pymol-users Mailing List for PyMOL Molecular Graphics System

dear users,

Since recently, I've got an error message when I try to 'open' a pdb (or
mol2) from the pymol tcl/tk GUI File/Open menu.
No problem when I open directly from the file (doble-clic)

Thanks


Alain

==========
Error: 1
CmdException Exception in Tk callback
  Function: <bound method Normal.file_open of <pmg_tk.skins.normal.Normal
instance at 0x04A9A8A0>> (type: <type 'instancemethod'>)
  Args: ()
Traceback (innermost last):
  File "C:\Program Files\DeLano
Scientific\PyMOL/modules\Pmw\Pmw_1_2\lib\PmwBase.py", line 1747, in
__call__
    return apply(self.func, args)
  File "C:\Program Files\DeLano
Scientific\PyMOL/modules\pmg_tk\skins\normal\__init__.py", line 438, in
file_open
    self.cmd.load(ofile,quiet=0)
  File "C:\Program Files\DeLano
Scientific\PyMOL/modules\pymol\importing.py", line 585, in load
    if _raising(r): raise pymol.CmdException
CmdException: <pymol.CmdException instance at 0x031E51C0>

Thank you all. I haven't tried to re-compile the pymol again yet. But
the pre-compiled version that I tried to install is the newest one. I
guess probably something is not right with my Fedora 6. I will try to
compile it from the source code later.

Nian Huang
Dept. of Biochemsitry
UT Southwestern Medical Center
Dallas, TX 75390

On Nov 25, 2007 12:32 AM, Nian Huang <hua...@gm...> wrote:
> Dear All,
> I tried to install precompiled pymol in Fedora 6, and found out I
> cannot input text. I have compiled pymol by myself before. It seemed
> that the problem was the Tcl/Tk, which didn't function correctly in
> Fedora 6. After replaced it with Active Tcl/Tk, I got a working pymol.
> But it was too bad that I didn't take note. Because I am not good at
> computer, I don't want spend a lot of time again to recompile the
> newest version of pymol. Could somebody provide a working pymol or any
> trick to fix the problem easily?
>
> Nian Huang
> Dept. of Biochemsitry
> UT Southwestern Medical Center
> Dallas, TX 75390
>

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CnJzYW5pc2h2aWxpQGFubC5nb3YNCg0K

Hi,

how is it possible in pymol, given a pdb protein dimer structure to get 
its monomers ?

Thanks

Nian,

We have now tried several Fedora 6 installs, but have been entirely unable
to reproduce this problem.  Therefore, we do not believe that this is a
general issue with PyMOL itself, but rather, with some specific Fedora 6
installations, apparently yours included.

Please confirm that the version of PyMOL you are using is 1.0r2.  If you do
not have it, you should be able to d/l it by going to http://delsci.com/dsc
from any UTSWMC on-campus computer.

Cheers,
Warren

--
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...
 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of Nian Huang
> Sent: Saturday, November 24, 2007 10:32 PM
> To: pym...@li...
> Subject: [PyMOL] Precompiled pymol won't work on Fedora 6
> 
> Dear All,
> I tried to install precompiled pymol in Fedora 6, and found 
> out I cannot input text. I have compiled pymol by myself 
> before. It seemed that the problem was the Tcl/Tk, which 
> didn't function correctly in Fedora 6. After replaced it with 
> Active Tcl/Tk, I got a working pymol.
> But it was too bad that I didn't take note. Because I am not 
> good at computer, I don't want spend a lot of time again to 
> recompile the newest version of pymol. Could somebody provide 
> a working pymol or any trick to fix the problem easily?
> 
> Nian Huang
> Dept. of Biochemsitry
> UT Southwestern Medical Center
> Dallas, TX 75390
> 
> --------------------------------------------------------------
> -----------
> This SF.net email is sponsored by: Microsoft Defy all 
> challenges. Microsoft(R) Visual Studio 2005.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

 
> I have a quick question for you.
> I am trying to look at the structure of the tetranucleosome (pdb file
1zbb).
> However, the structure is only composed by 2 nucleosomes. Is there a way
to duplicate the image to 4?

