pymol-users Mailing List for PyMOL Molecular Graphics System

Hello Vladimir,

May I request you turn off your virtual cards that come as
an attachment to every message you send to the list? I already
have a small collection of them :) Thanks.

Zach

> =20
>
>>Hello I made a Debian package for Pymol (only for x86 arch). Here are=20
>>instructions for how to get it and how to use it.
>>
>>There are two ways to install pymol from a Debian package :
>>
>>The automatic way:
>>add this line in your /etc/apt/sources.list file or ask your sys admin=20
>>to do so.
>>deb http://debian.acidspace.net custom/
>>
>>The advantage of this method is that you will always have an up to date=
=20
>>version of PyMOL
>>   =20
>>
>
>What are the advantages over running the official Debian pymol package?
>
>
>Michael
>
>
>
>
> =20
>

Sorry, I forgot to mention, my package is for Pymol v.0.97(and I will=20
keep it up to date). The official debian package is Pymol 0.95.

Vladimir

--=20

Daric Vladimir
Unit=E9 de Biochimie Structurale

Institut Pasteur
25 rue du Dr. Roux, 75724 Paris, France

Tel. +33 (0)1 40 61 35 46
Fax. +33 (0)1 45 68 86 04

http://www.pasteur.fr/recherche/unites/Bstruct
-----------------------------------------------

Hi,

I get the following error mesage when I select "Display" --> 
"Performance and Quality" --> "Maximum (or Reasonable) Performance" :
Error: unknown setting 'stick_balls'

I trace the error to "modules/pymol/util.py", where there are a couple 
of occurences of 'stick_balls' that I think should be 'stick_ball'.

I am not sure if the change in settings gets completed, since for the 
two choices that refer to 'stick_balls' I do not get the "PyMOL>rebuild" 
message like I get for the two higher quality choices that properly call 
for 'stick_ball'.

In any case, here is the diff file for those interested:

--- modules/pymol/util.py       2004-07-08 14:12:00.000000000 -0400
+++ modules/pymol/util.py.new   2004-07-29 14:56:53.673856552 -0400
@@ -267,7 +267,7 @@
       cmd.set('sphere_quality',1)
       cmd.set('cartoon_sampling',6)
       cmd.set('transparency_mode',2)
-      cmd.set('stick_balls',0.0)
+      cmd.set('stick_ball',0.0)
       cmd.do("rebuild")        
    else: # maximum performance
       cmd.set('line_smooth',0)
@@ -278,7 +278,7 @@
       cmd.set('sphere_quality',0)
       cmd.set('cartoon_sampling',3)
       cmd.set('transparency_mode',0)
-      cmd.set('stick_balls',0.0)
+      cmd.set('stick_ball',0.0)
       cmd.do("rebuild")        
   

Cheers,

Stéphane

-- 

=================================================
Stéphane M. Gagné, Ph.D.
Professeur, biochimie et CREFSIP
3255 pavillon Marchand
Université Laval, Québec, Canada     G1K 7P4
Téléphone (bureau):  (418) 656-7860
Téléphone (labo):    (418) 656-2131, poste 4530
Télécopieur (Fax):   (418) 656-7176
courrier électronique: sg...@rs...
================================================= 

On Thu, Jul 29, 2004 at 04:44:32PM +0200, Vladimir Daric wrote:
> Hello I made a Debian package for Pymol (only for x86 arch). Here are 
> instructions for how to get it and how to use it.
> 
> There are two ways to install pymol from a Debian package :
> 
> The automatic way:
> add this line in your /etc/apt/sources.list file or ask your sys admin 
> to do so.
> deb http://debian.acidspace.net custom/
> 
> The advantage of this method is that you will always have an up to date 
> version of PyMOL

What are the advantages over running the official Debian pymol package?


Michael

Hello I made a Debian package for Pymol (only for x86 arch). Here are 
instructions for how to get it and how to use it.

