pymol-users Mailing List for PyMOL Molecular Graphics System

Hi Warren,

I would be interested to see the OpenGL version implemented, despite the
lack of raytracing support. In a pinch the draw command could just be
sufficient to produce a good picture.

As for the implementation in a raytracer context I second Tsjerk's and
Harry's thoughts on the subject. Probably some sort of PovRay based
implementation would help in the interim. What I find most challenging
with that approach is the fact that the placement of the clipping
objects is difficult to achieve in PovRay since it lacks the
interactivity of a graphics program. I.e. finding the right cut through
a protein surface when depicting a ligand in a cut-away surface is
tough. Although there are other ways to achieve this they require some
"cheating" or creative use of Photoshop/PowerPoint to phrase it
differently. 
I am thinking that if it would be possible to write out the orientation
of the clipping planes/slabs as PovRay objects, they could be used as
bounding objects in PovRay. Since the placement of the clipping planes
is easily achieved in Pymol this could be done interactively. All the
user has to do is to associate clipping plane(s) with a graphics object,
place the planes and write out the corresponding PovRay code of the
object and the planes. Of course the code of the clipping objects needs
to be separate from the other stuff, so expanding the "PovRay tuple"
into (matrix,clipping,data) parts would help. 
Getting it all together requires some knowledge of PovRay but examples
in the Wiki should help to get over the initial pain. 

Any thoughts on this approach?

Carsten


> -----Original Message-----
> From: Warren DeLano [mailto:wa...@de...]
> Sent: Wednesday, April 29, 2009 10:36 PM
> To: Mankin Alexander; pym...@li...
> Subject: Re: [PyMOL] object-specific Z-clipping
> 
> Sorry, still not done (I have made two attempts, but both failed).
> 
> While OpenGL supports arbitrary clipping planes, accomplishing this
> correctly in the ray tracer is a much harder problem that one might
> think...
> 
> Cheers,
> Warren
> 
> > -----Original Message-----
> > From: Mankin Alexander [mailto:sh...@ui...]
> > Sent: Wednesday, April 29, 2009 6:18 AM
> > To: pym...@li...
> > Subject: [PyMOL] object-specific Z-clipping
> >
> > Dear all,
> > Does anyone know whether object-selective z-clipping has been
> > implemented in the newer Pymol version(s)? If not, has anyone found
> > any solution around (since 2002 no new threads on the matter)?
> > Thanks,
> > Shura Mankin
> >
> 
> 
> 
>
-----------------------------------------------------------------------
> -------
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Hi,

This is about the way I do it :) To make life easier, I have a
function to write the POV-Ray file in two pieces, using an #include
statement to include the object description in the overall scene setup
file. I've found this much easier to work with, since it allows to
change the light and camera and such much quicker than editing a
multi-Mb file, and the object description is easily modified with
sed/awk. But what it comes down to is memorizing this one line to
export your (part of a) scene to a POV-Ray include file:

open("part.inc","w").write(cmd.get_povray()[1])

Or to make it even easier:

def writepov(x="povray.inc"): open(x,"w").write(cmd.get_povray()[1])
cmd.extend("writepov", writepov)

Hope it helps,

Tsjerk

On Thu, Apr 30, 2009 at 8:48 AM, Harry M. Greenblatt
<Har...@we...> wrote:
> BS"D
>    There is a  workaround to this problem, which I used in a different
> program and have suggested in the past to Warren and others.  If getting the
> ray tracer to recognize the various clipping planes is difficult, this is
> probably the best solution.  It would be helpful, however, if Warren changed
> the POVray input files that are created by PyMOL a bit.
>     One can set up all the various parts of the picture, and then
> selectively show each element and clip it, with the others hidden.  Then
> output a POVray file.  This should only include the visible elements
> (correct, Warren?).  Hide this element, and show the next one, adjust the
> clipping plane, and output the POVray file.  One can then have a master
> POVray file which contains as many "include" statements as are needed to
> bring all the various elements together in one rendered image.
>   The difficulty in the current implementation of PyMOL is that the output
> for POVray contains both the scene definitions and the graphic primitives in
> one messy and potentially large file.  If the scene definitions could be
> stored in one small file, and the graphic primitives in another file, this
> process would be much easier.  One could then select one of the scene
> definitions files as the "master" and add "include" statements for all the
> graphic primitives as is needed.  I suppose this process is possible with
> the current POVray files, just not as simple.  I have examples if anybody is
> interested.
>
> Harry
>
> Sorry, still not done (I have made two attempts, but both failed).
> While OpenGL supports arbitrary clipping planes, accomplishing this
> correctly in the ray tracer is a much harder problem that one might
> think...
> Cheers,
> Warren
>
> -----Original Message-----
> From: Mankin Alexander [mailto:sh...@ui...]
> Sent: Wednesday, April 29, 2009 6:18 AM
> To: pym...@li...
> Subject: [PyMOL] object-specific Z-clipping
> Dear all,
> Does anyone know whether object-selective z-clipping has been
> implemented in the newer Pymol version(s)? If not, has anyone found
> any solution around (since 2002 no new threads on the matter)?
> Thanks,
> Shura Mankin
>
>
>
> ------------------------------------------------------------------------------
> Register Now & Save for Velocity, the Web Performance & Operations
> Conference from O'Reilly Media. Velocity features a full day of
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> leaders in dedicated Performance & Operations tracks. Use code vel09scf
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> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
> -------------------------------------------------------------------------
>
> Harry M. Greenblatt
>
> Associate Staff Scientist
>
> Dept of Structural Biology           har...@we...
>
> Weizmann Institute of Science        Phone:  972-8-934-3625
>
> Rehovot, 76100                       Facsimile:   972-8-934-4159
>
> Israel
>
>
>
> ------------------------------------------------------------------------------
> Register Now & Save for Velocity, the Web Performance & Operations
> Conference from O'Reilly Media. Velocity features a full day of
> expert-led, hands-on workshops and two days of sessions from industry
> leaders in dedicated Performance & Operations tracks. Use code vel09scf
> and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf
> _______________________________________________
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> 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

