvalFrameEx
 + 16640
 33  Python  0x0007aedc PyEval_EvalFrameEx
 + 16640
 34  Python  0x0007cac6 PyEval_EvalCodeEx +
 1734
 35  Python  0x000274ce PyClassMethod_New +
 2213
 36  Python  0xc2a8 PyObject_Call + 50
 37  Python  0x00015db7 PyClass_New + 1710
 38  Python  0xc2a8 PyObject_Call + 50
 39  Python  0x00076130
 PyEval_CallObjectWithKeywords + 211
 40  Python  0x000a3edf initthread + 1756
 41  libSystem.B.dylib   0x91446259 _pthread_start + 345
 42  libSystem.B.dylib   0x914460de thread_start + 34
 )
 Trace/BPT trap



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[PyMOL] Fwd: Problem with distance command(?)

2011-12-15 Thread Troels Emtekær Linnet
Hi James.

I think it is because you create a object, which have
identical ID's in the object.

new:
2x ID 7, 2x 5
and so on.

hide label, all
label new, index
hide label, all
label new, id

either use the index, to make selections
alter the chain name for one of the fragments, before creation

or so.

/T


Troels Emtekær Linnet
Slotsvej 2
4300 Holbæk
Mobil: +45 60210234



2011/12/15 James Davidson j.david...@vernalis.com

  **
 Dear All,

 I am currently having a problem with the distance command when applied to
 merged objects.  The real case is actually when I remove a ligand from a
 binding site and merge in a new ligand.  But as a simple example, I think I
 can demonstrate with the following:

 frag ala, ala1
 frag ala, ala2
 translate [4,0,0], ala2
 label all, ID
 distance d1, ala1  ID 3, ala2  ID 0

 This creates a distance object fine.  But if I now merge the two objects
 into a new object:

 create new, ala1 | ala2
 disable ala1 | ala2

 and manually create two single atom selections corresponding to the
 original ID 3 and ID 0 atoms (using atom select mode and renaming the
 selections to give 'sele1' and 'sele2'):

 distance d2, sele1, sele2

 gives me a distance between ID 0 and 3 both on what used to be ala2, and
 not between the two selected atoms!


 Am I doing something wrong with 'create'?  I don't recall having a problem
 with this sort of operation until maybe ~ 6 months ago...  I am using rev
 3971 under Windows.  Any help/advice greatly appreciated.

 Kind regards

 James

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Re: [PyMOL] Changing ligand conformation

2011-12-13 Thread Troels Emtekær Linnet
Or just use this script
http://www.pymolwiki.org/index.php/RemoveAlt

Troels Emtekær Linnet
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2011/12/13 Joel Tyndall joel.tynd...@otago.ac.nz

 Mark,

 You could always simply edit the pdb file (remove the trans option).
 Simply open up the pdb file in a text editor (gedit/notetab/wordpad) and
 delete the lines corresponding to the trans form. The pdb file (compare
 with the mol or mol2 files) is simple to edit manually. The others require
 connectivity etc to be edited.

 The last pdb file I saw with an alt conf looked like this:

 ATOM 53  CG2AVAL A   6  -5.306 -11.323  22.865  0.50 11.50  A
C
 ATOM 54  CG2BVAL A   6  -7.334 -10.108  21.413  0.50 12.94  A
C
 ATOM 55  CVAL A   6  -8.805 -10.428  23.682  1.00 11.53
AC
 ATOM 56  OVAL A   6  -9.347 -11.540  23.573  1.00 12.73
AO

 Where the AVAL and BVal correspond to different orientations.

 Hope this helps
 _
 Joel Tyndall, PhD

 Senior Lecturer in Medicinal Chemistry
 National School of Pharmacy
 University of Otago
 PO Box 56 Dunedin 9054
 New Zealand
 Skype: jtyndall
 http://www.researcherid.com/rid/C-2803-2008
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 Aotearoa

 Ph / Waea   +64 3 4797293
 Fax / Waeawhakaahua +64 3 4797034


 -Original Message-
 From: Mark Bostock [mailto:mjb...@cam.ac.uk]
 Sent: Saturday, 10 December 2011 10:26 a.m.
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Changing ligand conformation

 I have a pdb file of a protein which contains a lysine residue bound to a
 ligand. The ligand has two conformations due to a cis/trans isomerisation.
 I have created a pdb file (also .mol and .mol2) of lysine attached to the
 cis form and would like to replace the
 lysine-ligand(trans) form which is currently in the protein structure with
 the lysine-ligand(cis) form. Does anyone know how to do this; mutagenesis
 only gives me the option of standard amino acids and also does not remove
 the existing ligand.

 Many thanks,

 Mark.




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[PyMOL] Help converting shell script to python

2011-12-12 Thread Troels Emtekær Linnet
Hi guys.

I am trying to use the plugin: MSMShttp://www.pymolwiki.org/index.php/Msms on
a win machine.
The plugin is dependent on a shell script: pdb_to_xyzrn
But I cant execute it on a win machine, and I won't install cygwin.

Can someone help me convert the shell script to a python script?
Or know if it exist somewhere in .py script?

The script is:

#! /bin/sh
# extract x,y,z from PDB file, generate radius of each atom
# Hydrogens are presumed to be missing (united atom approach) unless -h
given
# later: options for alternate radius and pattern files
# --- Mike Pique, The Scripps Research Institute
#
# input: pdb file as argument or stdin
# output: new xyzr file to stdout
#
# Options:
#
# -h: use explicit hydrogen radii instead of default united atom radii
#
# examples:
#   pdb_to_xyzr  crambin.pdb  crambin.xyzr
#
#   foo_to_pdb -h mol.foo  | pdb_to_xyzr  mol.xyzr
#
#   foo_to_pdb mol.foo  | pdb_to_xyzr | awk '{print $4}'mol.r
#
#

# set which field to use for radii:
h_select=5
if test $# -ge 1 ;then
if test $1 = -h ; then
 h_select=4
shift
fi
fi
nawk 'BEGIN{
# read radius table and patterns from supplied file
npats=0
 numfile = ./atmtypenumbers
while ((getline  numfile)  0) {
 if(NF==0||substr($1,1,1)==#) continue;
if($1==radius) {
 n=$2 # atom number key
explicit_rad[$2] = $4

if(NF=4 || substr($5,1,1)==#) united_rad[n]=explicit_rad[n]
 else united_rad[n] = $5
continue;
}
 respat[npats] = $1
if(respat[npats] == *) respat[npats] = .*
 respat[npats] = ^respat[npats]$
atmpat[npats] = ^$2$
 gsub(_,  ,atmpat[npats])
atmnum[npats] = $3
if( ! (atmnum[npats] in explicit_rad) ) {
 # the key has no radius --- complain and fake one
print pdb_to_xyzr: error in library file,numfile,
  entry ,$1,$2,$3, has no corresponding radius value \
  | cat 12 # write to stderr
 explicit_rad[atmnum[npats]] = 0.01
united_rad[atmnum[npats]] = 0.01
}
 npats++
}
# for(pat=0;patnpats;pat++) print pat,respat[pat],atmpat[pat],atmnum[pat]
 }

$1==ATOM||$1==atom||$1==HETATM||$1==hetatm{
x = substr($0,31,8)
 y = substr($0,39,8)
z = substr($0,47,8)
resname=substr($0,18,3)

aname = substr($0,13,4)
# special handling needed for hydrogens in PDB files: they start with
 # digits not the letter H
#
if(substr(aname,1,2) ~ /[ 0-9][HhDd]/) aname=H
 # However, some bogus PDP files have the H in column 13 so we allow
# those too, which means we will treat as Hydrogen helium and hafnium
 # but we protect HG ... ... mp
#
if(substr(aname,1,2) ~ /[Hh][^Gg]/ ) aname=H


resnum=substr($0,23,4);