-------------------------------------------------------------
There are two ways to install pymol from a Debian package :

The automatic way:
add this line in your /etc/apt/sources.list file or ask your sys admin 
to do so.
deb http://debian.acidspace.net custom/

don't forget to do 'apt-get update' before doing 'apt-get install pymol'

The advantage of this method is that you will always have an up to date 
version of PyMOL

Manual installation :
Download pymol_0.97-1_i386.deb file from
http://debian.acidspace.net/custom/
or from
ftp://ftp.pasteur.fr/pub/GenSoft/unix/molecular_graphics/Pymol/

log as root and type :
dpkg -i pymol_0.97-1_i386.deb

------------------------------------------

Dear All.
Is it possible to save picture in vector postscript
format?
Thanks.
Petro


		
__________________________________
Do you Yahoo!?
New and Improved Yahoo! Mail - Send 10MB messages!
http://promotions.yahoo.com/new_mail 

> areas of the protein that undergo movement and show general trends.  There is
> also a server at Yale (http://www.molmovdb.org/molmovdb/ ) that will perform
> simulated annealing while morphing between two structures, thereby producing
> intermediate structures that violate fewer protein restraints.

You can also just download the script that does this.  If you know enough
about CNS, this also allows you to change which energy terms are used.
I've found that eliminating dihedrals from the equation sometimes produces
smoother movies - for example, RNA base flips aren't so sudden - but still
more realistic than linear interpolation.

This doesn't actually do simulated annealing, only energy minimization.
I'd like to figure out how to do generalized targeted molecular dynamics
(see for example http://sigler.bioch.bcm.tmc.edu/MaLab/gallery.php) in
the context of the morph server, but this is probably a fairly difficult
project.

If you have the molecules "mol01" and "mol02" open, you can type "mol_list 
= cmd.get_names()" to get the list of molecules put into the variable 
mol_list: ['mol01' ,'mol02'].

Now let's say you've got those two molecules open and you've made some 
selections within those two molecules.  The GL window will then have a 
list of objects like:  "mol01", "mol02", "pk1", "pkmol", "pkresi", ... 
"sel01", "sel02".  Does anyone know of a command analogous to 
cmd.get_names() that will return this list of objects from the GL window. 
( cmd.get_names() still returns only ['mol01', 'mol02'] )

Thanks,
Al Pierce

Hi,

I am a new user of PyMol. I work with spherical virus structures and
some of my questions could be specific to these structures :

1) I am trying to get a cut away view of the density and the plane where
the cut is made is always shaded in black color. I would like it to be 
some shade of the
color I use for the surface in general. how do I achieve this?

2) Is there a command for masking density : for example, given a radius 
and center of the
density volume, can we carve out the density INSIDE this specified 
sphere or OUTSIDE the
specified sphere as the case may be?!

3) Is it possible to color the spherical virus particle density using a 
radial color ramp ?

Thank you for your help in advance!
-Padma

______________________________
Padmaja Natarajan, Ph.D
The Scripps Research Institute
La Jolla, California, USA.

Hello, Frank.

I have done this and created a web page to tell others how to do it.  I used 
the Uppsala Software Factory program LSQMAN to generate structures that morph 
from one structure to another.  This is quick and easy and can be done on 
your own computer.  The intermediate structures should not be thought of 
actual intermediates in the motion, but they can be useful for identifying 
areas of the protein that undergo movement and show general trends.  There is 
also a server at Yale (http://www.molmovdb.org/molmovdb/ ) that will perform 
simulated annealing while morphing between two structures, thereby producing 
intermediate structures that violate fewer protein restraints.  

The page I wrote is 
http://ginsberg.med.virginia.edu/~dcoop/Help/morph.html

Good luck,
David

PS.  I wrote this over a year ago, and I haven't kept up with Pymol changes.  
If you find anything that needs to be changed, let me know.
-------------------------------------------
David Cooper, Ph.D.
University of Virginia
Molecular Physiology and Biological Physics
Jordan Hall, Box 800736
1300 Jefferson Park Ave
Charlottesville, VA 22908-0736
Phone: (434) 982-3151
Fax: (434) 982-1616



On Wednesday 28 July 2004 02:32 am, S. Frank Yan wrote:
> Hi,
>
> I have two static frames of a loop structure, one is in an open form,
> the other is in closed form.  I would like to make an animation which
> shows the transformation movement from open to closed.  I was wondering
> if Pymol can handle this.
>
> Thanks,
> Frank
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by BEA Weblogic Workshop
> FREE Java Enterprise J2EE developer tools!
> Get your free copy of BEA WebLogic Workshop 8.1 today.
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> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Hi,

I have two static frames of a loop structure, one is in an open form,
the other is in closed form.  I would like to make an animation which
shows the transformation movement from open to closed.  I was wondering
if Pymol can handle this.

