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Sent: 13 October 2004 23:45
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Today's Topics:
1. 2 colors for transparent surface and cartoon (Gabriel
=?iso-8859-1?Q?PA=CBS?=)
2. Re: 2 colors for transparent surface and cartoon (Tsjerk Wassenaar)
3. apbs map size (Lari =?iso-8859-1?b?TGVodGn2?=)
4. molecular Mechanics calculations (Gabriel =?iso-8859-1?Q?PA=CBS?=)
5. PyMol and Virtual Reality (Stein Jakob =?ISO-8859-1?Q?Nordb=F8?=)
6. rtools again (strange...) (Rummey, Christian)
7. Warning: Nvidia 6111 drivers for linux (peter.du...@cellbio.unige.ch)
8. using package Scientific from within pymol on OS X-X11 hybrid (gilleain
torrance)
9. Re: Warning: Nvidia 6111 drivers for linux (Yu Chen)
10. translating map/mesh (Viktor Hornak)
11. showing apbs map from a script (Osborne Michael)
12. Re: Warning: Nvidia 6111 drivers for linux (Stephane Gagne)
--__--__--
Message: 1
Date: Mon, 11 Oct 2004 17:41:34 -0000 (GMT)
From: Gabriel =?iso-8859-1?Q?PA=CBS?= <g...@dfuni.dk>
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] 2 colors for transparent surface and cartoon
Hi
I am pretty new using PyMol but it is really the best software i have ever
used from far! I love it, the pictures are so cute!
But i have a small question: i would like to use 2 different colors for a
transparent surface and the cartoon which is above, is it possible?
Thank you in adavce.
Gabriel
____________
Gabriel PAES
PhD Student
The Danish University of Pharmaceutical Sciences
Department of Medicinal Chemistry
Universitetsparken 2
2100 Copenhagen
DENMARK
Phone (+45) 35.30.62.46
E-mail g...@dfuni.dk
--__--__--
Message: 2
Date: Wed, 13 Oct 2004 09:41:19 +0200
From: Tsjerk Wassenaar <t.a.wassen...@chem.rug.nl>
To: PyMOL-users@lists.sourceforge.net
Subject: Re: [PyMOL] 2 colors for transparent surface and cartoon
Hi Gabriel,
You can set a specific color either for the surface or the cartoon with
set surface_color, color
set cartoon_color, color
or if you want to have more control over the colors you can create a new=20
object and show one in cartoon and the other in surface:
create newobj, obj
show surface, newobj
show cartoon, obj
Cheers,
Tsjerk
Gabriel PA=CBS wrote:
>Hi
>I am pretty new using PyMol but it is really the best software i have ev=
er
>used from far! I love it, the pictures are so cute!
>But i have a small question: i would like to use 2 different colors for =
a
>transparent surface and the cartoon which is above, is it possible?
>Thank you in adavce.
>Gabriel
>
>____________
>
>Gabriel PAES
>PhD Student
>The Danish University of Pharmaceutical Sciences
>Department of Medicinal Chemistry
>Universitetsparken 2
>2100 Copenhagen
>DENMARK
>
>Phone (+45) 35.30.62.46
>E-mail g...@dfuni.dk
>
>
>
>
>
>-------------------------------------------------------
>This SF.net email is sponsored by: IT Product Guide on ITManagersJournal
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s
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> =20
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--=20
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-- :)
-- :) Tsjerk A. Wassenaar, M.Sc.
-- :) Molecular Dynamics Group
-- :) Dept. of Biophysical Chemistry
-- :) University of Groningen
-- :) Nijenborgh 4
-- :) 9747 AG Groningen
-- :) The Netherlands
-- :)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-- :)
-- :) Hi! I'm a .signature virus!
-- :) Copy me into your ~/.signature to help me spread!
-- :)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
--__--__--
Message: 3
Date: Wed, 13 Oct 2004 12:41:34 +0300
From: Lari =?iso-8859-1?b?TGVodGn2?= <lari.leh...@helsinki.fi>
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] apbs map size
Hi,
I have a problem with apbs in pymol. I got it to work fine, if I cutted a=
=20
100 aminoacid stretch from my molecule and followed the instructions.=20
However my protein is a bit bigger, ~800aa, and I cannot get the apbs map=
=20
to cover my molecule. I get the whole surface, but only half of it is=20
coloured according to the electrostatics. I tried with and without an=20
external psize.py, but the result was the same. Does anyone know a=20
workaround for this?=20
~Lari~
_______________________________________
Lari Lehti=F6
University of Helsinki
Institute of Biotechnology
Macromolecular X-ray crystallography
P.O.Box 65
00014 HY
Finland
_______________________________________
--__--__--
Message: 4
Date: Wed, 13 Oct 2004 12:40:53 -0000 (GMT)
From: Gabriel =?iso-8859-1?Q?PA=CBS?= <g...@dfuni.dk>
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] molecular Mechanics calculations
Hi PyMolers
Is it possible to make some basic molecular mechanics calculations in
PyMOL, in fact I would like to measure the binding energy between a
protein and various ligands?