# trim any blanks
 gsub( , , resname);
gsub( , , aname);

for(pat=0;patnpats;pat++) {
if( aname ~ atmpat[pat]  resname ~ respat[pat] ) break
 }
if(pat==npats) {
# Not found
 print pdb_to_xyzr: error, file,FILENAME,line,NR,residue,
  resnum,
  atom pattern,resname, aname,was not found in  numfile  \
  | cat 12 # write to stderr
 print x,y,z,0.01
}
else printf(%f %f %f %f %d %s_%s_%d\n, x, y, z, \
  ('$h_select'== 5 ? united_rad[atmnum[pat]]:explicit_rad[atmnum[pat]]), 1,
aname, resname, resnum);
next;
 }' $*
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Re: [PyMOL] Help converting shell script to python

2011-12-12 Thread Troels Emtekær Linnet
Case closed.

Thanks to Hongbo Zhu for a solution.

Best
Troels


2011/12/12 Troels Emtekær Linnet tlin...@gmail.com

 Hi guys.

 I am trying to use the plugin: MSMShttp://www.pymolwiki.org/index.php/Msms 
 on
 a win machine.
 The plugin is dependent on a shell script: pdb_to_xyzrn
 But I cant execute it on a win machine, and I won't install cygwin.

 Can someone help me convert the shell script to a python script?
 Or know if it exist somewhere in .py script?

 The script is:
 
 #! /bin/sh
 # extract x,y,z from PDB file, generate radius of each atom
 # Hydrogens are presumed to be missing (united atom approach) unless -h
 given
 # later: options for alternate radius and pattern files
 # --- Mike Pique, The Scripps Research Institute
 #
 # input: pdb file as argument or stdin
 # output: new xyzr file to stdout
 #
 # Options:
 #
 # -h: use explicit hydrogen radii instead of default united atom radii
 #
 # examples:
 #   pdb_to_xyzr  crambin.pdb  crambin.xyzr
 #
 #   foo_to_pdb -h mol.foo  | pdb_to_xyzr  mol.xyzr
 #
 #   foo_to_pdb mol.foo  | pdb_to_xyzr | awk '{print $4}'mol.r
 #
 #

 # set which field to use for radii:
 h_select=5
 if test $# -ge 1 ;then
 if test $1 = -h ; then
  h_select=4
 shift
 fi
 fi
 nawk 'BEGIN{
 # read radius table and patterns from supplied file
 npats=0
  numfile = ./atmtypenumbers
 while ((getline  numfile)  0) {
  if(NF==0||substr($1,1,1)==#) continue;
 if($1==radius) {
  n=$2 # atom number key
 explicit_rad[$2] = $4

 if(NF=4 || substr($5,1,1)==#) united_rad[n]=explicit_rad[n]
  else united_rad[n] = $5
 continue;
 }
  respat[npats] = $1
 if(respat[npats] == *) respat[npats] = .*
  respat[npats] = ^respat[npats]$
 atmpat[npats] = ^$2$
  gsub(_,  ,atmpat[npats])
 atmnum[npats] = $3
 if( ! (atmnum[npats] in explicit_rad) ) {
  # the key has no radius --- complain and fake one
 print pdb_to_xyzr: error in library file,numfile,
   entry ,$1,$2,$3, has no corresponding radius value \
   | cat 12 # write to stderr
  explicit_rad[atmnum[npats]] = 0.01
 united_rad[atmnum[npats]] = 0.01
 }
  npats++
 }
 # for(pat=0;patnpats;pat++) print pat,respat[pat],atmpat[pat],atmnum[pat]
  }

 $1==ATOM||$1==atom||$1==HETATM||$1==hetatm{
 x = substr($0,31,8)
  y = substr($0,39,8)
 z = substr($0,47,8)
 resname=substr($0,18,3)

 aname = substr($0,13,4)
 # special handling needed for hydrogens in PDB files: they start with
  # digits not the letter H
 #
 if(substr(aname,1,2) ~ /[ 0-9][HhDd]/) aname=H
  # However, some bogus PDP files have the H in column 13 so we allow
 # those too, which means we will treat as Hydrogen helium and hafnium
  # but we protect HG ... ... mp
 #
 if(substr(aname,1,2) ~ /[Hh][^Gg]/ ) aname=H


 resnum=substr($0,23,4);

 # trim any blanks
  gsub( , , resname);
 gsub( , , aname);

 for(pat=0;patnpats;pat++) {
 if( aname ~ atmpat[pat]  resname ~ respat[pat] ) break
  }
 if(pat==npats) {
 # Not found
  print pdb_to_xyzr: error, file,FILENAME,line,NR,residue,
   resnum,
   atom pattern,resname, aname,was not found in  numfile  \
   | cat 12 # write to stderr
  print x,y,z,0.01
 }
 else printf(%f %f %f %f %d %s_%s_%d\n, x, y, z, \
   ('$h_select'== 5 ? united_rad[atmnum[pat]]:explicit_rad[atmnum[pat]]),
 1, aname, resname, resnum);
 next;
  }' $*

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Re: [PyMOL] Context sensitive mutation wizard

2011-12-08 Thread Troels Emtekær Linnet
Can this plugin solve it:
http://www.pymolwiki.org/index.php/Rotamer_Toggle

Note, that you have to collect the script yourself, and replace
the original pymol menu.py file.

Not a easy solution to problem.

Note, it the script: http://www.pymolwiki.org/index.php/Rotkit
You can mutate through a command line, and selecting which
rotamer to use. But that would not solve your problem of specifying which
plane
to select.
In http://www.pymolwiki.org/index.php/Propka#Mutagenesis_analysis
are some more examples of mutating in PyMOL and get the pKa
for the mutations.

Best
Troels


2011/12/8 Martin Hediger ma@bluewin.ch

 Dear PyMOL List
 I'm frequently using the PyMOL mutagenesis wizard. Consider the mutation
 of tryptophan to phenylalanin. If the sidechain is mutated from W to F,
 its reasonable to assume that the plane of the phenyl moiety of F
 would/should/could/might lie in the same plane as the indol part of the
 W if there was such a protein.
 Would it be possible to scriptically adjust the F side chain, after
 mutation, such that it lies in the W plane?
 Of course, this becomes ambiguous when, say, a A is mutated to a D,
 because what would then be the reference for the D side chain? However,
 N to D would be another case, where it would be desired to have the D
 end group be in as much overlay with the former N end group as possible.

 Any ideas on how this might be afforded? Probably not a one-liner though.

 Kind regards
 Martin


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Re: [PyMOL] Electrostatic calculations with ligand bound

2011-12-06 Thread Troels Emtekær Linnet
Hi Andrew.

I experienced something similar for the autodock_plugin.
http://www.pymolwiki.org/index.php/Autodock_plugin

During my trials, I notified two things for autodock.
It did not like funny atom names or Alternative configuration

Could this be a case for your protein / ligand?
I don't know if is the same for the APBS plugin, but you could try?
http://www.pymolwiki.org/index.php/Autodock_plugin#Example_1_-_Rename_of_funny_atom_names

Some of the preparation scripts for both plugins are coming from the same
research groups.
I think they both use: pdb2pqr or something.