BS"D

    There is a  workaround to this problem, which I used in a  
different program and have suggested in the past to Warren and  
others.  If getting the ray tracer to recognize the various clipping  
planes is difficult, this is probably the best solution.  It would be  
helpful, however, if Warren changed the POVray input files that are  
created by PyMOL a bit.
     One can set up all the various parts of the picture, and then  
selectively show each element and clip it, with the others hidden.   
Then output a POVray file.  This should only include the visible  
elements (correct, Warren?).  Hide this element, and show the next  
one, adjust the clipping plane, and output the POVray file.  One can  
then have a master POVray file which contains as many "include"  
statements as are needed to bring all the various elements together  
in one rendered image.

   The difficulty in the current implementation of PyMOL is that the  
output for POVray contains both the scene definitions and the graphic  
primitives in one messy and potentially large file.  If the scene  
definitions could be stored in one small file, and the graphic  
primitives in another file, this process would be much easier.  One  
could then select one of the scene definitions files as the "master"  
and add "include" statements for all the graphic primitives as is  
needed.  I suppose this process is possible with the current POVray  
files, just not as simple.  I have examples if anybody is interested.


Harry

> Sorry, still not done (I have made two attempts, but both failed).
>
> While OpenGL supports arbitrary clipping planes, accomplishing this
> correctly in the ray tracer is a much harder problem that one might
> think...
>
> Cheers,
> Warren
>
>> -----Original Message-----
>> From: Mankin Alexander [mailto:sh...@ui...]
>> Sent: Wednesday, April 29, 2009 6:18 AM
>> To: pym...@li...
>> Subject: [PyMOL] object-specific Z-clipping
>>
>> Dear all,
>> Does anyone know whether object-selective z-clipping has been
>> implemented in the newer Pymol version(s)? If not, has anyone found
>> any solution around (since 2002 no new threads on the matter)?
>> Thanks,
>> Shura Mankin
>>
>
>
>
> ---------------------------------------------------------------------- 
> --------
> Register Now & Save for Velocity, the Web Performance & Operations
> Conference from O'Reilly Media. Velocity features a full day of
> expert-led, hands-on workshops and two days of sessions from industry
> leaders in dedicated Performance & Operations tracks. Use code  
> vel09scf
> and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

------------------------------------------------------------------------ 
-
Harry M. Greenblatt
Associate Staff Scientist
Dept of Structural Biology           har...@we...
Weizmann Institute of Science        Phone:  972-8-934-3625
Rehovot, 76100                       Facsimile:   972-8-934-4159
Israel

Sorry, still not done (I have made two attempts, but both failed).

While OpenGL supports arbitrary clipping planes, accomplishing this
correctly in the ray tracer is a much harder problem that one might
think...

Cheers,
Warren

> -----Original Message-----
> From: Mankin Alexander [mailto:sh...@ui...]
> Sent: Wednesday, April 29, 2009 6:18 AM
> To: pym...@li...
> Subject: [PyMOL] object-specific Z-clipping
> 
> Dear all,
> Does anyone know whether object-selective z-clipping has been
> implemented in the newer Pymol version(s)? If not, has anyone found
> any solution around (since 2002 no new threads on the matter)?
> Thanks,
> Shura Mankin
> 

Whoops, my bad -- I duped the approval before seeing your repost!  

Answer:


# first create a phony molecular trajectory

load $PYMOL_PATH/test/dat/pept.pdb, obj

for a in range(2,31): cmd.create("obj","obj",1,a)

unbond 5/c, 6/n

protect not ((5/c or 6/n) extend 4)

sculpt_activate obj, 30

sculpt_iterate obj, 30, 100

smooth obj, 30, 3



# then program a bond-break/re-form movie

mset 1 x30 1 -30 30 x30 30 -1 

mdo 45: unbond 5/c, 6/n, quiet=1

mdo 100: bond 5/c, 6/n, quiet=1

frame 100

as sticks

orient 5-6/n+ca+c

mplay


# NOTE: only tested on PyMOL 1.2.x

Cheers,
warren

> -----Original Message-----
> From: Guilherme Menegon Arantes [mailto:gar...@iq...]
> Sent: Wednesday, April 29, 2009 6:44 PM
> To: pym...@li...
> Subject: [PyMOL] form and break bonds in movie
> 
> 
> Hi there,
> 
> I would like to produce a movie where bonds break and form. However,
> when I load the .pdb files in PyMOL, the bond status (formed or broken)
> stays the same as seen for the first state, even if the bond
> lenghts change considerably.
> 
> Any tips on how to do this are welcome. I have goggled and searched the
> archives, but found nothing.
> 
> Greetings,
> 
> G
> 
> --
> 
> Guilherme Menegon Arantes, PhD       São Paulo, Brasil
> ______________________________________________________
> 
> 
> --------------------------------------------------------------------------
> ----
> Register Now & Save for Velocity, the Web Performance & Operations
> Conference from O'Reilly Media. Velocity features a full day of
> expert-led, hands-on workshops and two days of sessions from industry
> leaders in dedicated Performance & Operations tracks. Use code vel09scf
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> _______________________________________________
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> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 
> 
> 

Hi there,

First post here, so hello to everybody!

I would like to produce a movie where covalent bonds break and form. 
However, when I load the .pdb files in PyMOL and play a movie, the bond 
status (formed or broken) stays the same as seen on the first state, 
even if bond lenghts change considerably. 

Any tips on how to do this are welcome. I have googled and searched the 
archives, but found nothing. 