Thanks,
Frank

> Is there a way for me to define a plane of atoms say 4 Nitrogens in a
> heme complex and then determine how far out-of-plane the Fe atom is?  If
so
> either in Pymol or another program I'd love to know the secret.

Hello Kristl,

have you tried to just individually add up the x, y, and z coordinates of
the four nitrogens and calculate the mean? This will give you a virtual
centre point of the plane. Finally, just create a new pdb file containing
the pseudo atom, load it into PyMOL and determine the distance between this
pseudo atom and your iron atom.

Best regards,
Bartholomeus

On Mon, 26 Jul 2004 10:40:47 +0100, Roger Dodd <rb...@he...> =20
wrote:

> Hi everyone,
>
> I've recently updated to the 0.97 release of pymol and although it ran =
=20
> fine to start with, it's now generating a segmentation fault. I =20
> installed from the * pymol-0_97-bin-linux-libc6-i386.tgz* =20
> <http://prdownloads.sourceforge.net/pymol/pymol-0_97-bin-linux-libc6-i3=
86.tgz?download> =20
> file into /usr/local/pymol and ran setup.sh. Then when running the =20
> pymol.com script I get the following:
>
> ./pymol.com: line 14: 31156 Segmentation fault      =20
> $PYMOL_PATH/pymol.exe $*
>
> I'm not sure exactly what's causing this and any help would be =20
> appreciated. I've tried completely removing the pymol directory and =20
> reinstalling but I still get the same error.

$PYMOL_PATH/pymol.exe $* <- this looks suspicious.

Did you tried to compile pymol as a monolythic thing? I don't beleive tha=
t =20
still works.
I use $PYMOL_PATH/ext/bin/python $PYMOL_PATH/modules/pymol/__init__.py $*

I'll send you my Rules.make and pymol.com.
I was able to build it simply with a symlink from ext to /usr


>
> Cheers
>
> Roger
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by BEA Weblogic Workshop
> FREE Java Enterprise J2EE developer tools!
> Get your free copy of BEA WebLogic Workshop 8.1 today.
> http://ads.osdn.com/?ad_id=3D4721&alloc_id=3D10040&op=3Dclick
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>



--=20
Don't go around saying the world owes you a living.
The world owes you nothing.  It was here first.
          -- Mark Twain

Hi everyone,

I've recently updated to the 0.97 release of pymol and although it ran 
fine to start with, it's now generating a segmentation fault. I 
installed from the * pymol-0_97-bin-linux-libc6-i386.tgz* 
<" rel="nofollow">http://prdownloads.sourceforge.net/pymol/pymol-0_97-bin-linux-libc6-i386.tgz?download> 
file into /usr/local/pymol and ran setup.sh. Then when running the 
pymol.com script I get the following:

./pymol.com: line 14: 31156 Segmentation fault      $PYMOL_PATH/pymol.exe $*

I'm not sure exactly what's causing this and any help would be 
appreciated. I've tried completely removing the pymol directory and 
reinstalling but I still get the same error.

Cheers

Roger

On Jul 23, 2004, at 4:16 PM, Chris Larkin wrote:
> hi michael-
> such a figure should be no problem, could you send me an example of 
> what you're ending up with and maybe I can figure out your problem.
>
> chris


Hi Chris, thanks for your willingness to help me troubleshoot:

I may have been too hasty; I am only now learning how to use scripts in 
pymol, and at the same time experimenting with the surface 
representations, and transparency.  So I'm juggling several layers of 
new tricks and its easier to make mistakes  :0)
What I'm discovering is that several residues I anticipated to be 
surface exposed are actually buried, and that's part of the reason why 
I wasn't seeing them on the surface.  I think I now understand how to 
do this.