Best
Troels

2011/12/7 Michael Lerner mgler...@gmail.com

 Hi Andrew,

 The main limitation for problems like this is that you need to have
 parameters for the ligand. Making sure that you have good parameters
 is often an expert-level topic, and you're probably best served by the
 APBS or PDB2PQR listservs as well as the literature ... but, you can
 get a decent start on things with PDB2PQR itself. See
 http://www.poissonboltzmann.org/pdb2pqr/examples/ligand-parameterization
 for some good starting instructions. Once you have a PQR file that
 includes both the protein and the ligand, the PyMOL/APBS plugin should
 do everything that you need.

 If that doesn't solve your problem, please let me know.

 Cheers,
 -Michael

 On Tue, Nov 29, 2011 at 11:44 AM, Malaby, Andrew
 andrew.mal...@umassmed.edu wrote:
  Hey guys,
 
  I am trying to calculate electrostatics with a ligand bound to my
 molecule using ABPS.  I am not having success.  Everything I've read seems
 to say that this is a normal limitation with APBS, and I've tried other
 programs to no avail.  I have not been able to rebuild my molecule in the
 correct format either.  Any help here is greatly appreciated.
 
  Andrew
  UMass Med School, Worcester, MA
 
 
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Re: [PyMOL] Select smart

2011-12-05 Thread Troels Emtekær Linnet
Hi Jared.

That is so cool!

I missed that feature :-)

Best
T



2011/12/5 Sampson, Jared jared.samp...@nyumc.org

 Hi Troels, Jason -

 I've often wondered about these as well, so I've just updated the wiki
 page
 http://www.pymolwiki.org/index.php/Single-word_Selectors#More_selectorsto 
 reflect the single-word selectors from Selector.c.  I think I got them
 all, but feel free to double check!

 Cheers,
 --
 Jared Sampson
 Xiangpeng Kong Lab
 NYU Langone Medical Center
 550 First Ave MSB 329
 New York, NY 10016
 212-263-7898

 On Dec 4, 2011, at 12:02 PM, Jason Vertrees wrote:

  HI Troels,
 
  pymol/layer3/Selector.c near line 355.
 
  Cheers,
 
  -- Jason
 
  2011/12/4 Troels Emtekær Linnet tlin...@gmail.com:
  Hi.
 
  I sometimes see, that you can do
  select polymer
  select organic
 
  Is there a list somewhere with these keywords and what they select?
 
  Best
  Troels
 
 
 
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  (e) jason.vertr...@schrodinger.com
  (o) +1 (603) 374-7120
 
 
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[PyMOL] Select smart

2011-12-04 Thread Troels Emtekær Linnet
Hi.

I sometimes see, that you can do
select polymer
select organic

Is there a list somewhere with these keywords and what they select?

Best
Troels
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Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)

2011-12-02 Thread Troels Emtekær Linnet
Try Following this script.

http://www.pymolwiki.org/index.php/Linux_Install#Ubuntu.2FMint_Compile_and_install_with_MPEG_support

Please report if you are successful.
It would be interesting to see how it works on CentOS

/T



2011/12/2 grantaka36 grantak...@gmail.com

 Referring the following, I'm trying to install PyMOL 1.4.1 with
 attached 'compile_pymol.sh', but no success. Would you please help to
 finish installation, or give me some advices? If information
 inadequate, please contact me.

 http://www.pymolwiki.org/index.php/Linux_Install
 - Requirements
 - Get latest Source from SVN
 - Compile and install
 - Problems - gcc-4.5 is broken for pymol install, use gcc-4.4
 -- My distribution has gcc4.5, so installed /usr/bin/gcc44, /usr/bin/g++44.

 Attached 'install_error.txt' gathers some information:
 - Original module files are in $HOME/install_module/pymol-archive
 - Intends to install in $HOME/pymol-svn
 - Original log has some Japanese messages so I added /* means ... */

 Regards,
 Masataka


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Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)

2011-12-02 Thread Troels Emtekær Linnet
Hi Marius.

The last test I had on a Ubuntu/Mint box (1 month ago), it would not
compile with gcc 4.5.
So, it is necessary to change to gcc 4.4
I have made a script that auto compile on Ubuntu/Mint.
I have not checked the last release with hcc 4.5

I have not tried CentOS.
It would be interesting to have a compile script, for RPM package system.
I do not know if gcc 4.5 works on CentOS.

Best
Troels




2011/12/2 Marius Retegan marius.s.rete...@gmail.com

 Could you please specified what exactly did the gcc 4.5 broke in Pymol?
 Maybe this is not the case for every linux distribution.

 Cheers,
 Marius

 2011/12/2 Troels Emtekær Linnet tlin...@gmail.com:
  Try Following this script.
 
 
 http://www.pymolwiki.org/index.php/Linux_Install#Ubuntu.2FMint_Compile_and_install_with_MPEG_support
 
  Please report if you are successful.
  It would be interesting to see how it works on CentOS
 
  /T
 
 
 
  2011/12/2 grantaka36 grantak...@gmail.com
 
  Referring the following, I'm trying to install PyMOL 1.4.1 with
  attached 'compile_pymol.sh', but no success. Would you please help to
  finish installation, or give me some advices? If information
  inadequate, please contact me.
 
  http://www.pymolwiki.org/index.php/Linux_Install
  - Requirements
  - Get latest Source from SVN
  - Compile and install
  - Problems - gcc-4.5 is broken for pymol install, use gcc-4.4
  -- My distribution has gcc4.5, so installed /usr/bin/gcc44,
  /usr/bin/g++44.
 
  Attached 'install_error.txt' gathers some information:
  - Original module files are in $HOME/install_module/pymol-archive
  - Intends to install in $HOME/pymol-svn
  - Original log has some Japanese messages so I added /* means ... */
 
  Regards,
  Masataka
 
 
 
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Re: [PyMOL] creating PDB structure

2011-11-24 Thread Troels Emtekær Linnet
Hi James.

Look here for windows:
http://www.pymolwiki.org/index.php/Windows_Install#Pre-compiled_PyMOL
Basically:

You can make a pymolrc.pym file, and put it under C:\Users\YOU. In the
file you can write the following listed. This folder is now in your PyMOL
search path, so you can put pymol wiki scripts here. Note the forward
slashes /.

import syssys.path.append(C:/Python27/PyMOL/scripts)

Then put all scripts here, and write in pymol.
import filename_to_script  (without .py)
If the script filename is forster.py), you write
import forster

Then you have access to the functions which have cmd.extend(forster
,forster)

cd /homes/YOU/Documents/Atto-dyes/Spectre/ALEXA488-ALEXA633import forster
forster D_Exi=ALEXA488Exi.txt, D_Emi=ALEXA488Emi.txt,
A_Exi=ALEXA633Exi.txt, A_Emi=ALEXA633Emi.txt, A_e_Max_Y=159000,
A_e_Max_X=621, Qd=0.92

And you have access to other functions with name of file in front of
function
Area=forster.numintegrator(fluarray, col1=0, col2=1)

Best
Troels



Troels Emtekær Linnet
Slotsvej 2
4300 Holbæk
Mobil: +45 60210234



2011/11/23 James Starlight jmsstarli...@gmail.com

 Thanks Thomas!

 Those scripts works fine. Could you tell me if there any way to install
 all of those scripts as the pymol plugins ( that I need not to load this
 scripts every time when I sttart pymol de novo )?