Greetings,

G

--

Guilherme Menegon Arantes, PhD       São Paulo, Brasil
______________________________________________________

Hi there,

I would like to produce a movie where bonds break and form. However,
when I load the .pdb files in PyMOL, the bond status (formed or broken)
stays the same as seen for the first state, even if the bond
lenghts change considerably. 

Any tips on how to do this are welcome. I have goggled and searched the 
archives, but found nothing. 

Greetings,

G

--

Guilherme Menegon Arantes, PhD       São Paulo, Brasil
______________________________________________________

Dear all,
Does anyone know whether object-selective z-clipping has been  
implemented in the newer Pymol version(s)? If not, has anyone found   
any solution around (since 2002 no new threads on the matter)?
Thanks,
Shura Mankin

Folks,

Thanks to mail-archive.com, the PyMOL-Users list is now once again
searchable:

http://www.mail-archive.com/pym...@li...

The new search syntax is summarized at:

http://www.mail-archive.com/faq.html#search

For example, you can now quickly identify all 22 posts which have
discussed "surface area":

http://www.mail-archive.com/search?l=p...@li...&q
=%22surface+area%22

Or you can check out Tsjerk's ~170+ helpful contributions to the list
over the past six years:

http://www.mail-archive.com/search?l=p...@li...&q
=from%3AWassenaar

Please everyone get in the habit of consulting this archive before
posting questions which may have the potential for being
frequently-asked.  There are nearly 7,000 posts at your beck and call.

Cheers,
Warren

Jan,

Perform the structure alignment after loading the structure and map:

load 1zziA_pbeq.pdb
load 1zziA_pbeq.dx, 1zziA_map 

# add

load target.pdb

align 1zziA_pbeq////CA, target////CA

matrix_copy 1zziA_pbeq, 1zziA_map

# Then continue with the rest of your script.

Cheers,
Warren

> -----Original Message-----
> From: Jan Kosinski [mailto:ko...@ge...] 
> Sent: Tuesday, April 28, 2009 8:03 AM
> To: Carlos Huerta
> Cc: pym...@li...
> Subject: Re: [PyMOL] rotating map
> 
> I cannot do that, because the CHARMM-GUI server that I use 
> for calculating the electrostatic potential changes the 
> orientation of the input structures (I reported that to the authors).
> 
> Cheers,
> Janek
> 
> Carlos Huerta wrote:
> > Janek,
> >
> > You need to align your structure with the reference, then 
> re-calculate the electrostatic potentials.
> >
> > Sincerely,
> >
> > Carlos
> >
> >   
> >>>> Jan Kosinski <ko...@ge...> 04/28/09 9:04 AM >>>
> >>>>         
> > I am visualizing in PyMol electrostatic potential generated by PBEQ 
> > Solver from CHARMM-GUI at 
> > http://www.charmm-gui.org/?doc=input/pbeqsolver
> >
> > The maps loads and colors nicely with the following 
> commands suggested 
> > by the PBEQ Solver server:
> > load 1zziA_pbeq.pdb
> > load 1zziA_pbeq.dx, 1zziA_map
> > show surface, 1zziA_pbeq
> > ramp_new 1zziA_elvl, 1zziA_map,[-2,0,2] set surface_color, 
> 1zziA_elvl, 
> > 1zziA_pbeq set surface_solvent, 1, 1zziA_pbeq
> >
> > Now I want to fit my structure to some reference one using super or 
> > align commands. As expected, the map no longer works, I cannot 
> > re-generate the original coloring after fitting. I suppose 
> that I need 
> > to change the orientation of the map accordingly to the rotation of 
> > the structure. But... how to do that? Is it at all possible?
> >
> > Cheers,
> > Janek
> >
> > 
> ----------------------------------------------------------------------
> > -------- Register Now & Save for Velocity, the Web Performance & 
> > Operations Conference from O'Reilly Media. Velocity features a full 
> > day of expert-led, hands-on workshops and two days of sessions from 
> > industry leaders in dedicated Performance & Operations tracks. Use 
> > code vel09scf and Save an extra 15% before 5/3. 
> > http://p.sf.net/sfu/velocityconf 
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
> >
> >
> >
> >   
> 
> 
> --------------------------------------------------------------
> ----------------
> Register Now & Save for Velocity, the Web Performance & 
> Operations Conference from O'Reilly Media. Velocity features 
> a full day of expert-led, hands-on workshops and two days of 
> sessions from industry leaders in dedicated Performance & 
> Operations tracks. Use code vel09scf and Save an extra 15% 
> before 5/3. http://p.sf.net/sfu/velocityconf 
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 
> 
> 
> 
> 

I cannot do that, because the CHARMM-GUI server that I use for 
calculating the electrostatic potential changes the orientation of the 
input structures (I reported that to the authors).

Cheers,
Janek

Carlos Huerta wrote:
> Janek,
>
> You need to align your structure with the reference, then re-calculate the electrostatic potentials.
>
> Sincerely,
>
> Carlos
>
>   
>>>> Jan Kosinski <ko...@ge...> 04/28/09 9:04 AM >>>
>>>>         
> I am visualizing in PyMol electrostatic potential generated by PBEQ 
> Solver from CHARMM-GUI at http://www.charmm-gui.org/?doc=input/pbeqsolver
>
> The maps loads and colors nicely with the following commands suggested 
> by the PBEQ Solver server:
> load 1zziA_pbeq.pdb
> load 1zziA_pbeq.dx, 1zziA_map
> show surface, 1zziA_pbeq
> ramp_new 1zziA_elvl, 1zziA_map,[-2,0,2]
> set surface_color, 1zziA_elvl, 1zziA_pbeq
> set surface_solvent, 1, 1zziA_pbeq
>
> Now I want to fit my structure to some reference one using super or 
> align commands. As expected, the map no longer works, I cannot 
> re-generate the original coloring after fitting. I suppose that I need 
> to change the orientation of the map accordingly to the rotation of the 
> structure. But... how to do that? Is it at all possible?
>
> Cheers,
> Janek
>
> ------------------------------------------------------------------------------
> Register Now & Save for Velocity, the Web Performance & Operations 
> Conference from O'Reilly Media. Velocity features a full day of 
> expert-led, hands-on workshops and two days of sessions from industry 
> leaders in dedicated Performance & Operations tracks. Use code vel09scf 
> and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
>
>
>   

Janek,

You need to align your structure with the reference, then re-calculate the electrostatic potentials.

