pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] Cheap VRML hack for 3D printing surfaces

[Chris W. <cw...@ua...>]

I recently got a color 3D printer that only accepts color
output from vrml files.

Attached is a patch for current CVS that does the following:

1) When a surface display is shown, it dumps the surface to a
VRML 2.0 file in /tmp/pymol.wrl

2) everytime the color scheme of the surface is changed, it
rewrites that wrl file.

I know this isn't a very elegant way to add a feature like this
(should have GUI elements, etc), but it was the quickest way
to get the job done for me, with my very limited knowledge of
the source code.

Here's some pics involving the demo file 1tii.pdb file, using
the "chainbow" coloring scheme:

http://bebop.cns.ualberta.ca/~cwant/pymol_wrl/pymol_1tii.jpg
http://bebop.cns.ualberta.ca/~cwant/pymol_wrl/pymol_1tii_print.jpg

Anyways, maybe somebody else will find the patch useful ...

Regards,
Chris


-- 
  ____________________________________________________________________
( Chris Want                                                         )
( Research Computing Support                                         )
( Academic Information and Communication Technologies (AICT)         )
( University of Alberta                                              )
( Tel: 1-780-492-9418                                                )
  --------------------------------------------------------------------

[PyMOL] Cutaway surface

[Stephen G. <ste...@us...>]

Hi all,

Is there any way good way in pymol of displaying a slice through a
surface and block colouring the 'inner' face of the surface.=20
Basically, I would like to generate a figure that looks like part (b)
of http://www.nature.com/nature/journal/v432/n7014/fig_tab/nature02988_F3.h=
tml
using pymol.  I have tried playing with the lighting models and
backpace culling (a-la set ambient=3D0; set direct=3D0.7; set reflect=3D0.0=
;
set backface_cull=3D0) but they are not quite what I am after.

Can anyone recommend a good way to achieve this effect?

Thanks,

Stephen

--
Stephen Graham
Crystallography Group
School of Molecular and Microbial Biosciences
University of Sydney

[PyMOL] show NMR constraints script help

[Anjali D. <anj...@re...>]

 hii,=0A=0AIam trying to run the script "show NMR constraints" after loadin=
g pdb on the pymol screen. but iam not getting any output. i have tried to =
put 'fname'for upl both within the script and also in the command line. Is =
there any specific format for Upl too that it will read.please guide me how=
 to run this script.=0AThanks in advance=0Abest regards=0Aanjali=0A=0A

[PyMOL] show NMR constraints script help

[Anjali D. <anj...@re...>]

 hii,=0A=0AIam trying to run the script "show NMR constraints" after loadin=
g pdb on the pymol screen. but iam not getting any output. i have tried to =
put 'fname'for upl both within the script and also in the command line. Is =
there any specific format for Upl too that it will read.please guide me how=
 to run this script.=0AThanks in advance=0Abest regards=0Aanjali=0A=0A

[PyMOL] Menu Bar viewed in stereo on Geowall

[Matthew B. <mw...@mr...>]

Dear All,
	I am sure that around 3 months ago I found a command that would  
allow the menu bar in pymol to be seen and used while viewing a  
session in stereo on a geowall.  However, try as I might I cannot  
find the command now, any ideas?  Many thanks in advance, Matt.



Matthew Bowler
MRC Dunn Human Nutrition Unit
Wellcome Trust / MRC Building
Hills Road
Cambridge CB2 2XY
Tel: 0044 (0) 1223 252826
Fax: 0044 (0) 1223 252825

Re: [PyMOL] getting pov-ray temp files

[Tsjerk W. <ts...@gm...>]

Hi Balaji,

In addition you can try the strategy I proposed earlier. Split your scene
into separate objects and exdport them to povray one at a time (by turning
all other objects off). In this way, you'll keep pymol from rendering the
whole scene at once, which can lead to memory problems. Subsequently, you
take one of the output .pov files and add an #include statement for each
.inc file generated, thus combining them to a single povray scene. And then
you pray that povray will be able to manage. With 1 or 2 Gb of ram and a
good cpu you might get away with a large scene, though it may still take a
while to render.