 James

 2011/11/23 James Starlight jmsstarli...@gmail.com

 Thanks thomas

 Those scripts works fine. Could you tell me if there any way to install
 all of those scripts as the pymol plugins ( that I need not to load this
 scripts every time when I sttart pymol de novo )?


 James


 2011/11/23 Thomas Holder spel...@users.sourceforge.net

 Hi James,

 check this PyMOLWiki page: 
 http://pymolwiki.org/index.**php/Fabhttp://pymolwiki.org/index.php/Fab

 However, the fab command does not take user defined phi/psi angles,
 only 4 predefined conformations (ss argument). User defined phi/psi can
 be handled by these scripts:

 http://pymolwiki.org/index.**php/CreateSecondaryStructurehttp://pymolwiki.org/index.php/CreateSecondaryStructure
 http://pldserver1.biochem.**queensu.ca/~rlc/work/pymol/#**modelhttp://pldserver1.biochem.queensu.ca/%7Erlc/work/pymol/#model

 Cheers,
  Thomas

 James Starlight wrote, On 11/23/11 11:43:

  Dear PyMol Users!

 I wounder to know about possible ways of creation of the peptide
 structures via PyMol Builder module. In particular I need create a linear
 structure of my protein ( with fixed phi and psi angles) for futher folding
 molecular dynamics simulation of that peptide. But in builder module I
 found only helix and sheet conformations for each aa. residue. How I can
 specify desired values for both torsion angles ?

 Also I'd like to know is there any module for pymol wich could be used
 for obtaining linear unfolded structure for the defined sequence or folded
 protein ( in pdb) ?

 Thanks,


 James


 --
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 Spemannstr. 35
 D-72076 Tübingen





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Re: [PyMOL] Questions about pymol plugins

2011-11-24 Thread Troels Emtekær Linnet
Have you told PyMOL to import the functions from a module?

What have you written in PyMOL?

/T

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2011/11/24 James Starlight jmsstarli...@gmail.com

 Dear PyMol Users!

 I've decided to make this topic for all questions wich could be arrise
 during working in diffent PyMol plugins.

 So My first question about installation of the plugins wich are separate
 python modules ( installed not via PyMolf itself)

 E.g I have old PyMol wicj lack CEalign plugin. I have CEalign source wich
 then I succesfull installed in my python.

 root@owntest:/home/own/Downloads/cealign-0.8-RBS# python setup.py build
 install
 running build
 running build_ext
 running install
 running install_lib
 running install_egg_info
 Writing /usr/local/lib/python2.6/dist-packages/cealign-0.8_RBS.egg-info

 but when I try use CEalign from pymol I've obtaind

 NameError: name 'cealign' is not defined

 How I could install such plugins correctly ?

 Thanks for help

 James



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Re: [PyMOL] Questions about pymol plugins

2011-11-24 Thread Troels Emtekær Linnet
Okay, well...

You need to know more about python search paths and importing modules...

You need to define and tell python to search in the directory where the
CEaling script is.
Then you need to import the module in PyMOL.

Then you can use the function.

Basically, you need to learn basic stuff of python.
Please consider how you ask questions.

Best
Troels



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2011/11/24 James Starlight jmsstarli...@gmail.com

 Troels,

 no I just typed command name
 cealign ref, target

 on another loptop I have more modern version of pymol with prebuilt CE.
 Here I can just type CEalign :)

 James


 2011/11/24 Troels Emtekær Linnet tlin...@gmail.com

 Have you told PyMOL to import the functions from a module?

 What have you written in PyMOL?

 /T

 Troels Emtekær Linnet
 Slotsvej 2
 4300 Holbæk
 Mobil: +45 60210234



 2011/11/24 James Starlight jmsstarli...@gmail.com

  Dear PyMol Users!

 I've decided to make this topic for all questions wich could be arrise
 during working in diffent PyMol plugins.

 So My first question about installation of the plugins wich are separate
 python modules ( installed not via PyMolf itself)

 E.g I have old PyMol wicj lack CEalign plugin. I have CEalign source
 wich then I succesfull installed in my python.

 root@owntest:/home/own/Downloads/cealign-0.8-RBS# python setup.py build
 install
 running build
 running build_ext
 running install
 running install_lib
 running install_egg_info
 Writing /usr/local/lib/python2.6/dist-packages/cealign-0.8_RBS.egg-info

 but when I try use CEalign from pymol I've obtaind

 NameError: name 'cealign' is not defined

 How I could install such plugins correctly ?

 Thanks for help

 James



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[PyMOL] Invitation to connect on LinkedIn

2011-11-19 Thread Troels Emtekær Linnet via LinkedIn
LinkedIn





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I'd like to add you to my professional network on LinkedIn.

- Troels Emtekær

Accept invitation from Troels Emtekær  Linnet
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Re: [PyMOL] Create a dummy atom

2011-11-14 Thread Troels Emtekær Linnet
Using pseudo atoms

http://www.pymolwiki.org/index.php/Pseudoatom

using pos=


pseudoatom tmpPoint2, resi=40, chain=ZZ, b=40, color=tv_blue, pos=[-10, 0, 10]


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2011/11/14 ABEL Stephane 175950 stephane.a...@cea.fr

 Dear all,

 I have a simple question but i have found no response: i have downloaded a
 pymol script COM.py from the pymol wiki to obtain the coordinates x, y and
 z of the center of mass of my protein. Now i would like to create a dummy
 at these coordinates. How to do that with pymol ?

 Thank for your help

 Stephane

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Re: [PyMOL] Antw.: Put scripts in a svn folder

2011-11-10 Thread Troels Emtekær Linnet
I personally think git hub is a good suggestion.

And we need you wikiguys (Jason etc. ) to catch the idea and implement it.
:-)

Security is an issue, and I also believe that you need to control this.
I don't know if github is able to make securities in groups of a owner of a
script and some super users.
So only a few users can change the script.
Would it possible to have the same user credentials to the github as the
wiki?

Host / mirror.
As far as I know, one can find each file at a github webpage.
So, maybe the pymolwiki could show that file in a window at the wiki?

People with github experience should throw in some experience. :-)

Best
Troels




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2011/11/10 Jason Vertrees jason.vertr...@schrodinger.com

 Hi Justin,

  I started this some time ago and also announced it on the mailing list.
 But
  it didn't caught much interest.

 The idea didn't get much traction because it was ahead of its time. I
 think now is its time.

 The plugin manager that Thomas is creating will be able to aggregate
 scripts from various locations and install them on the fly without one
 needing to restart PyMOL. Do you mind working with Thomas to help
 integrate with the git-hub repo?

 Downloading scripts and running them creates a security hazard. So, we
 need to be careful about that.

 Some points to consider for the repository:
  * it should mirror or host the code from the PyMOLWiki, not fork it
  * be secure from misuse (can anyone commit or just you?)

 What do you think?

 Cheers,

 -- Jason

 --
 Jason Vertrees, PhD
 PyMOL Product Manager
 Schrodinger, LLC

 (e) jason.vertr...@schrodinger.com
 (o) +1 (603) 374-7120


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[PyMOL] opensource pymol with MPEG support

2011-11-10 Thread Troels Emtekær Linnet
Hi Gals and Gils.

I have struggled with making a movie easy and fast. The MPEG way is just
snappy snappy fast.

I was pleased to see that installation instructions has been updated for
the pymol open source.

I added installation instructions (Ubuntu/Mint) with MPEG support for the
opensource pymol.

http://www.pymolwiki.org/index.php/Linux_Install#Ubuntu.2FMint_Compile_and_install_with_MPEG_support

Best
Troels
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Re: [PyMOL] Movie to export

2011-11-09 Thread Troels Emtekær Linnet
What codec do I need to install??