Thanks in advance
Gabriel
____________
Gabriel PA=CBS
PhD Student
The Danish University of Pharmaceutical Sciences
Department of Medicinal Chemistry
Universitetsparken 2
2100 Copenhagen
DENMARK
Phone (+45) 35.30.62.46
E-mail g...@dfuni.dk
--__--__--
Message: 5
From: Stein Jakob =?ISO-8859-1?Q?Nordb=F8?= <stein...@stud.ntnu.no>
To: pymol-users@lists.sourceforge.net
Date: Wed, 13 Oct 2004 11:41:18 +0200
Subject: [PyMOL] PyMol and Virtual Reality
Hi!
We are working on a project creating an OpenSource-library for a Virtual
Reality gloves/positioning device-combination that is going to be
integrated with a data analysis tool. However, the program is not in a
state where we can integrate our work yet, so we will create a prototype
to demonstrate the library's functionality.
Then, we came up with the idea of using PyMol as the prototype, using
the python API and creating a simple mapping between library events and
PyMol. Our question is simply: Is this feasible? We need to make
selections based on 3D coordinates, perform geometric transformations
(rotate/translate), viewing operations (panning, zooming, etc.), and
simple molecule manipulation. There doesn't seem to be support for 3D
coordinate selection (naturally), but is this difficult to implement (we
don't feel comfortable with altering too much the PyMol sources, but if
there was some easy way of doing it, by using some internal call or
something, we'd be interested)?
Best regards,
Stein Jakob Nordb=F8
--__--__--
Message: 6
Date: Wed, 13 Oct 2004 11:45:29 +0200
From: "Rummey, Christian" <christian.rum...@santhera.com>
To: <pymol-users@lists.sourceforge.net>
Subject: [PyMOL] rtools again (strange...)
Hi again,
1st of all thanks to Kristian -- the "time.sleep(1)" hint works fine. Maybe=
you
can help me with this one also:
calling a pdb file via
pdb CODE
usually checks if the file has already been downloaded and if yes, takes it=
from
the local repository.=20
however, calling this command from a script (within the same pymol session)=
via @script.pml (see below) ALWAYS tries to download the file, even if it =
is=20
already there. (I don't think it has anything to do with the loop).
Any ideas?=20
thanks,
christian
@script: ----------------------------
from pymol import cmd
time.sleep(1)
list =3D ('1n1m')
for strc in list:
pdb strc
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--__--__--
Message: 7
Date: Wed, 13 Oct 2004 18:12:11 +0200
From: peter.du...@cellbio.unige.ch
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Warning: Nvidia 6111 drivers for linux
Hello.
I did a scan (albeit brief) of the mailing list for this issue, but didn't find
it, so I decided to post it FYI.
I wanted to mention a serious issue I just discovered after installing the new
nvidia drivers for linux (specifically regarding the
"NVIDIA-Linux-x86-1.0-6111-pkg1.run" driver, though I imagine the same is true
for all other 6111 drivers), on a 2.4.x kernel, as well as the solution. It may
be important to make a note of this somewhere in the FAQ or installation
instructions (or perhaps it would be easy to fix in one of the pymol scripts).
PROBLEM:
========
Running Pymol gives the following message:
Traceback (most recent call last):
File "/usr/lib/python2.3/site-packages/pymol/__init__.py", line 90, in ?
import pymol
File "/usr/lib/python2.3/site-packages/pymol/__init__.py", line 306, in ?
import _cmd
ImportError: libnvidia-tls.so.1: cannot handle TLS data
SOLUTIONS:
==========
There are 2 solutions to this problem.
(1) either rename /usr/lib/tls to something else, or delete it entirely. Pymol
then works perfectly ok. However, since this is akin to "If it hurts, cut it
off", it might break something down the line. Do note though, that the files
contained within this dir are also in /usr/lib (not a symbolic link).
(2) edit /etc/default/nvidia-glx (if it exists, for me it didn't), and set
USE_TLS to 0. Reboot. Surely there must be another editable config file
somewhere with this option, but I haven't found it.