Based on the BIOMT records in the PDB file:

REMARK 350 BIOMOLECULE: 1
REMARK 350 APPLY THE FOLLOWING TO CHAINS: I, J, A, B, C, D, E, F, G,
REMARK 350 H, a, b, c, d, e, f, g, h
REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000
REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000
REMARK 350   BIOMT1   2 -1.000000  0.000000  0.000000      127.67500
REMARK 350   BIOMT2   2  0.000000  1.000000  0.000000        0.00000
REMARK 350   BIOMT3   2  0.000000  0.000000 -1.000000      237.12600

You can create the biological unit as follows:

# load the PDB file

fetch 1zbb, async=0

# create a copy

create 1zbb_2, 1zbb

# transform the copy according to the second matrix above

alter_state 1, 1zbb_2, (x,y,z)=(127.675-x, y, 237.126-z)

Cheers,
Warren

Hi Mark,

You can also directly change the vdw radius of sodium to its ionic radius:

alter r. na\+,vdw=1.02
rebuild

Cheers,

Tsjerk

On Nov 27, 2007 1:15 AM, Dr. Mark Mayer <ma...@ma...> wrote:

> hello,
>
> Can't find anything about this in docs or in settings:
>
> Where are sphere diameter settings controlled for individual atomic
> species: I'm trying to make fig with  ions and the sizes don't seem
> to be right - Cl too small and Na too big.
>
> Thanks
>
> --
> Mark Mayer Ph.D.
> LCMN NICHD NIH DHHS
> Bldg 35, Room 3B 1002 MSC 3712
> 35 Lincoln Drive
> Bethesda MD 20892 3712
> Phone: 301-496-9346 (office); 301-496-9347 (lab); FAX 301-496-2396
> Lab web site: http://mayerlab.nichd.nih.gov
>
> Send packages, Fedex and anything requiring a signature to:
>
> Bldg 35, Room 3B 1004
> 35 Lincoln Drive
> Bethesda MD 20892
>
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2005.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>



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

Okey, something wierd and I do not understand. I am attaching 2 pdb
files and 2 png's from pymol. 3.pdb, 4.pdb, 3.png and 4.png.

Now the only difference between 3 and 4 are in blank spaces. and the
sphere radius change between the two pdb files. In one Na is bigger
and in other Cl is ..

any ideas??.. bug or feature!!

On Nov 26, 2007 5:53 PM, Mayer, Mark (NIH/NICHD) [E]
<ma...@ma...> wrote:
> Thanks Abhinav,
>
> No other  posts yet; you are probably right that these are VDW values,
> but nice to know for sure, and also good to be able to change to ionic
> radii if desired.
>
>
>
> -----Original Message-----
> From: Abhinav Verma [mailto:abh...@gm...]
> Sent: Mon 11/26/2007 7:35 PM
> To: Mayer, Mark (NIH/NICHD) [E]
> Cc: pym...@li...
> Subject: Re: [PyMOL] sphere diameter
>
> set sphere_scale should scale the spheres, but they should be
> proportionate and they are van der waal spheres I guess, so chlorine
> is smaller than soduim..
> http://pt.chemicalstore.com/
> 227 vs 175 pm for na and cl respecively.
>
>
>
> On Nov 26, 2007 4:15 PM, Dr. Mark Mayer <ma...@ma...> wrote:
> > hello,
> >
> > Can't find anything about this in docs or in settings:
> >
> > Where are sphere diameter settings controlled for individual atomic
> > species: I'm trying to make fig with  ions and the sizes don't seem
> > to be right - Cl too small and Na too big.
> >
> > Thanks
> >
> > --
> > Mark Mayer Ph.D.
> > LCMN NICHD NIH DHHS
> > Bldg 35, Room 3B 1002 MSC 3712
> > 35 Lincoln Drive
> > Bethesda MD 20892 3712
> > Phone: 301-496-9346 (office); 301-496-9347 (lab); FAX 301-496-2396
> > Lab web site: http://mayerlab.nichd.nih.gov
> >
> > Send packages, Fedex and anything requiring a signature to:
> >
> > Bldg 35, Room 3B 1004
> > 35 Lincoln Drive
> > Bethesda MD 20892
> >
> >
> > -------------------------------------------------------------------------
> > This SF.net email is sponsored by: Microsoft
> > Defy all challenges. Microsoft(R) Visual Studio 2005.
> > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
>
>
>
> --
> Abhianv Verma
> Research Associate,
> Daggett Lab, Dept. of Medicinal Chemistry,
> University of Washington,
> Seattle, WA, 98195-7610  USA
>
>



-- 
Abhianv Verma
Research Associate,
Daggett Lab, Dept. of Medicinal Chemistry,
University of Washington,
Seattle, WA, 98195-7610  USA

set sphere_scale should scale the spheres, but they should be
proportionate and they are van der waal spheres I guess, so chlorine
is smaller than soduim..
http://pt.chemicalstore.com/
227 vs 175 pm for na and cl respecively.