MEncoder 1.0rc4-4.5.2 (C) 2000-2010 MPlayer Team
Option x264encopts: Unknown suboption nodct_decimat
success: format: 16  data: 0x0 - 0x0
MF file format detected.
[mf] search expr: *.png
[mf] number of files: 537 (4296)
[demux_mf] file type was not set! trying 'type=png'...
VIDEO:  [MPNG]  0x0  24bpp  25.000 fps0.0 kbps ( 0.0 kbyte/s)
[V] filefmt:16  fourcc:0x474E504D  size:0x0  fps:25.000  ftime:=0.0400
Opening video filter: [expand osd=1]
Expand: -1 x -1, -1 ; -1, osd: 1, aspect: 0.00, round: 1
==
Opening video decoder: [ffmpeg] FFmpeg's libavcodec codec family
Selected video codec: [ffpng] vfm: ffmpeg (FFmpeg PNG)
==
Could not find matching colorspace - retrying with -vf scale...
Opening video filter: [scale]
Movie-Aspect is undefined - no prescaling applied.
[swscaler @ 0x7f2555cc0620]BICUBIC scaler, from bgra to yuv420p using MMX2
FATAL: Cannot initialize video driver.
Movie-Aspect is undefined - no prescaling applied.
FATAL: Cannot initialize video driver.

Exiting...



2011/11/9 Marius Retegan marius.s.rete...@gmail.com

 On a Linux system you can use the following commands to stick them all
 together

 mencoder mf://*.png -mf fps=25 -ovc x264 -x264encopts

 bitrate=3000:threads=auto:frameref=8:bframes=0:nob_adapt:direct_pred=auto:subq=7:mixed_refs:nodct_decimat:no_psnr:me=umh:keyint=25
 -ofps 25 -nosound -noskip -of rawvideo -o movieLQ.264

 This will create a x264 compressed file which you will have to put in
 a mp4 container using the following command. You can modify the
 bitrate which is now set to 3000 and the framerate 25 fps.

 MP4Box -fps 25 -add movieLQ.264 movieLQ.mp4

 Best regards,
 Marius

 --
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 Tel +33 (0) 4 76 63 44 03
 GnuPG http://db.tt/rr7Hd0Y



 2011/11/8 Jason Vertrees jason.vertr...@schrodinger.com:
  Hi Troels,
 
  One benefit of the Incentive version of PyMOL is the Files  Save
  Movie as ...  MPEG feature. If you don't have that or you want to use
  a different compressor that's cool. In the past I had great luck with
  mencoder (http://www.pymolwiki.org/index.php/Making_Movies)-- but I
  think everyone's using VLC (http://www.videolan.org/) or ffmpeg
  (http://ffmpeg.org/) now. If the PyMOLWiki's out of date, please feel
  free to update it.
 
  Cheers,
 
  -- Jason
 
  2011/11/8 Troels Emtekær Linnet tlin...@gmail.com:
  Hi.
  I have made a nice little movie in Pymol.
  1500 frames.
  So now I am wondering what is the best method to export?
  At the moment I do export to .png with ray tracing each image.
  set ray_trace_frames = 1
  That takes a long time.
  And what program should I use to pack them together? The easy wasy?
  Can it be done faster with the MPEG method?
  Best
  Troels
 
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  (e) jason.vertr...@schrodinger.com
  (o) +1 (603) 374-7120
 
 
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[PyMOL] Put scripts in a svn folder

2011-11-09 Thread Troels Emtekær Linnet
Hi Pymolers.

I sometimes find small errors in my scripts, which I then correct.
But then I get a little sad, that now my unfinished script still lives
out there.

So I think, why is the pymolwiki scripts not under subversion control?

Then authors could push corrections to their scripts to the subversion
directory,
and users would get these corrections.

I dont know if the pymol wiki could fetch and display the scripts from the
subversion
folder.

How does this idea sounds?

Bes
Troels
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[PyMOL] Movie to export

2011-11-08 Thread Troels Emtekær Linnet
Hi.

I have made a nice little movie in Pymol.
1500 frames.

So now I am wondering what is the best method to export?

At the moment I do export to .png with ray tracing each image.
set ray_trace_frames = 1
That takes a long time.
And what program should I use to pack them together? The easy wasy?

Can it be done faster with the MPEG method?

Best
Troels

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Re: [PyMOL] how to activate pymol from remote server

2011-10-17 Thread Troels Emtekær Linnet
*This does not seem to be an issue of Pymol.*

If you can't open a display to any program, like gedit, you are not doing
it right.

Get an open display to any program, and then try Pymol.
Here is a start to do it.
*http://x.cygwin.com/docs/ug/using-remote-apps.html*http://x.cygwin.com/docs/ug/using-remote-apps.html

You NEED to pass *-Y* to the ssh program.

ssh *-Y* -l (loginname) (hostname)


But please come back again, if have problems regarding Pymol.

If you only neeed Pymol scripting, and no display, you can check here:
http://www.pymolwiki.org/index.php/Launching_PyMOL#Running_PyMOL_in_batch_mode
pymol -cq


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2011/10/17 grantaka36 grantak...@gmail.com

 Hi Thomas,

 I appreciate your advice very much, testing and cannot find green
 signal yet as [2]. For now, what I want to do is [1], so please give
 me, if any enough, advice or workaround.  If information might be
 inadequate, please contact me.

 [1]
  how to activate pymol from remote server?
  i.e. how to start pymol in [S] by scripting from [C]

 Sorry for lack of information, what all I'd like to do is:
 - Scripting in [C] (on Cygwin or telnet over Command Prompt etc.
 welcome), which includes login procedure to [S] by 'ssh -l (loginname)
 (hostname)'
 - pymol GUI open in [S]'s window (not in [C])

 I wonder, if even in this case X-forwarding is needed.

 [2]
  do you have a X server running on Windows? It works for me with Cygwin
 with
  installed X and GL libraries (but it's not very convenient because quite
  slow).
 
  ssh -Y linuxserver
  pymol

 Windows [C] didn't have X-server so I installed Xming 6.9.0.31 and
 kept running, 'pymol' returns:
 | freeglut (pymol): failed to open display ''
 | PyMOL: abrupt program termination.

 Another command returns:
 | $ gedit (one shell script).sh
 | (gedit:3887): Gtk-WARNING **: cannot open display:
 | (returned empty)
 | $

 | $ grep X11Forwarding /etc/ssh/sshd_config
 | X11Forwarding yes
 | $ grep X11DisplayOffset /etc/ssh/sshd_config
 | X11DisplayOffset 10

 So, I think X-forwarding setting done but not all of 'install X and GL
 libraries' might be intalled yet.


 Regards,
 Masataka


 2011/10/15 Thomas Holder spel...@users.sourceforge.net:
  Hi Masataka,
 
  do you have a X server running on Windows? It works for me with Cygwin
 with
  installed X and GL libraries (but it's not very convenient because quite
  slow).
 
  ssh -Y linuxserver
  pymol
 
  If pymol is set up on that linux server correct and runs there by just
  typing pymol, it should as well from an X-forwarded ssh connection. No
  need to export variables. Don't use the -R and -display arguments.
 