Kind Regards
--Michael

Hi PyMOL'ers

I'm trying to figure out how to do something that looks like the 
following figure:
http://www.uvm.edu/~mbovee/structures/surface.png

It seems any individual residues I color always map onto the cartoon 
ribbon representation rather than onto the surface representation.  Is 
this currently possible in PyMOL to do what is pictured in the link 
above?

Thanks,
--Michael Bovee, Ph.D.
Dept. of Biochemistry
University of Vermont

On Friday 23 July 2004 13:41, Dirk Kostrewa wrote:
> I wanted to have a program that can easily calculate cavities in proteins
> to be displayed with pymol (see e-mails below for details).
> Thanks to Gareth and Lari I've got two pointers to such programs:
> I've tried PASS, recommended by Lari and got a surface picture of my
> cavities within literally a few minutes, as Lari already wrote.

The rTools (http://www.rubor.de/bioinf/pymol_rubor.html) also contain a 
fucntion to interface PASS with PyMOL.

-- 
Lieven Buts
Department of Ultrastructure
Vrije Universiteit Brussel

Hello,

the old code of the scriptBox was converted into a modern PyMOL plugin, 
hopefully eliminating all installation problems and stripping down code 
size to 3 KB.

It is also available from
http://www.rubor.de/bioinf/pymol_extensions.html

Kristian Rother

I wanted to have a program that can easily calculate cavities in proteins t=
o=20
be displayed with pymol (see e-mails below for details).
Thanks to Gareth and Lari I've got two pointers to such programs:
I've tried PASS, recommended by Lari and got a surface picture of my caviti=
es=20
within literally a few minutes, as Lari already wrote.=20
I've ordered SURFNET, recommended by Gareth and will also try it (it needs =
a=20
signed license agreement returned by mail).

Many thanks again!

Best regards,

Dirk.

Gareth Stockwell wrote:
> One program which can do this is SURFNET:
>
> http://www.biochem.ucl.ac.uk/~roman/surfnet/surfnet.html
>
> There are two ways in which cavities can be displayed:
>
> i) SURFNET can write out PDB format files containing the atoms/residues
> lining each cleft, which you can view directly
>
> ii) If linked with the CCP4 libraries when compiled, SURFNET can write
> CCP4 format density maps which describe the shape of each cavity.  These
> can be loaded into PyMOL and contoured to show the location of each
> cleft.
>
> HTH
> Gareth

Lari Lehti=F6 wrote:
> I was looking for such a program couple of days ago, and I found "pass".
>
> http://www.ccl.net/cca/software/UNIX/pass/overview.shtml
>
> I saw the cavities in couple of minutes in pymol :) I'm not familiar with
> voidoo, so I don't know if you will find this usefull or not...
>
> My current problem is related to this one, so I'll post it here also.
> I would like to calculate surface of the cavity with pymol and show this =
as
> a cavity going in to the protein. But the surface is all grey, because it
> is the "inside". Is there a way to map the colours also to the other side
> of the surface?
>
> best regards,
>
> ~Lari~
>
>
> =BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=
=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB
> Lari Lehti=F6
> University of Helsinki
> Institute of Biotechnology
> Macromolecular X-ray crystallography
> P.O.Box 65
> 00014 HY
> Finland
> =BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=
=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB



> Quoting Dirk Kostrewa <dir...@ps...>:
>
> # Dear PyMol users,
> #
> # I'm looking for a program that can calculate and write out cavities in a
> #
> # format that can be converted such that I can display it with PyMol (I'm
> # not
> # satisfied with the results from VOIDOO). Could you please send me any
> # pointer
> # to a program that you found useful? BTW, this would be my wish for a
> # next
> # release of PyMol!
> #
> # Best regards,
> #
> # Dirk.
> #
> # --
> #
> # ****************************************
> # Dirk Kostrewa
> # Paul Scherrer Institut
> # Life Sciences, OFLC/110
> # CH-5232 Villigen PSI, Switzerland
> # Phone: 	+41-56-310-4722
> # Fax: 	+41-56-310-5288
> # E-mail:	dir...@ps...
> # http://sb.web.psi.ch
> # ****************************************
> #
> #
> #
> # -------------------------------------------------------
> # This SF.Net email is sponsored by BEA Weblogic Workshop
> # FREE Java Enterprise J2EE developer tools!
> # Get your free copy of BEA WebLogic Workshop 8.1 today.
> # http://ads.osdn.com/?ad_id=3D4721&alloc_id=3D10040&op=3Dclick
> # _______________________________________________
> # PyMOL-users mailing list
> # PyM...@li...
> # https://lists.sourceforge.net/lists/listinfo/pymol-users
> #