Sincerely,

Carlos

>>> Jan Kosinski <ko...@ge...> 04/28/09 9:04 AM >>>
I am visualizing in PyMol electrostatic potential generated by PBEQ 
Solver from CHARMM-GUI at http://www.charmm-gui.org/?doc=input/pbeqsolver

The maps loads and colors nicely with the following commands suggested 
by the PBEQ Solver server:
load 1zziA_pbeq.pdb
load 1zziA_pbeq.dx, 1zziA_map
show surface, 1zziA_pbeq
ramp_new 1zziA_elvl, 1zziA_map,[-2,0,2]
set surface_color, 1zziA_elvl, 1zziA_pbeq
set surface_solvent, 1, 1zziA_pbeq

Now I want to fit my structure to some reference one using super or 
align commands. As expected, the map no longer works, I cannot 
re-generate the original coloring after fitting. I suppose that I need 
to change the orientation of the map accordingly to the rotation of the 
structure. But... how to do that? Is it at all possible?

Cheers,
Janek

------------------------------------------------------------------------------
Register Now & Save for Velocity, the Web Performance & Operations 
Conference from O'Reilly Media. Velocity features a full day of 
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leaders in dedicated Performance & Operations tracks. Use code vel09scf 
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_______________________________________________
PyMOL-users mailing list
PyM...@li...
https://lists.sourceforge.net/lists/listinfo/pymol-users

I am visualizing in PyMol electrostatic potential generated by PBEQ 
Solver from CHARMM-GUI at http://www.charmm-gui.org/?doc=input/pbeqsolver

The maps loads and colors nicely with the following commands suggested 
by the PBEQ Solver server:
load 1zziA_pbeq.pdb
load 1zziA_pbeq.dx, 1zziA_map
show surface, 1zziA_pbeq
ramp_new 1zziA_elvl, 1zziA_map,[-2,0,2]
set surface_color, 1zziA_elvl, 1zziA_pbeq
set surface_solvent, 1, 1zziA_pbeq

Now I want to fit my structure to some reference one using super or 
align commands. As expected, the map no longer works, I cannot 
re-generate the original coloring after fitting. I suppose that I need 
to change the orientation of the map accordingly to the rotation of the 
structure. But... how to do that? Is it at all possible?

Cheers,
Janek

Bradley,
 
PyMOL runs with its own Python interpreter -- it does not (and cannot)
work with external interpreter code unless that interpreter exactly
matches the version 
 
Try pointing PYTHONPATH at installed BioPython directly, or try copying
BioPython into PyMOL's modules directory.
 
Cheers,
Warren


________________________________

From: Bradley Hintze [mailto:bra...@ag...] 
Sent: Friday, April 24, 2009 9:48 PM
To: pym...@li...
Subject: [PyMOL] importing in scripts



	I am trying to import a BioPython module into a pymol script but
pymol can' find it. When I import it from the DOS>python command line it
imports fine. Obviously pymol isn't looking in the right place for the
module. Is there a way to force pymol to look in the right place? 
	
	-- 
	Bradley J. Hintze
	Biochemistry Undergraduate
	Utah State University
	801-712-8799
	

I am trying to import a BioPython module into a pymol script but pymol can'
find it. When I import it from the DOS>python command line it imports fine.
Obviously pymol isn't looking in the right place for the module. Is there a
way to force pymol to look in the right place?

-- 
Bradley J. Hintze
Biochemistry Undergraduate
Utah State University
801-712-8799

When aligning two structures using the align function is there an easy  
way of generating the list of atoms kept for the final refinement?

Thanks,

Jason P. Rife, Ph. D.
Associate Professor

Mail:
P.O Box 980133
Department of Medicinal Chemistry
Virginia Commonwealth University
Richmond, VA 23298-0133

Parcel:
800 E. Leigh St. - Suite 212
Institute for Structural Biology & Drug Discovery
Richmond, VA 23298

(804) 828-7488
fax (804) 827-3664
Jas...@vc...