Tsjerk

On 1/25/06, Warren DeLano <wa...@de...> wrote:
>
> Balaji,
>
> One thing you might try is reducing "hash_max" to a smaller number -- 80
> or even 50.  This will use less RAM but cause rendering to take much
> much longer.
>
> Cheers,
> Warren
>
> --
> Warren L. DeLano, Ph.D.
> Principal Scientist
>
> . DeLano Scientific LLC
> . 400 Oyster Point Blvd., Suite 213
> . South San Francisco, CA 94080 USA
> . Biz:(650)-872-0942  Tech:(650)-872-0834
> . Fax:(650)-872-0273  Cell:(650)-346-1154
> . mailto:wa...@de...
>
>
> > -----Original Message-----
> > From: pym...@li...
> > [mailto:pym...@li...] On Behalf Of
> > Bhyravbhatla, Balaji
> > Sent: Wednesday, January 25, 2006 9:50 AM
> > To: Tsjerk Wassenaar
> > Cc: pym...@li...
> > Subject: RE: [PyMOL] getting pov-ray temp files
> >
> > Thanks Tsjerk,
> >
> > I still have the same issue of PyMOL aborting on me:
> >
> >
> >
> > RayRenderPovRay: processed 2956434 graphics primitives.
> >
> > VLAExpand-ERR: realloc failed.
> >
> > ****EEK! PyMOL just ran out of memory and crashed
> >
> >
> >
> > /usr/local/pymol/pymol.com: line 14: 3812 Aborted
> >
> >
> >
> >
> >
> > So I guess I really need to look for larger resources
> > (hardware) meanwhile is it possible to use PyMOL on a command
> > line and have it write out the output files? What I had in
> > mind was to install PyMOL on our cluster (Opteron based) that
> > has 8GB RAM on the node and submit it without the invocation
> > of the GUI? The cluster does only computations and no
> > graphics as most clusters are. Will it work?
> >
> >
> >
> > Thanks
> >
> >
> >
> > Balaji
> >
> >
> >
> > ________________________________
> >
> > From: Tsjerk Wassenaar [mailto:ts...@gm...]
> > Sent: Tuesday, January 24, 2006 3:41 PM
> > To: Bhyravbhatla, Balaji
> > Cc: pym...@li...
> > Subject: Re: [PyMOL] getting pov-ray temp files
> >
> >
> >
> >
> > Hi Balaji,
> >
> > The temporary povray file is written to the working
> > directory. However, you may want to use the attached script
> > instead. This will write your scene in two parts, a .pov file
> > containing all meta data, such as the lights, camera and
> > #defaults, and an include file (.inc) which contains the
> > structure. In this way you have maximum control over your
> > scene without having to edit a huge povray file. You may even
> > want to consider splitting your scene up in separate parts
> > (taken from the same perspective), which you combine in a
> > global .pov file using #include statements. This will give
> > even more control with regards to modifications to the scene.
> >
> > The magic word in pymol (after run make_pov.py) is make_pov
> >
> > NB. the .pov file contains a commented statement with regards
> > to a povray script, which allows transforming scenes and
> > objects from model space to camera space and vice versa. If
> > you want, you can get a copy of that script.
> >
> > Good luck!
> >
> > Tsjerk
> >
> > On 1/24/06, Bhyravbhatla, Balaji
> > <Bal...@um... > wrote:
> >
> > Hello All,
> > I am trying to render a large mega Dalton complex and can get
> > it up on the screen but rendering it causes a crash because
> > of memory issues (I have 1Gb on the system and tried on a 2Gb
> > system also). So what I would like is to get the temp pov ray
> > files that Pymol is writing out and use those with PoVRAY.
> > I am unable to find the location of those files. Can you
> > please point me to where they are written?
> >
> > If anyone also has ideas on how to get a decent publication
> > quality output for a complex (think in terms of viruses) that
> > would be helpful.
> > I do have a session file saved with my views.
> >
> > Thanks
> >
> > Balaji
> >
> >
> >
> > -------------------------------------------------------
> > This SF.net email is sponsored by: Splunk Inc. Do you grep
> > through log files for problems?  Stop!  Download the new AJAX
> > search engine that makes searching your log files as easy as
> > surfing the  web.  DOWNLOAD SPLUNK!
> > http://sel.as-us.falkag.net/sel?cmdlnk&kid3432&bid#0486&dat=1216
> > 42
> > <http://sel.as-us.falkag.net/sel?cmdlnk&kid%103432&bid#0486&dat=121642>
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
> >
> >
> >
> > --
> >
> > Tsjerk A. Wassenaar, M.Sc.
> > Groningen Biomolecular Sciences and Biotechnology Institute
> > (GBB) Dept. of Biophysical Chemistry University of Groningen
> > Nijenborgh 4 9747AG Groningen, The Netherlands
> > +31 50 363 4336
> >
> >
>



--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336

[PyMOL] apbs color ligand by potential using pml script

[Mike O. <mic...@um...>]

HI everyone
I have been able to show electrostatics from APBS by loading the .dx map
using a pml script. However, I would really like to display it on the
surface similar to the apbs plugin option which says "color by potential
on solvent accessible surface" in the visualization menu. Does anyone
know how to do this using a pml script?
Actually, when I use this the potentials on the surface look a lot
smoother. I was also wondering, which representation is best.
Thanks
MIke
--=20
Mike Osborne
Universit=C3=A9 de Montr=C3=A9al
Montreal, Quebec, H3T 1J4

[PyMOL] nucleic acid cartoon problem?