According to a thread on PyKDE, "The tls (thread local storage) stuff only
works if you are running a tls-enabled glibc on a 2.6 kernel, and when
installing nvidia-glx, you are normally asked by debconf on what to use."
This suggests anyone running the new nvidia drivers on a 2.4.x kernel may
encounter this problem. Admittedly, I haven't tested them on a 2.6.x kernel, so
I can't be sure the problem doesn't occur there either.
Hope this helps someone.
Cheers,
Peter
_.--'"`'--._ _.--'"`'--._ _.--'"`'--._ _
-:`.'|`|"':-. '-:`.'|`|"':-. '-:`.'|`|"':-. '.` :
'. | | | |'. '. | | | |'. '. | | | |'. '.:
'. '.| | | | '. '.| | | | '. '.| | | | '. '.
'. `.:_ | :_.' '. `.:_ | :_.' '. `.:_ | :_.' '. `.
`-..,..-' `-..,..-' `-..,..-' `
Laboratory of Dr. Didier Picard
University of Geneva
Department of Cell Biology
Scinces III
30, Quai Ernest-Ansermet
1211 Geneva 4
Switzerland
Tel: +41 22 379 3254
Fax: +41 22 379 6442
Email: du...@cellbio.unige.ch
http://www.picard.ch/DP/DPhome.html
_.--'"`'--._ _.--'"`'--._ _.--'"`'--._ _
-:`.'|`|"':-. '-:`.'|`|"':-. '-:`.'|`|"':-. '.` :
'. | | | |'. '. | | | |'. '. | | | |'. '.:
'. '.| | | | '. '.| | | | '. '.| | | | '. '.
'. `.:_ | :_.' '. `.:_ | :_.' '. `.:_ | :_.' '. `.
`-..,..-' `-..,..-' `-..,..-' `
--__--__--
Message: 8
From: "gilleain torrance" <gille...@hotmail.com>
To: pymol-users@lists.sourceforge.net
Date: Wed, 13 Oct 2004 17:47:48 +0000
Subject: [PyMOL] using package Scientific from within pymol on OS X-X11 hybrid
I guess this might seem obvious to some people, but I wanted to use Vectors
and Objects3D from pymol scripts, but I couldn't see how.
however, it turns out that if you copy the entire (python) source tree of
Scientific - IE:
"ScientificPython<version>/Scientific/"
into
"/Applications/PyMolX11blahHybridetc/py23/lib/python2.3/site-packages"
(er..and restart pymol (this foxed me for a while :) )
you can say :
from Scientific.Geometry import Vector
print Vector((0,0,0))
and get
[0 0 0]
hopefully! Anyway, there might be a better way, but this works. One tiny
glitch is the change from Numeric to numarray. This can be 'fixed'
('hacked') by using *cough*perl*cough*:
perl -i -p -e 's/Numeric/numarray/g' *.py */*.py
which should substitiute all instances of 'Numeric' with 'numarray'.
gilleain torrance
--__--__--
Message: 9
Date: Wed, 13 Oct 2004 13:54:19 -0400 (EDT)
From: Yu Chen <c...@hhmi.umbc.edu>
To: peter.du...@cellbio.unige.ch
cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Warning: Nvidia 6111 drivers for linux
Hi, Peter
What Linux are you using? Seems it's not a problem on RedHat linux, I am
running both 7.3 and EL-AS, with 2.4.20 and 2.4.21 kernel respectively,
and the exact same NVIDIA version without any problem at all.
Although we are using python2.2, looks like you are using python2.3, maybe
that's the problem?
Best
Chen
On Wed, 13 Oct 2004 peter.du...@cellbio.unige.ch wrote:
> Hello.
>
> I did a scan (albeit brief) of the mailing list for this issue, but didn't
> find
> it, so I decided to post it FYI.
>
> I wanted to mention a serious issue I just discovered after installing the new
> nvidia drivers for linux (specifically regarding the
> "NVIDIA-Linux-x86-1.0-6111-pkg1.run" driver, though I imagine the same is true
> for all other 6111 drivers), on a 2.4.x kernel, as well as the solution. It
> may
> be important to make a note of this somewhere in the FAQ or installation
> instructions (or perhaps it would be easy to fix in one of the pymol scripts).
>
>
> PROBLEM:
> ========
>
> Running Pymol gives the following message:
>
> Traceback (most recent call last):
> File "/usr/lib/python2.3/site-packages/pymol/__init__.py", line 90, in ?
> import pymol
> File "/usr/lib/python2.3/site-packages/pymol/__init__.py", line 306, in ?
> import _cmd
> ImportError: libnvidia-tls.so.1: cannot handle TLS data
>
>
> SOLUTIONS:
> ==========
>
> There are 2 solutions to this problem.