Thanks!!
Now it works!!
albert

En/na Warren DeLano ha escrit:
> (Sorry if this is dupe -- my email client is acting up...)
>  
> the rms_* and fit commands required that the atoms in each selection to have matching identifiers: such as chain, resi, segi, resn, etc.  You can use the "alter" command to set the identifiers to matching values before issuing such commands:
>  
> alter all, segi=''
>  
> alter c321 and chain E, chain='A'
>  
> alter c321 and chain I, chain='B'
>  
> etc.
>  
> Cheers,
> Warren
> 
> ________________________________
> 
> From: Albert Solernou [mailto:al...@mm...]
> Sent: Thu 4/23/2009 9:42 AM
> To: pym...@li...
> Subject: [PyMOL] rms_cur, rms, fit - No atoms selected
> 
> 
> 
> I'm new at pymol, and I'm trying to use the commands rms and rms_cur.
> 
> I have two pdb files, with two proteins in each.
> First, I load the files
> 
>> load 1acb_321000.pdb, c321
>> load 1acb_dock.pdb, dock
> 
> then I select the backbone of the B chain of each complex,
>> select lc, /c321//b//ca+c+n+o
>> select lr, /dock//b//ca+c+n+o
> 
> Everything works until here. Each selection is showed on the screen, and
> they are 207 atoms each. Now I want to get the rms value without
> superimposing:
> 
>> rms_cur lc, lr
> 
> but it does not work:
> ExecutiveRMS-Error: No atoms selected.
> It also does not work with rms or fit commands, although it works with
> align:
> 
>> align lc, lr
>  Match: read scoring matrix.
>  Match: assigning 69 x 69 pairwise scores.
>  MatchAlign: aligning residues (69 vs 69)...
>  ExecutiveAlign: 207 atoms aligned.
>  ExecutiveRMS: 5 atoms rejected during cycle 1 (RMS=0.01).
>  ExecutiveRMS: 2 atoms rejected during cycle 2 (RMS=0.01).
>  Executive: RMS =    0.006 (200 to 200 atoms)
> 
> 
> I've seen that someone has reported a bug at debian's, under the version
> 0.99rc6:
> 
> http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=486254
> 
> 
> I've tried the 1.0r2-1 version (commming with ubuntu, apt-get), and
> compliling the source code from the svn of the current version, 1.2-x.
> Same results.
> 
> Hope someone can help me,
> albert
> 
> ------------------------------------------------------------------------------
> Stay on top of everything new and different, both inside and
> around Java (TM) technology - register by April 22, and save
> $200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco.
> 300 plus technical and hands-on sessions. Register today.
> Use priority code J9JMT32. http://p.sf.net/sfu/p
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 
> 
> 
> 
> 
> 

Hi Warren, e.a.,

I agree that posts in which people react on the 'tone' of  the
communication of one another should in principle be kept private and
settled thus. For me, there were three reasons to bounce this mail to
the mailing list. First and for all, I had hoped for the response you
gave regarding the mailing list archive as this was a very good
illustration of the need for such. Second, the answer to the original
question should be archived anyway, which hadn't happened the first
time, as I simply pressed 'reply'. Third, the reference to 'how to ask
questions the smart way' is always a good one to be posted now and
again (and to be archived).

That being said, it doesn't hurt if a discussion like this comes by
once in a while. It makes both posters and repliers aware that there's
people involved with feelings that can be touched. This is especially
true when the list concerns people from all over the world and have
all different kinds of backgrounds. Then, you can't rely on your own
background to make inferences about what's written between the lines
or expect that what you write between the lines is picked up in the
way you intend. Actually that is one of the most exciting parts of
intercultural communication: try to choose your words such that they
are unlikely to be misinterpreted, and try to find the proper viewing
angle to interpret the words from others. Both of these are tough.
Here we usually put things quite explicitly, without hard feelings,
and suppose that the direct manner of speech leaves little room for
misinterpretation. However, I admit that this explicit way of putting
things is very likely to be overinterpreted from a background in which
signals are usually put implicitly.

Although there's some more on my mind, I think I'll leave it like
this. Just as a final comment, I think this is just a sign that both
Pymol and the user list really grow to be mature now. I'll be happy to
elaborate on this and possible consequences thereof privately with
anyone :)

Warren, if you feel I crossed boundaries here, I apologize. You know
I'm not troll enough to want to jeopardize the mailing list ;)

Mehmet, let's have a drink on intercultural and mailing list communication.