[Leven <lw...@ya...>]

Hi,

I came across a possible (and maybe debatable) problem
with RNA cartoons:

With default settings (i.e. cartoon_nucleic_acid_mode
= 0, so the ribbon goes through P's), the "rungs" or
sticks in the ladder representation don't always
intersect with the backbone ribbon. In other words,
sometimes the ladder sticks are floating in space.
This is exacerbated in highly kinked areas of the
backbone and fixed with cartoon_nucleic_acid_mode = 1
(ribbon through C3').

To be correct, I imagine the algorithm for drawing the
ladder should be different for each mode. Is there an
easy fix (keeping cartoon_nucleic_acid_mode = 0)? 

By the way, I'm using the latest Linux beta build
(0.99-37).

Thanks much,

Leven


__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com 

RE: [PyMOL] getting pov-ray temp files

[Bhyravbhatla, B. <Bal...@um...>]

Thanks Tsjerk,

I still have the same issue of PyMOL aborting on me:

=20

RayRenderPovRay: processed 2956434 graphics primitives.

VLAExpand-ERR: realloc failed.

****EEK! PyMOL just ran out of memory and crashed

=20

/usr/local/pymol/pymol.com: line 14: 3812 Aborted

=20

=20

So I guess I really need to look for larger resources (hardware)
meanwhile is it possible to use PyMOL on a command line and have it
write out the output files? What I had in mind was to install PyMOL on
our cluster (Opteron based) that has 8GB RAM on the node and submit it
without the invocation of the GUI? The cluster does only computations
and no graphics as most clusters are. Will it work?

=20

Thanks

=20

Balaji

=20

________________________________

From: Tsjerk Wassenaar [mailto:ts...@gm...]=20
Sent: Tuesday, January 24, 2006 3:41 PM
To: Bhyravbhatla, Balaji
Cc: pym...@li...
Subject: Re: [PyMOL] getting pov-ray temp files

=20


Hi Balaji,

The temporary povray file is written to the working directory. However,
you may want to use the attached script instead. This will write your
scene in two parts, a .pov file containing all meta data, such as the
lights, camera and #defaults, and an include file (.inc) which contains
the structure. In this way you have maximum control over your scene
without having to edit a huge povray file. You may even want to consider
splitting your scene up in separate parts (taken from the same
perspective), which you combine in a global .pov file using #include
statements. This will give even more control with regards to
modifications to the scene.=20

The magic word in pymol (after run make_pov.py) is make_pov

NB. the .pov file contains a commented statement with regards to a
povray script, which allows transforming scenes and objects from model
space to camera space and vice versa. If you want, you can get a copy of
that script.=20

Good luck!

Tsjerk

On 1/24/06, Bhyravbhatla, Balaji <Bal...@um... >
wrote:

Hello All,
I am trying to render a large mega Dalton complex and can get it up on=20
the screen but rendering it causes a crash because of memory issues (I
have 1Gb on the system and tried on a 2Gb system also). So what I would
like is to get the temp pov ray files that Pymol is writing out and use=20
those with PoVRAY.
I am unable to find the location of those files. Can you please point me
to where they are written?

If anyone also has ideas on how to get a decent publication quality
output for a complex (think in terms of viruses) that would be helpful.=20
I do have a session file saved with my views.

Thanks

Balaji



-------------------------------------------------------
This SF.net email is sponsored by: Splunk Inc. Do you grep through log
files=20
for problems?  Stop!  Download the new AJAX search engine that makes
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_______________________________________________
PyMOL-users mailing list
PyM...@li...=20
https://lists.sourceforge.net/lists/listinfo/pymol-users




--=20

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336

Re: [PyMOL] getting pov-ray temp files

[Tsjerk W. <ts...@gm...>]

# make_pov.py                                                                                       
# Do "run make_pov.py" from within pymol and then execute the script                                
# with "make_pov('povray.inp')" to create the povray.inp file.                                      
#                                                                                                   

from pymol import cmd

def make_pov(file, meta=True):
	f1, f2 = file, file[:-4] + '.inc'