On Nov 26, 2007 4:15 PM, Dr. Mark Mayer <ma...@ma...> wrote:
> hello,
>
> Can't find anything about this in docs or in settings:
>
> Where are sphere diameter settings controlled for individual atomic
> species: I'm trying to make fig with  ions and the sizes don't seem
> to be right - Cl too small and Na too big.
>
> Thanks
>
> --
> Mark Mayer Ph.D.
> LCMN NICHD NIH DHHS
> Bldg 35, Room 3B 1002 MSC 3712
> 35 Lincoln Drive
> Bethesda MD 20892 3712
> Phone: 301-496-9346 (office); 301-496-9347 (lab); FAX 301-496-2396
> Lab web site: http://mayerlab.nichd.nih.gov
>
> Send packages, Fedex and anything requiring a signature to:
>
> Bldg 35, Room 3B 1004
> 35 Lincoln Drive
> Bethesda MD 20892
>
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2005.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>



-- 
Abhianv Verma
Research Associate,
Daggett Lab, Dept. of Medicinal Chemistry,
University of Washington,
Seattle, WA, 98195-7610  USA

hello,

Can't find anything about this in docs or in settings:

Where are sphere diameter settings controlled for individual atomic 
species: I'm trying to make fig with  ions and the sizes don't seem 
to be right - Cl too small and Na too big.

Thanks

-- 
Mark Mayer Ph.D.
LCMN NICHD NIH DHHS
Bldg 35, Room 3B 1002 MSC 3712
35 Lincoln Drive
Bethesda MD 20892 3712
Phone: 301-496-9346 (office); 301-496-9347 (lab); FAX 301-496-2396
Lab web site: http://mayerlab.nichd.nih.gov

Send packages, Fedex and anything requiring a signature to:

Bldg 35, Room 3B 1004
35 Lincoln Drive
Bethesda MD 20892

Hi,

one of us just bought a 3Dconnexion SpaceNavigator.
There is no problem to install the base software on Linux, but how to
use it in pymol?
-- 
Joachim Reichelt

Dear Nian,

on my Fedora 6 system there was absolutely no problem compiling and 
later running PyMOL.  Here's the rundown:

Get Pmw from sf.net, unpack and put into python site-packages directory, 
eg. /usr/lib/python2.5/site-packages/Pmw.  In Pmw1.3, there is a 
setup.py that professes to do this automagically.  I had errors with 
'python setup.py install' so I did it manually after all.  Get Numeric 
from sf.net and install the same way.  I didn't try to make it work with 
NumPy, which apparently supersedes Numeric.

Then you need to 'yum install freetype-devel freeglut-devel libpng-devel'.

After that, 'python setup.py build', 'python setup.py install', and 
'python setup2.py install'.

Tell me if that's not working smoothly.


Andreas


Nian Huang wrote:
> Dear All,
> I tried to install precompiled pymol in Fedora 6, and found out I
> cannot input text. I have compiled pymol by myself before. It seemed
> that the problem was the Tcl/Tk, which didn't function correctly in
> Fedora 6. After replaced it with Active Tcl/Tk, I got a working pymol.
> But it was too bad that I didn't take note. Because I am not good at
> computer, I don't want spend a lot of time again to recompile the
> newest version of pymol. Could somebody provide a working pymol or any
> trick to fix the problem easily?
> 
> Nian Huang
> Dept. of Biochemsitry
> UT Southwestern Medical Center
> Dallas, TX 75390
> 

Dear All,
I tried to install precompiled pymol in Fedora 6, and found out I
cannot input text. I have compiled pymol by myself before. It seemed
that the problem was the Tcl/Tk, which didn't function correctly in
Fedora 6. After replaced it with Active Tcl/Tk, I got a working pymol.
But it was too bad that I didn't take note. Because I am not good at
computer, I don't want spend a lot of time again to recompile the
newest version of pymol. Could somebody provide a working pymol or any
trick to fix the problem easily?

Nian Huang
Dept. of Biochemsitry
UT Southwestern Medical Center
Dallas, TX 75390

On Thu, 22 Nov 2007 22:43:27 -0800 (PST), JJ <jos...@ya...> wrote:

> 
> >>
> From: Robert Campbell <robert.campbell@qu...> -
> 2007-11-22 21:56
> 
> Rather than use PyMOL's surface, I've used the
> triangulated surface output
> by Michel Sanner's msms program. <<
> 
> Thanks much Rob.  Can you please tell me why it might
> be better to use msms to calculate surface points
> rather than the pymol algorithm.  Are there advantages
> to one or the other?