Cheers,

Tsjerk



On Thu, Apr 23, 2009 at 5:44 PM, Warren DeLano <wa...@de...> wrote:
> Folks,
>
> Please endeavor to be respectful, kind, and patient with one another.
> Toxic interactions on the mailing list hurt all of us, so please avoid
> such posts altogether or keep them private.
>
> Unfortunately, is appears that we can no longer rely on either
> SourceForge or Google to provide a PyMOL mailing list search capacity,
> so we will be looking at what else we can do instead to provide
> convenient access to the accumulated knowledge contained inside the
> pymol-users archives.  Restoring this capability should help cut down on
> the number of repeat questions.
>
> Cheers,
> Warren
>
>> -----Original Message-----
>> From: Tsjerk Wassenaar [mailto:ts...@gm...]
>> Sent: Thursday, April 23, 2009 5:00 AM
>> To: Mehmet Cetin; pymol-users
>> Subject: Re: [PyMOL] solvent accessibility with pymol
>>
>> Hi Mehmet,
>>
>> > 1. I have just become a member today so I don't know who
>> posted what 2
>> > days ago. and as far as I can see there is no search
>> function on the archives.
>>
>> True, that's why I didn't answer 'search the archives', like
>> I would on other lists.
>>
>> > 2. I do search the web before asking. I couldn't find something
>> > satisfying, that's why I asked.
>>
>> The wiki did have the answer, maybe you searched but you
>> couldn't find it, or did not know of its existence. In that
>> case, indicate what you tried in order to find the answer
>> yourself (like noticing the archives have no search
>> function). That will make people like me feel to be taken
>> seriously and not used like some helpdesk. Maybe it is not a
>> bad idea to read http://www.catb.org/~esr/faqs/smart-questions.html
>>
>> > 3. I am not looking for a "substitute for my brain's
>> function" either.
>> > I just asked a simple question. just delete it if you don't
>> want to answer.
>> > and I suggest you think more carefully before you lecture
>> people you
>> > don't know.
>>
>> I gave you an answer, despite not being paid for it. You can
>> appreciate that and take the other comments for granted,
>> doing with it what you think is right. You can think badly of
>> me and hope for somebody more polite to answer, disregarding
>> what I said, or you can lecture me like you do here and make
>> me think twice before opening a post of yours and answering
>> your question.
>> The fact that you feel insulted by me, suggesting that you
>> would regard us as a 'substitute ...', is a good sign. It
>> gives the feeling that you're willing to learn and find
>> things out for yourself, although in this case you didn't
>> manage. Reflect that in your posts.
>> I've seen to many which boiled down to 'please do my homework for me'
>> or 'make me avoid straining my neurons', and after the years
>> involved in mailing lists like these mails invoking such
>> feelings trigger a response like the one I gave or even
>> worse. Not a personal thing though; I don't even know you.
>>
>> I hope this settles things a bit.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> >
>> > Mehmet
>> >
>> >
>> > --- On Thu, 4/23/09, Tsjerk Wassenaar <ts...@gm...> wrote:
>> >
>> > From: Tsjerk Wassenaar <ts...@gm...>
>> > Subject: Re: [PyMOL] solvent accessibility with pymol
>> > To: "Mehmet Cetin" <mm...@ya...>
>> > Date: Thursday, April 23, 2009, 2:43 AM
>> >
>> > Mehmet,
>> >
>> > Really, two days ago we got this post:
>> >
>> > ---
>> > Dear all,
>> >
>> > Is there any PyMOL command to calculate surface areas?
>> > Many thanks,
>> >
>> > Luisa Rodrigues
>> > ---
>> >
>> > And now you come with this:
>> >
>> > On Thu, Apr 23, 2009 at 4:30 AM, Mehmet Cetin
>> <mm...@ya...> wrote:
>> >>
>> >> Hi all, I am looking for a way to figure out the solvent
>> >> accessibility of a particular region on a protein. could
>> anyone tell
>> >> me if there is a command (or script) in Pymol that I can
>> use to do it? thanks in advance.
>> >>
>> >
>> > The answer given should be good enough for you.
>> >
>> > ---
>> > Did you try to search for information yourself first?
>> >
>> > Anyways, the pymolwiki.org
>> >
>> > is always a good place to go and then you would have found
>> something
>> > like this:
>> > http://pymolwiki.org/index.php/Get_Area
>> >
>> > I hope this is what you are looking for?
>> >
>> > Best regards,
>> > Folmer Fredslund
>> > ---
>> >
>> > Please do bear in mind that we're not an easy substitute
>> for your own
>> > brains function! Before posting, search the internet, and
>> especially
>> > search on the wiki pages. Also, be sure to read the questions and
>> > answers that come by on this list as these may provide you answers
>> > before you know you were looking for them.
>> >
>> > Cheers,
>> >
>> > Tsjerk
>> >
>> >
>> > --
>> > 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
>> >
>> >
>>
>>
>>
>> --
>> 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
>>
>
>
> ------------------------------------------------------------------------------
> Stay on top of everything new and different, both inside and
> around Java (TM) technology - register by April 22, and save
> $200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco.
> 300 plus technical and hands-on sessions. Register today.
> Use priority code J9JMT32. http://p.sf.net/sfu/p
> _______________________________________________
> 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

(Sorry if this is dupe -- my email client is acting up...)
 
the rms_* and fit commands required that the atoms in each selection to have matching identifiers: such as chain, resi, segi, resn, etc.  You can use the "alter" command to set the identifiers to matching values before issuing such commands:
 
alter all, segi=''
 
alter c321 and chain E, chain='A'
 
alter c321 and chain I, chain='B'
 
etc.
 
Cheers,
Warren

________________________________

From: Albert Solernou [mailto:al...@mm...]
Sent: Thu 4/23/2009 9:42 AM
To: pym...@li...
Subject: [PyMOL] rms_cur, rms, fit - No atoms selected



I'm new at pymol, and I'm trying to use the commands rms and rms_cur.

I have two pdb files, with two proteins in each.
First, I load the files

> load 1acb_321000.pdb, c321
> load 1acb_dock.pdb, dock

then I select the backbone of the B chain of each complex,
> select lc, /c321//b//ca+c+n+o
> select lr, /dock//b//ca+c+n+o

Everything works until here. Each selection is showed on the screen, and
they are 207 atoms each. Now I want to get the rms value without
superimposing:

> rms_cur lc, lr

but it does not work:
ExecutiveRMS-Error: No atoms selected.
It also does not work with rms or fit commands, although it works with
align:

> align lc, lr
 Match: read scoring matrix.
 Match: assigning 69 x 69 pairwise scores.
 MatchAlign: aligning residues (69 vs 69)...
 ExecutiveAlign: 207 atoms aligned.
 ExecutiveRMS: 5 atoms rejected during cycle 1 (RMS=0.01).
 ExecutiveRMS: 2 atoms rejected during cycle 2 (RMS=0.01).
 Executive: RMS =    0.006 (200 to 200 atoms)


I've seen that someone has reported a bug at debian's, under the version
0.99rc6:

http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=486254


I've tried the 1.0r2-1 version (commming with ubuntu, apt-get), and
compliling the source code from the svn of the current version, 1.2-x.
Same results.

Hope someone can help me,
albert

------------------------------------------------------------------------------
Stay on top of everything new and different, both inside and
around Java (TM) technology - register by April 22, and save
$200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco.
300 plus technical and hands-on sessions. Register today.
Use priority code J9JMT32. http://p.sf.net/sfu/p
_______________________________________________
PyMOL-users mailing list
PyM...@li...
https://lists.sourceforge.net/lists/listinfo/pymol-users

On Wed, Apr 22, 2009 at 6:37 PM, Craig Smith <boi...@ma...> wrote:

> I was looking at the demos in pymol (wizard --> demo) and saw
> interesting features called roving detail and roving density.  I
> looked in the manual on how to do this feature but couldn't find it.
> Could anyone point me in the right direction or show me how to
> interactively display electron density as I move through my structure.
>

This is what I do (sorry, it's in Python, but easily converted to PyMOL
commands).  It assumes that you have two maps loaded, named "2fofc" and
"fofc".    (Some of it is cribbed from the C code for the roving density
demo.)