        (header,data) = cmd.get_povray()
        povfile = open(f1,'w')
	if meta: povfile.write(header)
	povview = cmd.get_view()

	povfile.write("""\n
// Uncomment the following lines if you have the pymolmacro.inc include file and want to use it.
/*
#include \"pymolmacro.inc\"
PYMOL_VIEW( %10.5f, %10.5f, %10.5f,
            %10.5f, %10.5f, %10.5f,
	    %10.5f, %10.5f, %10.5f,
	    %10.5f, %10.5f, %10.5f,
	    %10.5f, %10.5f, %10.5f,
	    %10.5f, %10.5f, %10.5f )
*/

""" % povview)
	povfile.write('#include "%s"\n\n' % f2)
	povfile.close()
	povfile = open(f2,'w')
        povfile.write(data)
        povfile.close()

cmd.extend('make_pov',make_pov)

[PyMOL] getting pov-ray temp files

[Bhyravbhatla, B. <Bal...@um...>]

Hello All,
I am trying to render a large mega Dalton complex and can get it up on
the screen but rendering it causes a crash because of memory issues (I
have 1Gb on the system and tried on a 2Gb system also). So what I would
like is to get the temp pov ray files that Pymol is writing out and use
those with PoVRAY.
I am unable to find the location of those files. Can you please point me
to where they are written?

If anyone also has ideas on how to get a decent publication quality
output for a complex (think in terms of viruses) that would be helpful.
I do have a session file saved with my views.

Thanks

Balaji

[PyMOL] two problems with pyMOL beta

[Michael W. <we...@st...>]

I think I have found two problems with pyMOl that might require a fix:

1) I experience sporadic crashes of pyMOL on two Windows XP Pro machines =
(more I have not tested): AMD Athlon-A 1.1 GHz (TBird), ASUS A7V =
mainboard, Leadtek A280 graphics board (Geforce 4), 768 MB RAM and on my =
Fujitsu-Siemens Notebook Amilo A series, AMD Athlon-64 3000+ =
(Clawhammer), ATI Radeon 9700+, 512 MB RAM. The program sometimes simply =
shuts down after loading a PDB file or after some manipulations of =
files. I do not see any reason for that. I previously also had the same =
problem on the same machines with the stable release client pyMOL 0.98.

2) Another problem that seems new with version 0.99beta31 is that =
selections disappear as soon as the measurement wizard is activated. I =
mean, the selection is no longer seen in the right-hand-side window =
while the corresponding atoms remain unchanged incl. all settings =
applied to them.

I do not know whether this is important. Although sometimes a bit =
annoying, I can live with this. ;-)

Michael.

- - - - - - - - - -
Michael H.W. Weber
Philipps-Universit=E4t Marburg
Germany

- - - - - - - - - -
Proteins are nanomachines or nanomachine building blocks.
Examples: The ribosome and RNA polymerase holoenzyme.

- - - - - - - - - -
This e-mail was scanned for potential virus contamination.

RE: [PyMOL] Surface of cavity

[Warren D. <wa...@de...>]

Paul,

PyMOL generally shows all sides of an exposed atom, but perhaps you
could load both the GOLD output and the original structure.

You could then only show the surface on the atoms in the original
structure with corresponding atoms in the gold output as follows:

load orig.pdb
load gold.pdb

then=20

show surface, orig in gold

or

show surface, orig like gold

That might produce something close to what you want.  Note that:

"in" matches chains, segments, residue names, residue ids, and atom
names.

"like" just matches residue ids and atom names.

You can use

alter all, segi=3D''
alter all, chain=3D''

to clear out the segment and/or chain IDs before using "in" to
selectively reduce its stringency.

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Paul Wilhelm Elsinghorst
> Sent: Friday, January 20, 2006 11:33 PM
> To: pym...@li...
> Subject: [PyMOL] Surface of cavity
>=20
> Hi,
>=20
>=20
> a little question regarding cavity surfaces :-)
>=20
>=20
> I have a set of active atoms (GOLD output) that surround a=20
> cavity. Now I want to dipslay the surface only for the cavity=20
> wall, not on the outside.
>=20
>=20
> Any ideas?
>=20
>=20
> Paul=20
>=20

Re: [PyMOL] Surface of cavity

[Betty <beh...@st...>]

Hi Paul,

> I have a set of active atoms (GOLD output) that surround a cavity. Now I
> want to dipslay the surface only for the cavity wall, not on the
> outside.

try this: show surface for the whole protein and then hide surface for 
"not the active residues" - something like this:

####
from pymol import cmd
from pymol import stored

# load your protein and the active atoms as GOLD output
cmd.load("protein.pdb", "prot")
cmd.load("active_atoms.pdb", "act_res")

# create a list of the activ residue-id's stored.act_res=[]
cmd.iterate("act_res", "stored.act_res.append(resi)")

# create selection of the actives
cmd.select("act_res","resi %s" %stored.act_res[0])
for i in stored.act_res:
	cmd.select("act_res","act_res or resi %s" %i)