Simply that the msms program already could write out a file of the
vertices.  It was easier than trying to sift through the PyMOL code.

And later John wrote:
> I should have also asked in my original post, is there a way in pymol to
> determine the solvent-accessible surface  for a particular atom? Or more
> to the point, identify the atoms that shape the solvent-accessible
> surface and the percent of the surface attributed to each?

That's what I use my "msms_pymol.py" script for.  It creates a temporary
PDB file from an object, pipes that through a pdb_to_xyzrn awk script (I
modified the original msms version to include chain IDs) and feeds that to
msms to create a file containing areas for each atom.  The msms_pymol.py
script can include a selection, such that the total area for just that
selection is calculated (e.g. for looking at interfaces).  You can also
pre-calculate the area file with msms and feed that file to msms_pymol.py
with the "file_name" option. E.g.

After using:
PyMOL> run msms_pymol.py
to load the script into pymol,

type:
PyMOL> calc_msms_area object_name, file_name=object.area, selection=resi
PyMOL> 10-20

This will report the area for residues 10-20 from the pre-calculated file
"object.area"

Another example:
PyMOL> calc_msms_area enzyme, enzyme within 5 of inhibitor

will take the "enzyme" object, create a PDB file, feed that to msms and
then sum up the area only for the atoms of the "enzyme" object that are
within 5A of the atoms of the "inhibitor" object.

It is important in this case to have the enzyme and inhibitor as two
object, so that the surface at the interface between them is calculated
(true for both msms and PyMOL's own surface calculation).

Get this from:
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/msms_pymol.py
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/pdb_to_xyzrn

My surface complementarity/similarity scripts are now up at:

http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/

They are in python because it is easy for me, but they would no doubt run
much faster if written in C.  If anybody wants to do that, I'd be happy to
hear about it!

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821            Fax: 613-533-2497
<rob...@qu...>    http://pldserver1.biochem.queensu.ca/~rlc

Just as a matter of general philosophy:  PyMOL is primarily intended as a
display program and communications program, with (admittedly) rather limited
emphasis placed on rigorous analysis and generation of quantitative
information.  There's only so much time in the day, so we have to choose our
battles and set our priorities.  

The ongoing vision for core PyMOL is that remain firmly anchored the
visualization realm while leveraging Python to easily link out to rigorous
tools that specialize in various forms of number-crunching and analysis --
written by teams of people who make rigor their top priority.  Examples
include GROMACS, MMTK, APBS, Rosetta, Modeller, DSSP, MSMS, PHENIX, CCP4,
Maestro, MOE, Discovery Studio, and so on.

--
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...
 
"Not yet a PyMOL Subscriber, but want to support the project?  Email
sa...@de... to quote your lab, school, or employer.  Thank you for
sponsoring this open-source endeavor!" -WLD
 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of JJ
> Sent: Thursday, November 22, 2007 10:43 PM
> To: pym...@li...
> Subject: Re: [PyMOL] obtaining coordinates of solvent-surface points
> 
> 
> >>
> From: Robert Campbell <robert.campbell@qu...> -
> 2007-11-22 21:56
> 
> Rather than use PyMOL's surface, I've used the triangulated 
> surface output by Michel Sanner's msms program. <<
> 
> Thanks much Rob.  Can you please tell me why it might be 
> better to use msms to calculate surface points rather than 
> the pymol algorithm.  Are there advantages to one or the other?
> 
> John
> 
> 
> 
> 
> 
> 
>       
> ______________________________________________________________
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>>
From: JJ <josh8912@ya...> - 2007-11-22 20:36
Hello:
Im new at pymol and would like to obtain the
coordinates of the dots that make up the
solvent-accessible surface.<<

I should have also asked in my original post, is there
a way in pymol to determine the solvent-accessible
surface  for a particular atom? Or more to the point,
identify the atoms that shape the solvent-accessible
surface and the percent of the surface attributed to
each?

Thanks,  
John 


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>>
From: Robert Campbell <robert.campbell@qu...> -
2007-11-22 21:56

Rather than use PyMOL's surface, I've used the
triangulated surface output
by Michel Sanner's msms program. <<

Thanks much Rob.  Can you please tell me why it might
be better to use msms to calculate surface points
rather than the pymol algorithm.  Are there advantages
to one or the other?