    cmd.set("roving_detail", 20)
    cmd.set("roving_isomesh", 20)
    cmd.set("roving_origin", 1)
    cmd.set("roving_sticks", 0)
    cmd.set("roving_ribbon", 0)
    cmd.set("roving_lines", 0)
    cmd.set("roving_spheres", 0)
    cmd.set("roving_nb_spheres", 0)
    cmd.set("roving_polar_contacts", 0)
    cmd.set("roving_polar_cutoff", 0)
    cmd.set("roving_map1_name", "2fofc")
    cmd.set("roving_map1_level", 1)
    cmd.set("roving_map2_name", "fofc")
    cmd.set("roving_map3_name", "fofc")
    cmd.set("roving_map2_level", 3)
    cmd.set("roving_map3_level", -3)

    cmd.isomesh("rov_m1", "2fofc", 1.0, "center", 20)
    cmd.isomesh("rov_m2", "fofc", 3.0, "center", 20)
    cmd.isomesh("rov_m3", "fofc", -3.0, "center", 20)
    cmd.color("skyblue", "rov_m1")
    cmd.color("green", "rov_m2")
    cmd.color("red", "rov_m3")

This might not be ideal - some of those 'set' commands may be unnecessary or
incorrect.  However, the end result works more or less like Coot, which is
what I was aiming for.

-Nat

Sign,

Sorry, PyMOL has no volume calculation capabilities at present.

Cheers,
Warren 

> -----Original Message-----
> From: Kin Sing Stephen Lee [mailto:si...@ch...] 
> Sent: Thursday, April 23, 2009 9:18 AM
> To: pym...@li...
> Subject: [PyMOL] Binding pocket volume calculation
> 
> Dear all,
> 
> I'm just wondering is it possible to calculate the ligand 
> volume and also the volume of the binding pocket from pymol? 
> If no, do you have any program that allow me to do so?
> 
> Thank you very much
> 
> All the best,
> 
> Sing
> 
> 
> --------------------------------------------------------------
> ----------------
> Stay on top of everything new and different, both inside and 
> around Java (TM) technology - register by April 22, and save 
> $200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco.
> 300 plus technical and hands-on sessions. Register today. 
> Use priority code J9JMT32. http://p.sf.net/sfu/p 
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 
> 
> 
> 
> 

Dear all,

I'm just wondering is it possible to calculate the ligand volume and  
also the volume of the binding pocket from pymol? If no, do you have  
any program that allow me to do so?

Thank you very much

All the best,

Sing

Folks,

Please endeavor to be respectful, kind, and patient with one another.
Toxic interactions on the mailing list hurt all of us, so please avoid
such posts altogether or keep them private.  

Unfortunately, is appears that we can no longer rely on either
SourceForge or Google to provide a PyMOL mailing list search capacity,
so we will be looking at what else we can do instead to provide
convenient access to the accumulated knowledge contained inside the
pymol-users archives.  Restoring this capability should help cut down on
the number of repeat questions.

Cheers,
Warren

> -----Original Message-----
> From: Tsjerk Wassenaar [mailto:ts...@gm...] 
> Sent: Thursday, April 23, 2009 5:00 AM
> To: Mehmet Cetin; pymol-users
> Subject: Re: [PyMOL] solvent accessibility with pymol
> 
> Hi Mehmet,
> 
> > 1. I have just become a member today so I don't know who 
> posted what 2 
> > days ago. and as far as I can see there is no search 
> function on the archives.
> 
> True, that's why I didn't answer 'search the archives', like 
> I would on other lists.
> 
> > 2. I do search the web before asking. I couldn't find something 
> > satisfying, that's why I asked.
> 
> The wiki did have the answer, maybe you searched but you 
> couldn't find it, or did not know of its existence. In that 
> case, indicate what you tried in order to find the answer 
> yourself (like noticing the archives have no search 
> function). That will make people like me feel to be taken 
> seriously and not used like some helpdesk. Maybe it is not a 
> bad idea to read http://www.catb.org/~esr/faqs/smart-questions.html
> 
> > 3. I am not looking for a "substitute for my brain's 
> function" either. 
> > I just asked a simple question. just delete it if you don't 
> want to answer.
> > and I suggest you think more carefully before you lecture 
> people you 
> > don't know.
> 
> I gave you an answer, despite not being paid for it. You can 
> appreciate that and take the other comments for granted, 
> doing with it what you think is right. You can think badly of 
> me and hope for somebody more polite to answer, disregarding 
> what I said, or you can lecture me like you do here and make 
> me think twice before opening a post of yours and answering 
> your question.
> The fact that you feel insulted by me, suggesting that you 
> would regard us as a 'substitute ...', is a good sign. It 
> gives the feeling that you're willing to learn and find 
> things out for yourself, although in this case you didn't 
> manage. Reflect that in your posts.
> I've seen to many which boiled down to 'please do my homework for me'
> or 'make me avoid straining my neurons', and after the years 
> involved in mailing lists like these mails invoking such 
> feelings trigger a response like the one I gave or even 
> worse. Not a personal thing though; I don't even know you.
> 
> I hope this settles things a bit.
> 
> Cheers,
> 
> Tsjerk
> 
> >
> > Mehmet
> >
> >
> > --- On Thu, 4/23/09, Tsjerk Wassenaar <ts...@gm...> wrote:
> >
> > From: Tsjerk Wassenaar <ts...@gm...>
> > Subject: Re: [PyMOL] solvent accessibility with pymol
> > To: "Mehmet Cetin" <mm...@ya...>
> > Date: Thursday, April 23, 2009, 2:43 AM
> >
> > Mehmet,
> >
> > Really, two days ago we got this post:
> >
> > ---
> > Dear all,
> >
> > Is there any PyMOL command to calculate surface areas?
> > Many thanks,
> >
> > Luisa Rodrigues
> > ---
> >
> > And now you come with this:
> >
> > On Thu, Apr 23, 2009 at 4:30 AM, Mehmet Cetin 
> <mm...@ya...> wrote:
> >>
> >> Hi all, I am looking for a way to figure out the solvent 
> >> accessibility of a particular region on a protein. could 
> anyone tell 
> >> me if there is a command (or script) in Pymol that I can 
> use to do it? thanks in advance.
> >>
> >
> > The answer given should be good enough for you.
> >
> > ---
> > Did you try to search for information yourself first?
> >
> > Anyways, the pymolwiki.org
> >
> > is always a good place to go and then you would have found 
> something 
> > like this:
> > http://pymolwiki.org/index.php/Get_Area
> >
> > I hope this is what you are looking for?
> >
> > Best regards,
> > Folmer Fredslund
> > ---
> >
> > Please do bear in mind that we're not an easy substitute 
> for your own 
> > brains function! Before posting, search the internet, and 
> especially 
> > search on the wiki pages. Also, be sure to read the questions and 
> > answers that come by on this list as these may provide you answers 
> > before you know you were looking for them.
> >
> > Cheers,
> >
> > Tsjerk
> >
> >
> > --
> > 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
> >
> >
> 
> 
> 
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
> 