# create selection of the "non-actives"
cmd.select("not_act_res", "prot and not act_res")

# show surface
cmd.show("surface", "prot")
cmd.hide("surface", "not_act_res" )

cmd.delete("not_act_res")
####



Cheers,
Betty

Re: [PyMOL] Surface of cavity

[Andrea S. <and...@gm...>]

Hi,
you may try to use caver:

http://viper.chemi.muni.cz/caver/concept.php

or castp

http://cast.engr.uic.edu/cast/oldindex.php

regards

andrea

2006/1/21, Paul Wilhelm Elsinghorst <pa...@un...>:
>  Hi,
>
>
>  a little question regarding cavity surfaces :-)
>
>
>  I have a set of active atoms (GOLD output) that surround a cavity. Now I
> want to dipslay the surface only for the cavity wall, not on the outside.
>
>
>  Any ideas?
>
>
>  Paul
> -----BEGIN PGP SIGNATURE-----
> Version: GnuPG v1.4.0 (GNU/Linux)
>
> iD8DBQBD0eKigFneuXxhreARAnFLAJ9Z3o6zMiphEzzKpVzMXtdXxh6dBwCeMp9u
> ZIoavXwL2DE+hMObJhTiD8o=3D
> =3DuZkv
> -----END PGP SIGNATURE-----
>
>
>


--
"La conoscenza libera il genere umano dalla superstizione"
J. Watson

[PyMOL] Surface of cavity

[Paul W. E. <pa...@un...>]

Hi,


a little question regarding cavity surfaces :-)


I have a set of active atoms (GOLD output) that surround a cavity. Now I
want to dipslay the surface only for the cavity wall, not on the
outside.


Any ideas?


Paul

RE: [PyMOL] GUI

[David A. H. <dh...@wf...>]

Hi-
I'd second this; my brain doesn't do well keeping track of whether I'm,
for example, in maximum or reasonable performance mode.=20
David

-----------------------------=20
David A. Horita, Ph.D.
Department of Biochemistry
Wake Forest University School of Medicine
Winston-Salem, NC 27157-1016=20
Tel: 336 713-4194
Fax: 336 716-7671=20
email:  dh...@wf...
web:  http://www1.wfubmc.edu/biochem/faculty/Horita.htm

-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Mark A
Saper
Sent: Friday, January 20, 2006 3:01 PM
To: Pymol
Subject: [PyMOL] GUI

Hi Warren,

Why can't we have little check marks in the main menu that indicate the
current setting?
For example, Setting>Rendering>Antialias   gets a check, but =20
selecting Setting>Rendering>Shadows>None doesn't give a check (as do any
of the other rendering options).

Mark
_________________________________
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry Biophysics Research
Division, University of Michigan Chemistry Building Room 3040 930 N
University Ave Ann Arbor MI 48109-1055 U.S.A.

sa...@um...        (734) 764-3353        fax (734) 764-3323
http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html




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[PyMOL] GUI

[Mark A S. <sa...@um...>]

Hi Warren,

Why can't we have little check marks in the main menu that indicate  
the current setting?
For example, Setting>Rendering>Antialias   gets a check, but  
selecting Setting>Rendering>Shadows>None doesn't give a check (as do  
any of the other rendering options).

Mark
_________________________________
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry
Biophysics Research Division, University of Michigan
Chemistry Building Room 3040
930 N University Ave
Ann Arbor MI 48109-1055 U.S.A.

sa...@um...        (734) 764-3353        fax (734) 764-3323
http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html

RE: [PyMOL] GUI output font size too small

[Warren D. <wa...@de...>]

Hi Bjorn,

Unfortunately, this isn't configurable at runtime yet.  We'll need to do =
something about this...

For now, you'll need to directly edit the code in =
modules/pmg_tk/skins/normal/__init__.py

look for self.font and text.configure.

Cheers,
Warren


--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
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=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Bj=F6rn Kauppi
> Sent: Thursday, January 19, 2006 5:02 AM
> To: pym...@li...
> Subject: [PyMOL] GUI output font size too small
>=20
> Hi,
>=20
>=20
> How do I control the GUI output window font size? It is too=20
> small for my eyes on a 1600x1200 screen. I can change it=20
> manually to 12 points in the GUI window Setting/Output size,=20
> but I can not find a command to do it for my .pymolrc!=20
> Preferably to more than 12 points as well...
> I use 0.99beta33 on Linux and windows.
>=20
>=20
> Thanks,
>=20
>=20
> Bj=F6rn Kauppi
>=20
> **************************************************************
> *************
> This e-mail may contain confidential information proprietary=20
> to Karo Bio AB and is meant for the intended addressee(s)=20
> only. Any unauthorized review, use, disclosure or=20
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[PyMOL] RE: Program or Script to Calculate Atom-Atom Distances in pdb files

[Warren D. <wa...@de...>]

Irida,

> I am looking for a free program=20
> or script that can calculate all sulfur-sulfur distances in=20
> pdb files from the Protein Data Bank.