  Cheers,
   Thomas
 
 
  grantaka36 wrote, On 10/14/11 07:35:
 
  Dear list members,
 
  Would you please tell me the way, how to activate pymol from remote
  server? i.e. how to start pymol in [S] by scripting from [C]
 
  --
  - From Windows client [C], SSH2 logging in to the remote server [S]
  (Linux x64, Ubuntu 10)
  - [S]
  -- installed PyMOL 1.2 r2, PATH includes '/usr/bin/pymol' so only
  'pymol' entering enable to activate pymol GUI
  -- 'python' returns
  -- Python 2.6.6 (r266:84292, Sep 15 2010, 16:22:56)
  -- [GCC 4.4.5] on linux2
  - [C]
  -- first trying the following:
  PYMOL_PATH=/usr/bin/pymol
  HOST_ID=`uname -n`
  pymol -R -display:${HOST_ID}:0.0
  -- returns:
  Traceback (most recent call last):
   File /usr/lib/python2.6/runpy.py, line 122, in _run_module_as_main
 __main__, fname, loader, pkg_name)
   File /usr/lib/python2.6/runpy.py, line 34, in _run_code
 exec code in run_globals
   File /usr/lib/pymodules/python2.6/pymol/__init__.py, line 495, in
  module
 invocation.parse_args(pymol_argv)
   File /usr/lib/pymodules/python2.6/pymol/invocation.py, line 251,
  in parse_args
 options.stereo_mode = int(av.pop())
  IndexError: pop from empty list
  --
 
  By referring,
 
 
 http://www.pymolwiki.org/index.php/Launching_PyMOL#Launching_PyMOL_from_an_external_application
 
  If PYMOL_PATH, LD_LIBRARY_PATH, and TCL_LIBRARY are correctly defined,
  then you can launch PyMOL from an external Python program
 
  But I don't know which path to designate LD_LIBRARY_PATH and TCL_LIBRARY
 
 
  Regards,
  Masataka
 
  --
  Thomas Holder
  MPI for Developmental Biology
  Spemannstr. 35
  D-72076 Tübingen
 


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Re: [PyMOL] Segmentation fault while starting Pymol in ubuntu 11

2011-10-17 Thread Troels Emtekær Linnet
What version do you have installed?

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2011/10/17 Tao-wei Huang yelve...@gmail.com

 Hi all,

 I have problems with starting pymol in ubuntu. When I started it from
 terminal, I just received the error message: Segmentation fault. I
 tried googling pymol segmentation fault, but I don't find effective
 information to fix this problem. If you have any idea or experience
 about this, please tell me. Thank you very much.


 Cheers,
 Tao


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Re: [PyMOL] Rotation of a Protein

2011-10-09 Thread Troels Emtekær Linnet
Create two new molecules from the originial.
then

import rotkit
*rotateline Pos1=**atomcoordM1**, Pos2=atomcoordM2, degangle=60,
molecule=dim1*




2011/10/9 kanika sharma ksharma...@gmail.com

 I need to rotate the second unit of the dimeric protein on the line joining
 their center of masses. rotate it at a atep of 60 degrees till 240 degree..


 2011/10/8 Troels Emtekær Linnet tlin...@gmail.com

 If you need rotations around an line, instead of axis, check out

 http://www.pymolwiki.org/index.php/Rotkit

 Troels Emtekær Linnet
 Karl-Liebknecht-Straße 53, 2 RE http://maps.google.dk/
 04107 Leipzig, Tyskland
 Mobil: +49 1577-8944752



 2011/10/7 kanika sharma ksharma...@gmail.com

  Hello everyone,
 I Have a protein with 2 chains.
 I have to rotate the second chain of the protein by 60,120,180,240
 degrees each.
 Is there a script in PyMol that can do that?

 Best,
 Kanika


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Re: [PyMOL] Rotation of a Protein

2011-10-07 Thread Troels Emtekær Linnet
If you need rotations around an line, instead of axis, check out

http://www.pymolwiki.org/index.php/Rotkit

Troels Emtekær Linnet
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04107 Leipzig, Tyskland
Mobil: +49 1577-8944752



2011/10/7 kanika sharma ksharma...@gmail.com

 Hello everyone,
 I Have a protein with 2 chains.
 I have to rotate the second chain of the protein by 60,120,180,240 degrees
 each.
 Is there a script in PyMol that can do that?

 Best,
 Kanika


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Re: [PyMOL] Mutate residues in batch mode

2011-09-22 Thread Troels Emtekær Linnet
# Firs load files in dirextory with:
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/
# load_sep.py
# Load multiple PDB files into a multiple PyMOL objects
#  e.g. load_sep prot_*.pdb, prot
# will create objects with names, prot1, prot2, prot3, etc.

# Now the rest
cd /home/tlinnet/Desktop

# Test protein
fetch 4INS, async=0

# Get all loaded PDB object names in pymol
PDBs = cmd.get_names()

python
### We need to find a way to get the information of chain and resi from the
loaded list
### Create empty list
ProtChainResiList = []
for PDB in PDBs:
#print PDB
### Get the ID numbers of CA atom in protein
CAindex = cmd.identify(%s and name CA%PDB)
for CAid in CAindex:
### We need to find a way to get the information of chain and resi
from ID
pdbstr = cmd.get_pdbstr(%s and id %s%(PDB,CAid))
pdbstr_lines = pdbstr.splitlines()
chain = pdbstr_lines[0].split()[4]
resi = pdbstr_lines[0].split()[5]
#print CAid: %s Chain: %s resi: %s%(CAid, chain,resi)
ProtChainResiList.append([PDB,chain,resi])
#for entry in ProtChainResiList:
#print entry
python end

### We devide it up in several python blocks, so python dont speed ahead:
python
### Start the wizard
cmd.wizard(mutagenesis)
## REMOVE [0:3]
for p,c,r in ProtChainResiList[0:4]:
#print p,c,r
cmd.do(refresh_wizard)
cmd.get_wizard().set_mode(LYS)
selection=/%s//%s/%s%(p,c,r)
#print selection
cmd.get_wizard().do_select(selection)
### Select frame 1, which is most probable
cmd.frame(1)
cmd.get_wizard().apply()
### Stop the wizard
cmd.set_wizard(done)
python end

Troels Emtekær Linnet



2011/9/22 Fabio Gozzo fgo...@gmail.com

 Hi Pymolers,

 I need to perform a batch operation but I need a help with script
 modification.
 A have a set (~100) of pdb files that I would like to mutate all residues
 to lysine. I modified mutate02.py script in pymol to perform this task, but
 I would need two extra features:

 1) the script would need to save the file with a different name. For
 example, load test.pdb, mutate all residues to lysine and then save the
 mutated version to test_K.pdb
 2) the script would need to perform this task for all the pdb files in a
 directory.

 Right now, I am not concerned about the possible rotamers of lysine, any
 lysine rotamer would work.
 Could anyone give a hint on how to do it ?
 Thanks !
 Fabio.



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Re: [PyMOL] Mutate residues in batch mode

2011-09-22 Thread Troels Emtekær Linnet
And to save it, add this python block

python
for PDB in PDBs:
cmd.save(%s-K.pdb%PDB,%s%PDB)
python end

Troels Emtekær Linnet
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2011/9/22 Troels Emtekær Linnet tlin...@gmail.com

 # Firs load files in dirextory with:
 http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/
 # load_sep.py
 # Load multiple PDB files into a multiple PyMOL objects
 #  e.g. load_sep prot_*.pdb, prot
 # will create objects with names, prot1, prot2, prot3, etc.