=2D-=20

****************************************
Dirk Kostrewa
Paul Scherrer Institut
Life Sciences, OFLC/110
CH-5232 Villigen PSI, Switzerland
Phone: 	+41-56-310-4722
=46ax: 	+41-56-310-5288
E-mail:	dir...@ps...
http://sb.web.psi.ch
****************************************

Hi,

I'm trying to add some labels to a diagram using the cyl_text method, 
but I can't find any way to change the font size. In the only example 
I've found:

# draw text using cgo
from pymol import cmd
from pymol.cgo import *
from pymol.vfont import plain

cgo = []
axes = [[2.0,0.0,0.0],[0.0,2.0,0.0],[0.0,0.0,2.0]]
pos = [0.0,-3.0,0.0]
cyl_text(cgo,plain,pos,'Hello Universe',0.10,axes=axes)
cmd.load_cgo(cgo,'txt')
cmd.zoom("all",2.0)

Changing the '0.10' parameter only alters the thickness of the text, 
not the font size. Is there a way of altering font size here?

Alex Gutteridge
European Bioinformatics Institute
Cambridge CB10 1SD
UK

Tel: 01223 492550
Email: al...@eb...

Dear PyMOL users,

One of our students and i have written a plugin that colors proteins by 
the amino acid scales on www.Expasy.ch.

It is available at http://www.rubor.de/bioinf

Also, i have updated the PyMOL tips pages to reflect some topics 
discussed here in recent months.

Yours,

   Kristian Rother

Okay, it seems that "set auto_zoom, off" does work for PDB files, but not 
for SDF files.  I have a python script that gives these three commands:

set auto_zoom, off
load gsk_77553_l.sdf
show sticks, gsk_77553_l

But when you call the script, this is what happens in pymol

PyMOL>set auto_zoom, off
 Setting: auto_zoom set to off.
PyMOL>load gsk_77553_l.sdf
 Executive: object "gsk_77553_l" created.
PyMOL>zoom (gsk_77553_l)
PyMOL>show sticks, gsk_77553_l

Related the issue of inside-surface coloring, a useful feature to add to =
pymol would be the ability to flip surface normals for selected =
surfaces.

Just a thought.