I'm new at pymol, and I'm trying to use the commands rms and rms_cur.

I have two pdb files, with two proteins in each.
First, I load the files

> load 1acb_321000.pdb, c321
> load 1acb_dock.pdb, dock

then I select the backbone of the B chain of each complex,
> select lc, /c321//b//ca+c+n+o
> select lr, /dock//b//ca+c+n+o

Everything works until here. Each selection is showed on the screen, and
they are 207 atoms each. Now I want to get the rms value without
superimposing:

> rms_cur lc, lr

but it does not work:
ExecutiveRMS-Error: No atoms selected.
It also does not work with rms or fit commands, although it works with
align:

> align lc, lr
 Match: read scoring matrix.
 Match: assigning 69 x 69 pairwise scores.
 MatchAlign: aligning residues (69 vs 69)...
 ExecutiveAlign: 207 atoms aligned.
 ExecutiveRMS: 5 atoms rejected during cycle 1 (RMS=0.01).
 ExecutiveRMS: 2 atoms rejected during cycle 2 (RMS=0.01).
 Executive: RMS =    0.006 (200 to 200 atoms)


I've seen that someone has reported a bug at debian's, under the version
0.99rc6:

http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=486254


I've tried the 1.0r2-1 version (commming with ubuntu, apt-get), and
compliling the source code from the svn of the current version, 1.2-x.
Same results.

Hope someone can help me,
albert

Hi Mehmet,

> 1. I have just become a member today so I don't know who posted what 2 days
> ago. and as far as I can see there is no search function on the archives.

True, that's why I didn't answer 'search the archives', like I would
on other lists.

> 2. I do search the web before asking. I couldn't find something satisfying,
> that's why I asked.

The wiki did have the answer, maybe you searched but you couldn't find
it, or did not know of its existence. In that case, indicate what you
tried in order to find the answer yourself (like noticing the archives
have no search function). That will make people like me feel to be
taken seriously and not used like some helpdesk. Maybe it is not a bad
idea to read http://www.catb.org/~esr/faqs/smart-questions.html

> 3. I am not looking for a "substitute for my brain's function" either. I
> just asked a simple question. just delete it if you don't want to answer.
> and I suggest you think more carefully before you lecture people you don't
> know.

I gave you an answer, despite not being paid for it. You can
appreciate that and take the other comments for granted, doing with it
what you think is right. You can think badly of me and hope for
somebody more polite to answer, disregarding what I said, or you can
lecture me like you do here and make me think twice before opening a
post of yours and answering your question.
The fact that you feel insulted by me, suggesting that you would
regard us as a 'substitute ...', is a good sign. It gives the feeling
that you're willing to learn and find things out for yourself,
although in this case you didn't manage. Reflect that in your posts.
I've seen to many which boiled down to 'please do my homework for me'
or 'make me avoid straining my neurons', and after the years involved
in mailing lists like these mails invoking such feelings trigger a
response like the one I gave or even worse. Not a personal thing
though; I don't even know you.

I hope this settles things a bit.

Cheers,

Tsjerk

>
> Mehmet
>
>
> --- On Thu, 4/23/09, Tsjerk Wassenaar <ts...@gm...> wrote:
>
> From: Tsjerk Wassenaar <ts...@gm...>
> Subject: Re: [PyMOL] solvent accessibility with pymol
> To: "Mehmet Cetin" <mm...@ya...>
> Date: Thursday, April 23, 2009, 2:43 AM
>
> Mehmet,
>
> Really, two days ago we got this post:
>
> ---
> Dear all,
>
> Is there any PyMOL command to calculate surface areas?
> Many thanks,
>
> Luisa Rodrigues
> ---
>
> And now you come with this:
>
> On Thu, Apr 23, 2009 at 4:30 AM, Mehmet Cetin <mm...@ya...> wrote:
>>
>> Hi all, I am looking for a way to figure out the solvent accessibility of
>> a particular region on a protein. could anyone tell me if there is a command
>> (or script) in Pymol that I can use to do it? thanks in advance.
>>
>
> The answer given should be good enough for you.
>
> ---
> Did you try to search for information yourself first?
>
> Anyways, the pymolwiki.org
>
> is always a good place to go and then you
> would have found something like this:
> http://pymolwiki.org/index.php/Get_Area
>
> I hope this is what you are looking for?
>
> Best regards,
> Folmer Fredslund
> ---
>
> Please do bear in mind that we're not an easy substitute for your own
> brains function! Before posting, search the internet, and especially
> search on the wiki pages. Also, be sure to read the questions and
> answers that come by on this list as these may provide you answers
> before you know you were looking for them.
>
> Cheers,
>
> Tsjerk
>
>
> --
> 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
>
>



-- 
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