 # Now the rest
 cd /home/tlinnet/Desktop

 # Test protein
 fetch 4INS, async=0

 # Get all loaded PDB object names in pymol
 PDBs = cmd.get_names()

 python
 ### We need to find a way to get the information of chain and resi from the
 loaded list
 ### Create empty list
 ProtChainResiList = []
 for PDB in PDBs:
 #print PDB
 ### Get the ID numbers of CA atom in protein
 CAindex = cmd.identify(%s and name CA%PDB)
 for CAid in CAindex:
 ### We need to find a way to get the information of chain and resi
 from ID
 pdbstr = cmd.get_pdbstr(%s and id %s%(PDB,CAid))
 pdbstr_lines = pdbstr.splitlines()
 chain = pdbstr_lines[0].split()[4]
 resi = pdbstr_lines[0].split()[5]
 #print CAid: %s Chain: %s resi: %s%(CAid, chain,resi)
 ProtChainResiList.append([PDB,chain,resi])
 #for entry in ProtChainResiList:
 #print entry
 python end

 ### We devide it up in several python blocks, so python dont speed ahead:
 python
 ### Start the wizard
 cmd.wizard(mutagenesis)
 ## REMOVE [0:3]
 for p,c,r in ProtChainResiList[0:4]:
 #print p,c,r
 cmd.do(refresh_wizard)
 cmd.get_wizard().set_mode(LYS)
 selection=/%s//%s/%s%(p,c,r)
 #print selection
 cmd.get_wizard().do_select(selection)
 ### Select frame 1, which is most probable
 cmd.frame(1)
 cmd.get_wizard().apply()
 ### Stop the wizard
 cmd.set_wizard(done)
 python end

 Troels Emtekær Linnet



 2011/9/22 Fabio Gozzo fgo...@gmail.com

  Hi Pymolers,

 I need to perform a batch operation but I need a help with script
 modification.
 A have a set (~100) of pdb files that I would like to mutate all residues
 to lysine. I modified mutate02.py script in pymol to perform this task, but
 I would need two extra features:

 1) the script would need to save the file with a different name. For
 example, load test.pdb, mutate all residues to lysine and then save the
 mutated version to test_K.pdb
 2) the script would need to perform this task for all the pdb files in a
 directory.

 Right now, I am not concerned about the possible rotamers of lysine, any
 lysine rotamer would work.
 Could anyone give a hint on how to do it ?
 Thanks !
 Fabio.



 --
 All the data continuously generated in your IT infrastructure contains a
 definitive record of customers, application performance, security
 threats, fraudulent activity and more. Splunk takes this data and makes
 sense of it. Business sense. IT sense. Common sense.
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Re: [PyMOL] pymol wildcards usage

2011-09-13 Thread Troels Emtekær Linnet
Have you tried

delete all and not obj1

Troels Emtekær Linnet
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04107 Leipzig, Tyskland
Mobil: +49 1577-8944752



2011/9/13 Андрей Гончар gontc...@gmail.com

 Hi all! I have a question about wildcards usage in pymol.
 For example if I want to delete all except obj1 I write:
 delete not obj1
 but this expression does not works as expected...

 Is there a way in pymol to delete all except [something]?
 In selections these experssions work. But in object names they don't.


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Re: [PyMOL] Show Sticks - Turns Molecule Blue

2011-09-11 Thread Troels Emtekær Linnet
This should get you on the way on compiling from svn.

http://www.pymolwiki.org/index.php/Linux_Install#Mint11_Linux_.28Ubuntu.29_-_Tested_for_PyMOL_1.4.1

Best
Troels


2011/9/9 Sean Law magic...@hotmail.com

  Hi PyMOLers,

 I have tried installing both PyMOL 1.3 and PyMOL 1.4.1 on OpenSuse (old
 Pentium 4) and am finding that when I load a molecule and click Show --
 Sticks that the entire molecular gets colored blue (originally the green
 default lines color).  After trying to change the color (Color --
 Elements), it doesn't alter the color at all.  However, hiding the sticks
 representation takes me back to the hidden green default lines color.  I'm
 not sure if this is because I'm using an old computer or if I'm missing
 something (i.e. libraries).

 Any suggestions would be greatly appreciated.

 Thanks

 Sean


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Re: [PyMOL] print hydrogen bonds involved residues

2011-09-11 Thread Troels Emtekær Linnet
You have to make .pml file and put the python commands inside pymol blocks.

Try look here for an example.

http://www.pymolwiki.org/index.php/Propka#Mutagenesis_analysis

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2011/9/11 lina lina.lastn...@gmail.com



 On Sun, Sep 11, 2011 at 3:59 AM, Thomas Holder 
 spel...@users.sourceforge.net wrote:

 Hi Lina,

 have a look at:
 http://pymolwiki.org/index.**php/Polarpairshttp://pymolwiki.org/index.php/Polarpairs

 it takes two selections and has a state argument.


 Thanks for the link.

 I still have a question:

 1]  save the script as polar_pairs.py
 2] in pymol run polar_pairs.py
 3] For

 pairs = polarpairs('chain A', 'chain B')for p in pairs:
 dist = cmd.get_distance('(%s`%s)' % p[0], '(%s`%s)' % p[1])
 print p, 'Distance: %.2f' % (dist)

 I don't know how to proceed this part, do I need to put those code in
 another .py file?

 sorry and thanks for your patience,


 Cheers,
  Thomas

 lina wrote, On 09/10/11 15:21:

  Hi,

 After dist hb, proA, proB, mode=2

 I can get the hydrogen bonds formation between protein A and protein B.

 But I don't know how to get the detailed involved residues very quickly,
 suppose I have had 10 models in this structure.

 I googled before,
 http://www.mail-archive.com/**pymol-users@lists.sourceforge.**
 net/msg06211.htmlhttp://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg06211.html
 is helpful for the single one selections,
 here I got two.

 Thanks for any suggestions,

 --
 Best Regards,

 lina


 --
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 MPI for Developmental Biology
 Spemannstr. 35
 D-72076 Tübingen




 --
 Best Regards,

 lina




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Re: [PyMOL] Writing a script yo pymol

2011-09-11 Thread Troels Emtekær Linnet
Well, not hard.

I made a script that can rotate a molecule around a line.
And I made a large tutorial to take one through the available functions of
this script.
It is a pymol command file, .pml.

Check out:
http://www.pymolwiki.org/index.php/Rotkit


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Mobil: +49 1577-8944752



2011/9/11 Yotam Avital yota...@gmail.com

 Hi.

 How hard it is to write a (python?) script that will rotate the figure and
 color some atoms? Nothing fancy... I searched a little bit but couldn't find
 a quick and dirty tutorial for script writing.

 Thanks

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Re: [PyMOL] Mutagenesis script

2011-09-04 Thread Troels Emtekær Linnet
So.
cmd.(something) ALWAYS has to be in string format.
So there is the cmd.frame wrong.

Then you dont quit the mutagenesis wizard
And you have a space in the cmd.save

*It total, try:*
#Initialize
fetch 1shr, async=0
create test, 1shr
cmd.wizard(mutagenesis)
cmd.do(refresh_wizard)

# Mutate
cmd.get_wizard().set_mode(HIS)
cmd.get_wizard().do_select(/test//B/36)

cmd.frame(1)
cmd.get_wizard().apply()
cmd.set_wizard(done)

# Save
cmd.save(kill.pdb)

or look at:
http://www.pymolwiki.org/index.php/Rotkit
import rotkit
*mutate test, chain=B, resi=36, target=HIS, mutframe=1*


2011/9/2 Rozaimi Razali rozaimiraz...@gmail.com

 Can someone please explain to me why my script is not working properly?