JP Cartailler

> -----Original Message-----
> From: pym...@li... [mailto:pymol-users-
> ad...@li...] On Behalf Of Lari Lehti=F6
> Sent: Thursday, July 22, 2004 9:07 AM
> To: Dirk Kostrewa
> Cc: PyMOLBB
> Subject: Re: [PyMOL] Cavity display?
>=20
> I was looking for such a program couple of days ago, and I found =
"pass".
>=20
> http://www.ccl.net/cca/software/UNIX/pass/overview.shtml
>=20
> I saw the cavities in couple of minutes in pymol :) I'm not familiar =
with
> voidoo, so I don't know if you will find this usefull or not...
>=20
> My current problem is related to this one, so I'll post it here also.
> I would like to calculate surface of the cavity with pymol and show =
this
> as
> a cavity going in to the protein. But the surface is all grey, because =
it
> is the "inside". Is there a way to map the colours also to the other =
side
> of the surface?
>=20
> best regards,
>=20
> ~Lari~
>=20
>=20
> =
=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=
=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB
> Lari Lehti=F6
> University of Helsinki
> Institute of Biotechnology
> Macromolecular X-ray crystallography
> P.O.Box 65
> 00014 HY
> Finland
> =
=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=
=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB
>=20
> Quoting Dirk Kostrewa <dir...@ps...>:
>=20
> # Dear PyMol users,
> #
> # I'm looking for a program that can calculate and write out cavities =
in a
> #
> # format that can be converted such that I can display it with PyMol =
(I'm
> # not
> # satisfied with the results from VOIDOO). Could you please send me =
any
> # pointer
> # to a program that you found useful? BTW, this would be my wish for a
> # next
> # release of PyMol!
> #
> # Best regards,
> #
> # Dirk.
> #
> # --
> #
> # ****************************************
> # Dirk Kostrewa
> # Paul Scherrer Institut
> # Life Sciences, OFLC/110
> # CH-5232 Villigen PSI, Switzerland
> # Phone: 	+41-56-310-4722
> # Fax: 	+41-56-310-5288
> # E-mail:	dir...@ps...
> # http://sb.web.psi.ch
> # ****************************************
> #
> #
> #
> # -------------------------------------------------------
> # This SF.Net email is sponsored by BEA Weblogic Workshop
> # FREE Java Enterprise J2EE developer tools!
> # Get your free copy of BEA WebLogic Workshop 8.1 today.
> # http://ads.osdn.com/?ad_id=3D4721&alloc_id=3D10040&op=3Dclick
> # _______________________________________________
> # PyMOL-users mailing list
> # PyM...@li...
> # https://lists.sourceforge.net/lists/listinfo/pymol-users
> #
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by BEA Weblogic Workshop
> FREE Java Enterprise J2EE developer tools!
> Get your free copy of BEA WebLogic Workshop 8.1 today.
> http://ads.osdn.com/?ad_idG21&alloc_id=10040&op=3Dick
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

One program which can do this is SURFNET:

http://www.biochem.ucl.ac.uk/~roman/surfnet/surfnet.html

There are two ways in which cavities can be displayed:

i) SURFNET can write out PDB format files containing the atoms/residues
lining each cleft, which you can view directly

ii) If linked with the CCP4 libraries when compiled, SURFNET can write
CCP4 format density maps which describe the shape of each cavity.  These
can be loaded into PyMOL and contoured to show the location of each
cleft.

HTH
Gareth




On Thu, 2004-07-22 at 14:28, Dirk Kostrewa wrote:
> Dear PyMol users,
> 
> I'm looking for a program that can calculate and write out cavities in a 
> format that can be converted such that I can display it with PyMol (I'm not 
> satisfied with the results from VOIDOO). Could you please send me any pointer 
> to a program that you found useful? BTW, this would be my wish for a next 
> release of PyMol!
> 
> Best regards,
> 
> Dirk.


-- 
Gareth Stockwell
European Bioinformatics Institute

I was looking for such a program couple of days ago, and I found "pass".

http://www.ccl.net/cca/software/UNIX/pass/overview.shtml

I saw the cavities in couple of minutes in pymol :) I'm not familiar with
voidoo, so I don't know if you will find this usefull or not...

My current problem is related to this one, so I'll post it here also.
I would like to calculate surface of the cavity with pymol and show this =
as
a cavity going in to the protein. But the surface is all grey, because it
is the "inside". Is there a way to map the colours also to the other side
of the surface?

best regards,

~Lari~


=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=
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Lari Lehti=F6
University of Helsinki
Institute of Biotechnology
Macromolecular X-ray crystallography
P.O.Box 65
00014 HY
Finland
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Quoting Dirk Kostrewa <dir...@ps...>:

# Dear PyMol users,
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# I'm looking for a program that can calculate and write out cavities in =
a
#=20
# format that can be converted such that I can display it with PyMol (I'm
# not=20
# satisfied with the results from VOIDOO). Could you please send me any
# pointer=20
# to a program that you found useful? BTW, this would be my wish for a
# next=20
# release of PyMol!
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# Best regards,
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# Dirk.
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# --=20
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# ****************************************
# Dirk Kostrewa
# Paul Scherrer Institut
# Life Sciences, OFLC/110
# CH-5232 Villigen PSI, Switzerland
# Phone: 	+41-56-310-4722
# Fax: 	+41-56-310-5288
# E-mail:	dir...@ps...
# http://sb.web.psi.ch
# ****************************************
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