This is the kind of problem you can solve in PyMOL with just a few lines
of Python code.  For example:

from pymol import cmd
from glob import glob

for file in glob("*.pdb"):
    print file
    cmd.load(file,'prot')
    for a in cmd.index("elem s and bound_to elem s"):
        if cmd.select("s1","%s`%d"%a) and \
           cmd.select("s2","elem s and bound_to %s`%d"%a):
            if cmd.select("(s1|s2) and not ?skip"):
                cmd.iterate("s1|s2","print ' ',chain,resn,resi,name")
                print '   ',round(cmd.dist("tmp","s1","s2"),3)
                cmd.select("skip","s1|s2|?skip")
    cmd.delete("all")
   =20
Would generate the following output in a directory with pdb files:

1alk.pdb
  A CYS 168 SG
  A CYS 178 SG
    1.975
  A CYS 286 SG
  A CYS 336 SG
    1.995
  B CYS 168 SG
  B CYS 178 SG
    1.996
  B CYS 286 SG
  B CYS 336 SG
    2.032
1btu.pdb
   CYS 42 SG
   CYS 58 SG
    2.039
   CYS 136 SG
   CYS 201 SG
    2.031
   CYS 168 SG
   CYS 182 SG
    2.001
   CYS 191 SG
   CYS 220 SG
    2.019
...

Note that the above is for bonded sulfurs in disulfides.  For all
intra-cysteine gamma sulfur distances, you'd want to do something more
like:

from pymol import cmd
from glob import glob

for file in glob("*.pdb"):
    print file
    cmd.load(file,'prot')
    for a in cmd.index("CYS/SG"):
        for b in cmd.index("CYS/SG"):
            if a[1]<b[1]:
                cmd.select("s1","%s`%d"%a)
                cmd.select("s2","%s`%d"%b)
                if cmd.select("(s1|s2) and not ?skip"):
                    cmd.iterate("s1|s2","print '
',chain,resn,resi,name")
                    print '   ',round(cmd.dist("tmp","s1","s2"),3)
                    cmd.select("skip","s1|s2|?skip")
    cmd.delete("all")

1alk.pdb
  A CYS 168 SG
  A CYS 178 SG
    1.975
  A CYS 168 SG
  A CYS 286 SG
    35.845
  A CYS 168 SG
  A CYS 336 SG
    35.029
  A CYS 168 SG
  B CYS 168 SG
    63.64
  A CYS 168 SG
  B CYS 178 SG
    63.775
  A CYS 168 SG
  B CYS 286 SG
    39.02
  A CYS 168 SG
  B CYS 336 SG
    39.314
1btu.pdb
   CYS 42 SG
   CYS 58 SG
    2.039
   CYS 42 SG
   CYS 136 SG
...


http://delsci.com/pymol

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: own...@cc... [mailto:own...@cc...]=20
> Sent: Wednesday, January 18, 2006 6:03 PM
> To: Warren DeLano
> Subject: CCL: Program or Script to Calculate Atom-Atom=20
> Distances in pdb files
>=20
> Sent to CCL by: "Irida  Kastrati" [ikastr2[a]uic.edu]
> Hello CCLers,
> Because of some excellent feedback I received when I asked=20
> for help about a year ago, I thought of using the CCL members=20
> expertise again this time.  I am looking for a free program=20
> or script that can calculate all sulfur-sulfur distances in=20
> pdb files from the Protein Data Bank. The program or script=20
> should be able to read the massive database of protein=20
> structures from the Protein Data Bank, or a local copy of PDB=20
> files. Then, pinpoint S-S distances within a certain value,=20
> or calculate the actual distance. I have access to SYBYL.
> Any suggestion is very welcome!
> Thank you in advance for your time and help.
>=20
> Sincerely,
> Irida Kastrati
> e-mail: ikastr2{=3D}uic.edu
> University of IL at Chicago
> College of Pharmacy, Medicinal Chemistry
>=20
>=20
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RE: [PyMOL] Possible to select the nth residue?