 #Initialize
 fetch 1shr, async=0
 create test, 1shr
 cmd.wizard(mutagenesis)
 cmd.do(refresh_wizard)

 # Mutate
 cmd.get_wizard().set_mode(HIS)
 cmd.get_wizard().do_select(/test//B/36)

 cmd.frame(1)
 cmd.get_wizard().apply()

 # Save
 cmd.save (kill.pdb)

 Thanks!


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[PyMOL] New script: rotkit: Rotate molecule around line and more script in the kit.

2011-08-30 Thread Troels Emtekær Linnet
Hi PyMOLers.

I was tired, not to be able to load a dye molecule, and put it next to my
protein with full control.
Especially, I needed to be able to rotate my dye molecule around a line,
which is not supported in PyMOL.
So I investigated the PyMOL TTT matrixes, and made some handy scripts.

Check the scripts kit out: rotkit.py http://pymolwiki.org/index.php/Rotkit

I have made there a little tutorial to take one through the functions.

*Available in PyMOL*

   - rotateline(Pos1,Pos2,degangle,molecule): Pos1-Pos2 define a line
   whereabout molecule will be rotated degangle degrees *rotateline
   Pos1=P513C_CA, Pos2=P513C_CB, degangle=5, molecule=Atto590* *rotateline
   Pos1=dyeatom87, Pos2=dyeatom85, degangle=10, molecule=Atto590*
   - mutate(molecule,chain,resi,target=CYS,mutframe=1): Mutate a
   /molecule//chain/resi into a target, and selecting most probable frame 1
   *mutate 1HP1, chain=A, resi=515, target=CYS, mutframe=1*
   - toline(Pos1,Pos2,atom,molecule,dist=1): Translate molecule atom, 1
   angstrom away in the same direction Pos1-Pos2 specify *toline
   Pos1=P513C_CA, Pos2=P513C_CB, atom=dyeatom87, molecule=Atto590, dist=3*

*Available through PyMOL mini shell*

   - printMat(matrix): prints the TTT matrix in a readable format. (4X4)
   - getxyz(Sel): output is a list [x,y,z] in float. The input can be a
   list, a string(list) or a selection.
   - vector(Sel1,Sel2): Finds the vector between points. Gets the xyz list
   from getxyz, so input can be anything.
   - vectorstr(vector): turn a vector in list format into string. No real
   function actually.
   - transmat(vector,dist=1): Makes a TTT translation matrix for according
   to the input vector. The vector is multiplied with dist.
   - unitvector(vector): Make a vector a unitvector.
   - radangle(angle): Convert degree to radians. Not that all input are
   assumed to be in degrees, and are converted automatically.
   - rotmat(angle,vectornorm,pointcoord): This function is the most
   important. That makes the TTT matrix that rotates a molecule around a
   normalized vector, which goes through a coordinate point.
   - crossprod(Vector1, Vector2): Makes a crossproduct between two vectors
   - crosspoint(Pos1, crossprod): Returns the endpoint for the Position plus
   the crossproduct vector. Suitable if one would like to rotate around a
   crossvector.


Best
Troels Emtekær Linnet
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Re: [PyMOL] Run script synchronized

2011-08-28 Thread Troels Emtekær Linnet
Thanks Jason. But still no luck...

So, I changed it to a python script. It was important that the ending of the
file is .py :-)
But, I can see from the list of objects, that PyMOL fetches the next protein
before it has finished propka first.
Does pymol run external script in some kind of asynchron mode as default?

-
import pymol
from pymol import cmd
import os
os.chdir(/homes/linnet/Documents/Speciale/5NT-project/Mutant-construct/predict_reactivity/Comparison/Match)

cmd.cartoon(auto)
cmd.set(cartoon_fancy_helices,1)
cmd.bg_color(white)
cmd.set(fog,0)
cmd.set(cartoon_transparency,0.7)
cmd.set(auto_zoom,off)

import propka
#resis =
[[1bj6,36],[1bj6,39],[1bj6,49],[1ag1,14],[1gu9,133],[1gu9,130],[1omu,56],[1khg,273],[2trx,35],
#[1tde,32],[1tde,35],[2ovo,56],[1m8b,56],[1hic,39],[1m8c,56],[1ppo,25],[1qlp,232]]
resis = [[1ppo,25],[1qlp,232]]
i = 0
results = []
for p,r in resis:
cmd.fetch(p,async=0)
cmd.refresh()
# When we import a module in python, the namespace is normally:
module.function
# And we see, that propka expect resi to be in str format.
# And we don't want the logtime function
pkavalues = propka.propka(molecule=p,resi=r,resn=CYS,logtime=i)
results.append(pkavalues)
cmd.refresh()
i = i + 1
cmd.zoom(all)
print results[0]
print results[1]



2011/8/28 Jason Vertrees jason.vertr...@schrodinger.com

 Hi Troels,

 In PyMOL, it you try the following, what happens for you?

 # make this a file called chill.py
 import time
 def chill():
rightThisSecond = time.time()
i = 0
while time.time()  rightThisSecond + 3.0:
i+=1
print The farthest I could count in 3 seconds was %d. % i

 # make this a file called troels.py
 import pymol
 from pymol import cmd
 import chill
 resis = [ [1bj6,36], [1bj6,39], [1bj6,49],
  [1ag1,14],
   [1gu9,133], [1gu9,130], ]
 for p,r in resis:
# fetch a protein
cmd.fetch(p,async=0)
print -- Fetched %s % p
# do something slow
chill.chill()
# some post processing
print %s has %d atoms % (p, cmd.count_atoms(p))
print %s/%s has %d atoms % (p, r, cmd.count_atoms(%s and i. %s %
 (p,r)))
cmd.delete(p)
print -- Deleted protien


 Now load PyMOL and try,

 run ~/troels.py

 Does PyMOL wait for the chill calls to finish? The idea is, wrap your
 call in a module/file and import it. Then, call through that function.

 It's about 3 AM my time and I'm sure there's a better solution--but
 this might work for now.

 Cheers,

 -- Jason




 2011/8/26 Troels Emtekær Linnet tlin...@gmail.com:
  Well, I cant get it to work.
  Pymol speeds ahead of calling propka.propka
 
  Can you give an example of subprocess?
  ---
 
  import propka
 
  python
  resis = [[1bj6,36],[1bj6,39]]
  #resis =
 
 [[1bj6,36],[1bj6,39],[1bj6,49],[1ag1,14],[1gu9,133],[1gu9,130],[1omu,56],[1khg,273],[2trx,35],
 
 #[1tde,32],[1tde,35],[2ovo,56],[1m8b,56],[1hic,39],[1m8c,56]]
  i = 0
  for resi in resis:
  cmd.fetch(resi[0],async=0)
  cmd.refresh()
  # When we import a module in python, the namespace is normally:
  module.function
  # And we see, that propka expect resi to be in str format.
  # And we don't want the logtime function
  propka.propka(molecule=resi[0],resi=resi[1],logtime=i)
  cmd.refresh()
  i = i + 1
  python end
  zoom all
 
 
  hth
  Martin
 
  On 23.08.11 10:48, Troels Emtekær Linnet wrote:
 
  Hi.
 
  If one writes a pymol script, and calls an external function, the pymol
  script continues its operation before waiting for the success of the
  external function.
 
  Is it possible to give a keyword, so it waits for the external
 function
  before preceding?
 
  Kind of the same function with:
  fetch 1hp1, async=0
 
  Best
  Troels
 
 
 
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