John






      ____________________________________________________________________________________
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Make Yahoo! your homepage.
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Dear all,
   I would like to know if there is a way to measure between surfaces 
(actually two parts of one surface) in pymol or another program.  We would 
like to measure the active site of our enzyme structure, and noticed that 
authors of related structures had done this type of measurement with GRASP 
surfaces.  
   I apologize if this question is too simple, since I am still not that 
familiar with all of pymol's facilities.
   Thank you for any suggestions,
    Jim

-----Original Message-----
From: Robert Campbell <rob...@qu...>
To: pym...@li...
Date: Thu, 22 Nov 2007 16:56:01 -0500
Subject: Re: [PyMOL] obtaining coordinates of solvent-surface points

> Hello John,
> 
> On Thu, 22 Nov 2007 12:36:32 -0800 (PST), JJ <jos...@ya...>
> wrote:
> 
> > Hello:
> > Im new at pymol and would like to obtain the
> > coordinates of the dots that make up the
> > solvent-accessible surface.  I can obtain the vertices
> > using cmd.get_povray()[1], but that will give me a
> > list of coordinates of open cylinders with spheres at
> > either end.  Perhaps these sphere and cylinders are so
> > small that I could use any of them as the coordinates
> > for the surface dot. Or, would it be more exact to use
> > the midpoint of the cylinder?  Any suggestions?
> 
> Rather than use PyMOL's surface, I've used the triangulated surface
> output
> by Michel Sanner's msms program.  I've written a few python scripts
> that
> allow various manipulations.  Just today, in fact, I wrote a script to
> calculate surface areas from within PyMOL.  I also have previously
> written some python code that does a calculation similar to the CCP4
> program "sc" (surface complementarity).  This allows me to colour the
> surface of, for example, an inhibitor according to how complementarity
> it is to an enzyme active site.  I hadn't added these to my PyMOL
> scripts
> web page, but I will do so now.  Look for "msms_pymol.py" at
> 
>   http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/
> 
> Of course, one needs to obtain msms, but that can be simply found at
> 
>   http://mgltools.scripps.edu/downloads
> 
> The msms_complementarity calculation is done outside pymol and the
> resulting vertex and triangle files are read by a separate script to
> create
> a CGO representation of the msms surface.  I'll get those up on the web
> site tomorrow, perhaps.
> 
> Cheers,
> Rob
> -- 
> Robert L. Campbell, Ph.D.
> Senior Research Associate/Adjunct Assistant Professor 
> Botterell Hall Rm 644
> Department of Biochemistry, Queen's University, 
> Kingston, ON K7L 3N6  Canada
> Tel: 613-533-6821            Fax: 613-533-2497
> <rob...@qu...>   
> http://pldserver1.biochem.queensu.ca/~rlc
> 
> -----------------------------------------------------------------------
> --
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2005.
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> _______________________________________________
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> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

'turn z, 270'

(sorry)

On Tue, 20 Nov 2007, Vincent Chaptal wrote:

     Hello,
     
     I am trying to make a picture for a cover and I am wondering how to make 
     a vertical image.
     (Pymol creates horizontal images, and journal covers are vertical)
     Is there a way to creates those vertical images other than turning the 
     image 90 degrees with the 'turn z, 90' command?
     
     thanks
     vincent
     
     
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     ----------------------------------------------------------
     
     
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     IMPORTANT WARNING:  This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential.  You, the recipient, are obligated to maintain it in a safe, secure and confidential manner.  Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the recipient, please immediately notify us by return email, and delete this message from your computer.
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     ------------------------------
     

Hello John,

On Thu, 22 Nov 2007 12:36:32 -0800 (PST), JJ <jos...@ya...>
wrote:

> Hello:
> Im new at pymol and would like to obtain the
> coordinates of the dots that make up the
> solvent-accessible surface.  I can obtain the vertices
> using cmd.get_povray()[1], but that will give me a
> list of coordinates of open cylinders with spheres at
> either end.  Perhaps these sphere and cylinders are so
> small that I could use any of them as the coordinates
> for the surface dot. Or, would it be more exact to use
> the midpoint of the cylinder?  Any suggestions?