[Warren D. <wa...@de...>]

res_list =3D []

iterate name ca, res_list.append(chain+"/"+resi+"/")

cmd.indicate(res_list[2])
=20

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of Dan Kulp
> Sent: Thursday, January 19, 2006 9:37 AM
> To: dw...@ma...
> Cc: Alex Luso; pym...@li...
> Subject: Re: [PyMOL] Possible to select the nth residue?
>=20
> Sorry the below actually won't work, you'll need something more...
>=20
> nth_residue =3D 3
> previous =3D -1
> cur_res  =3D 0
> nth_resi =3D 0
> for at in cmd.get_model("molecule1 and chainA").atom:
>     if (at.resi !=3D previous):
>          cur_res++
>=20
>     if (cur_res =3D=3D nth_residue):
>          nth_resi =3D at.resi
>          break
>=20
> # Now do the selection...
> cmd.select("myselection", "molecule1 and chain A and resi %s"=20
> % (nth_resi))
>=20
>=20
> There might be a cleaner way, but something along these lines=20
> should work.
>=20
> Sorry for the first email,
> Dan
>=20
> This looks better. However you'll want to put it in a script,=20
> wrap it with a function, etc...  I haven't test the above though.
>=20
>=20
> Dan Kulp wrote:
> > I just needed to do this and this was my solution
> >
> > NTH_RESIDUE=3D3
> > cmd.select("myselection", "molecule1 and chain A and resi %s" %=20
> > (cmd.get_model("molecule1 and chain A").atom[NTH_RESIDUE]))
> >
> > will create a selection named myselection and contain only the=20
> > NTH_RESIDUE of molecule1 and chain  A.
> >
> > Hope this helps,
> > ~Dan
> >
> > Alex Luso wrote:
> >>   One more question.
> >>
> >>   Someone asked me this: is it possible in Pymol to select
> >> the nth (e.g. the 3rd) residue in a molecule/chain without
> >> knowing the pdb residue # itself?
> >>
> >>   -Alex
> >>
> >> __________________________________________________
> >> Do You Yahoo!?
> >> Tired of spam?  Yahoo! Mail has the best spam protection around=20
> >> http://mail.yahoo.com
> >>
> >> -------------------------------------------------------
> >> This SF.net email is sponsored by: Splunk Inc. Do you grep through=20
> >> log files
> >> for problems?  Stop!  Download the new AJAX search engine=20
> that makes
> >> searching your log files as easy as surfing the  web. =20
> DOWNLOAD SPLUNK!
> >>=20
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D103432&bid=3D230486&
> dat=3D121642
> >> _______________________________________________
> >> PyMOL-users mailing list
> >> PyM...@li...
> >> https://lists.sourceforge.net/lists/listinfo/pymol-users
> >>
> >>  =20
> >
> >
>=20
>=20
> --=20
>    Dan Kulp
>    Biophysics Graduate Student @ UPenn
>    dw...@ma...
>    http://dwkulp.homelinux.net/tiki/tiki-index.php
> --
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep=20
> through log files
> for problems?  Stop!  Download the new AJAX search engine that makes
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>=20
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RE: [PyMOL] selection disordered

[Warren D. <wa...@de...>]

Frank,

That PDB file has bogus/inconsistent segment identifiers that are
screwing up atomic ordering (since atoms are sorted into segments by
default).

set ignore_pdb_segi

before loading the pdb file and then everything should work file.

Cheers,
Warren


--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Frank Dressel
> Sent: Thursday, January 19, 2006 7:36 AM
> To: pym...@li...
> Subject: [PyMOL] selection disordered
>=20
> Hi there,
>=20
> i have the following problem: selecting all ca atoms in chain=20
> A of 1ao0 the amino acids in the selection are disordered=20
> with respect to their occurrence in the protein.
>=20
> After loading the protein i tried the following:
>=20
>     numbers=3D[]
>     iterate (chain a)&(name ca),(numbers.append(resi))
>     print numbers
>=20
> And what i get is the following:
>=20
>     ['56', '1', '2', '3', '4', '5', '6', '7', '8', '9', '10',=20
> '11', '12', '13', '14', '15', '16', '17', '18', '19', '20',=20
> '21', '22', '23', '24', '25', '26', '27','28', '29', '30',=20
> '31', '32', '33', '34', '35', '36', '37', '38', '39', '40',=20
> '41', '42', '43', '44', '45', '46', '47', '48', '49', '50',=20
> '51', '52', '53', '54', '55', '57', '58', '59', '60', '61', ...]
>=20
> So the 56th amino acid is BEFORE the first one. Whats going wrong?
>=20
>     Thanks:
>=20
>        Frank
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep=20
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RE: [PyMOL] reinitialize fails to clear PyMOL Viewer

[Warren D. <wa...@de...>]

Pete,

Does tbe image go away as soon as you drag the mouse in the viewer area?

Cheers,
Warren


--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Peter Adrian Meyer
> Sent: Thursday, January 19, 2006 8:00 AM
> To: pym...@li...
> Subject: [PyMOL] reinitialize fails to clear PyMOL Viewer
>=20
> Hi all,
>=20
> I've run into a small glitch that I was wondering if anyone=20
> else had seen (or knew of a way to fix).  At somewhat=20
> unpredicatable intervals, the reinitialize command doesn't=20
> actually clear the viewer display (objects show as deleted,=20
> but are still visible).
>=20
> Any ideas?
>=20
> Pete
>=20
> Pete Meyer
> Fu Lab
> BMCB grad student
> Cornell University
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep=20
> through log files for problems?  Stop!  Download the new AJAX=20
> search engine that makes searching your log files as easy as=20
> surfing the  web.  DOWNLOAD SPLUNK!
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D103432&bid=3D230486&
> dat=3D121642
> _______________________________________________
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> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
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>=20

RE: [PyMOL] Labels throw shadows in Ray traced images - possible to turn off?

[Alex L. <tap...@ya...>]

  Thanks, that works. I missed that option (didn't look far
enough to the right when i hit set label "tab").

  And, yes, in build 33, they are on by default (I think).

  -Alex

--- Warren DeLano <wa...@de...> wrote:

> In the current development version, shadows are off for
> labels by
> default...
> 
> set label_shadow_mode, 0
> 
> If that doesn't work in your build, it will in the next
> release.
> 
> Cheers,
> Warren
> 
> 
> --
> Warren L. DeLano, Ph.D.                     
> Principal Scientist
> 
> . DeLano Scientific LLC  
> . 400 Oyster Point Blvd., Suite 213           
> . South San Francisco, CA 94080 USA   
> . Biz:(650)-872-0942  Tech:(650)-872-0834     
> . Fax:(650)-872-0273  Cell:(650)-346-1154
> . mailto:wa...@de...      
>  
> 
> > -----Original Message-----
> > From: pym...@li... 
> > [mailto:pym...@li...] On
> Behalf Of 
> > Alex Luso
> > Sent: Thursday, January 19, 2006 9:09 AM
> > To: pym...@li...
> > Subject: [PyMOL] Labels throw shadows in Ray traced
> images - 
> > possible to turn off?
> > 
> > 
> >   Hi,
> > 
> >   I noticed that Ray traced output of images containing
> text 
> > labels will show the shadows thrown by and on these
> labels. 
> > This is a nice feature but is there also an easy way to
> turn 
> > this off (i.e. selectively turn off shadows from/on
> text 
> > while mantaining global shadows)?
> > 
> >   Thanks,
> >   -Alex
> > 
> > __________________________________________________
> > Do You Yahoo!?
> > Tired of spam?  Yahoo! Mail has the best spam
> protection 
> > around http://mail.yahoo.com 
> > 
> > 
> > -------------------------------------------------------
> > This SF.net email is sponsored by: Splunk Inc. Do you
> grep 
> > through log files
> > for problems?  Stop!  Download the new AJAX search
> engine that makes
> > searching your log files as easy as surfing the  web.  
> > DOWNLOAD SPLUNK!
> >
>
http://sel.as-us.falkag.net/sel?cmd=lnk&kid=103432&bid=230486&
> > dat=121642
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> >
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> > 
> > 
> > 
> > 
> 


__________________________________________________
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RE: [PyMOL] Labels throw shadows in Ray traced images - possible to turn off?

[Warren D. <wa...@de...>]

In the current development version, shadows are off for labels by
default...

set label_shadow_mode, 0

If that doesn't work in your build, it will in the next release.

Cheers,
Warren


--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Alex Luso
> Sent: Thursday, January 19, 2006 9:09 AM
> To: pym...@li...
> Subject: [PyMOL] Labels throw shadows in Ray traced images -=20
> possible to turn off?
>=20
>=20
>   Hi,
>=20
>   I noticed that Ray traced output of images containing text=20
> labels will show the shadows thrown by and on these labels.=20
> This is a nice feature but is there also an easy way to turn=20
> this off (i.e. selectively turn off shadows from/on text=20
> while mantaining global shadows)?
>=20
>   Thanks,
>   -Alex
>=20
> __________________________________________________
> Do You Yahoo!?
> Tired of spam?  Yahoo! Mail has the best spam protection=20
> around http://mail.yahoo.com=20
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep=20
> through log files
> for problems?  Stop!  Download the new AJAX search engine that makes
> searching your log files as easy as surfing the  web. =20
> DOWNLOAD SPLUNK!
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D103432&bid=3D230486&
> dat=3D121642
> _______________________________________________
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> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
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