Rather than use PyMOL's surface, I've used the triangulated surface output
by Michel Sanner's msms program.  I've written a few python scripts that
allow various manipulations.  Just today, in fact, I wrote a script to
calculate surface areas from within PyMOL.  I also have previously
written some python code that does a calculation similar to the CCP4
program "sc" (surface complementarity).  This allows me to colour the
surface of, for example, an inhibitor according to how complementarity
it is to an enzyme active site.  I hadn't added these to my PyMOL scripts
web page, but I will do so now.  Look for "msms_pymol.py" at

  http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/

Of course, one needs to obtain msms, but that can be simply found at

  http://mgltools.scripps.edu/downloads

The msms_complementarity calculation is done outside pymol and the
resulting vertex and triangle files are read by a separate script to create
a CGO representation of the msms surface.  I'll get those up on the web
site tomorrow, perhaps.

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821            Fax: 613-533-2497
<rob...@qu...>    http://pldserver1.biochem.queensu.ca/~rlc

Hello:
Im new at pymol and would like to obtain the
coordinates of the dots that make up the
solvent-accessible surface.  I can obtain the vertices
using cmd.get_povray()[1], but that will give me a
list of coordinates of open cylinders with spheres at
either end.  Perhaps these sphere and cylinders are so
small that I could use any of them as the coordinates
for the surface dot. Or, would it be more exact to use
the midpoint of the cylinder?  Any suggestions?

Thanks,
John 


      ____________________________________________________________________________________
Be a better sports nut!  Let your teams follow you 
with Yahoo Mobile. Try it now.  http://mobile.yahoo.com/sports;_ylt=At9_qDKvtAbMuh1G1SQtBI7ntAcJ

iterate name, print chain,resi,name

# or if you want to get really fancy, you can do something 
# where iterate calls another PyMOL method:

load $TUT/1hpv.pdb

# NOTE the following text should all appear one line

iterate A/50/CA around 5, print
chain,resi,name,cmd.get_distance("A/50/CA","///%s/%s/%s"%(chain,resi,name))

Cheers,
Warren

 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of Wiktor Jurkowski
> Sent: Wednesday, November 21, 2007 2:48 AM
> To: pym...@li...
> Subject: [PyMOL] selection print out
> 
> How to list residues within given selection? E.g. if I have selection:
> select name, resi 134 around 4.0
> How to get details about atoms, residues which could be used 
> by extrenal code or just copied to text file? 
> Wiktor
> 
> 
> --------------------------------------------------------------
> -----------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2005.
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> https://lists.sourceforge.net/lists/listinfo/pymol-users

How to list residues within given selection? E.g. if I have selection:
select name, resi 134 around 4.0 
How to get details about atoms, residues which could be used by extrenal
code or just copied to text file? 
Wiktor

Try the command "png filename.png, 1200, 1600, -1, 1" to create an 
output image 1200 pixels wide by 1600 pixels tall, raytraced. To disable 
raytracing, change the last argument to zero.

Cheers,

-- 
------------------------------------------------------------------------
Roger S. Rowlett
Professor
Colgate University Presidential Scholar
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rro...@ma...

Vincent Chaptal wrote:
> Hello,
>
> I am trying to make a picture for a cover and I am wondering how to make 
> a vertical image.
> (Pymol creates horizontal images, and journal covers are vertical)
> Is there a way to creates those vertical images other than turning the 
> image 90 degrees with the 'turn z, 90' command?
>
> thanks
> vincent
>
>
> ----------------------------------------------------------
> IMPORTANT WARNING:  This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential.  You, the recipient, are obligated to maintain it in a safe, secure and confidential manner.  Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the recipient, please immediately notify us by return email, and delete this message from your computer.
> ----------------------------------------------------------
>
>
> ----------------------------------------------------------
> IMPORTANT WARNING:  This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential.  You, the recipient, are obligated to maintain it in a safe, secure and confidential manner.  Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the recipient, please immediately notify us by return email, and delete this message from your computer.
> ----------------------------------------------------------
>
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2005.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>   

Hello,

I am trying to make a picture for a cover and I am wondering how to make 
a vertical image.
(Pymol creates horizontal images, and journal covers are vertical)
Is there a way to creates those vertical images other than turning the 
image 90 degrees with the 'turn z, 90' command?

thanks
vincent


----------------------------------------------------------
IMPORTANT WARNING:  This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential.  You, the recipient, are obligated to maintain it in a safe, secure and confidential manner.  Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the recipient, please immediately notify us by return email, and delete this message from your computer.
----------------------------------------------------------


----------------------------------------------------------
IMPORTANT WARNING:  This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential.  You, the recipient, are obligated to maintain it in a safe, secure and confidential manner.  Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the recipient, please immediately notify us by return email, and delete this message from your computer.
----------------------------------------------------------