>
> (1) either rename /usr/lib/tls to something else, or delete it entirely. Pymol
> then works perfectly ok. However, since this is akin to "If it hurts, cut it
> off", it might break something down the line. Do note though, that the files
> contained within this dir are also in /usr/lib (not a symbolic link).
>
> (2) edit /etc/default/nvidia-glx (if it exists, for me it didn't), and set
> USE_TLS to 0. Reboot. Surely there must be another editable config file
> somewhere with this option, but I haven't found it.
>
> According to a thread on PyKDE, "The tls (thread local storage) stuff only
> works if you are running a tls-enabled glibc on a 2.6 kernel, and when
> installing nvidia-glx, you are normally asked by debconf on what to use."
>
> This suggests anyone running the new nvidia drivers on a 2.4.x kernel may
> encounter this problem. Admittedly, I haven't tested them on a 2.6.x kernel,
> so
> I can't be sure the problem doesn't occur there either.
>
> Hope this helps someone.
>
> Cheers,
> Peter
>
>
> _.--'"`'--._ _.--'"`'--._ _.--'"`'--._ _
> -:`.'|`|"':-. '-:`.'|`|"':-. '-:`.'|`|"':-. '.` :
> '. | | | |'. '. | | | |'. '. | | | |'. '.:
> '. '.| | | | '. '.| | | | '. '.| | | | '. '.
> '. `.:_ | :_.' '. `.:_ | :_.' '. `.:_ | :_.' '. `.
> `-..,..-' `-..,..-' `-..,..-' `
>
> Laboratory of Dr. Didier Picard
> University of Geneva
> Department of Cell Biology
> Scinces III
> 30, Quai Ernest-Ansermet
> 1211 Geneva 4
> Switzerland
>
> Tel: +41 22 379 3254
> Fax: +41 22 379 6442
>
> Email: du...@cellbio.unige.ch
>
> http://www.picard.ch/DP/DPhome.html
>
> _.--'"`'--._ _.--'"`'--._ _.--'"`'--._ _
> -:`.'|`|"':-. '-:`.'|`|"':-. '-:`.'|`|"':-. '.` :
> '. | | | |'. '. | | | |'. '. | | | |'. '.:
> '. '.| | | | '. '.| | | | '. '.| | | | '. '.
> '. `.:_ | :_.' '. `.:_ | :_.' '. `.:_ | :_.' '. `.
> `-..,..-' `-..,..-' `-..,..-' `
>
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: IT Product Guide on ITManagersJournal
> Use IT products in your business? Tell us what you think of them. Give us
> Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out more
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> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
--__--__--
Message: 10
Date: Wed, 13 Oct 2004 15:01:04 -0400
From: Viktor Hornak <hor...@csb.sunysb.edu>
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] translating map/mesh
Hello,
I loaded an Xplor map and created a mesh:
load grid.xplor, map1
isomesh mesh1, map1, 30
Now I need to translate the mesh by 1.0A in all three directions
(x,y,z). In other words, I need to shift the mesh object by some offset
vector. Is there any way to do that in pymol? It seems like
"alter_state" (alter_state 1,(mesh1),x=x+1.0, etc.) and undocumented
"translate" (translate [1,1,1],mesh1) only work for atoms/molecules and
not for arbitrary objects.
Thanks for help,
-Viktor
--
Viktor Hornak
SUNY at Stony Brook
--__--__--
Message: 11
Date: Wed, 13 Oct 2004 14:59:57 -0400
From: "Osborne Michael" <michael.osbo...@umontreal.ca>
To: <pymol-users@lists.sourceforge.net>
Subject: [PyMOL] showing apbs map from a script
HI everyone
I'm pretty new to pymol and I'm trying to show an electrostatic surface. =
I have managed to use the apbs plugin to do this - however I REALLY want =
to be able to do this from a .pml script since this would make it easier =
to do some movies. Anyone have any ideas how to do this?
Thanks in advance=20
Mike
------------------
Mike Osborne
NMR manager IRIC -Universite de Montreal
--__--__--
Message: 12
Date: Wed, 13 Oct 2004 17:48:08 -0400
From: Stephane Gagne <sga...@rsvs.ulaval.ca>
Subject: Re: [PyMOL] Warning: Nvidia 6111 drivers for linux
To: pymol-users@lists.sourceforge.net
Hi Peter,
Just to provide report that 611 driver works without problem with:
- pymol 0.97
- python 2.3.3
- 2.6.7-gentoo-r12 kernel
- nvidia-kernel-1.0.6111
- nvidia-glx-1.0.6111
- xfree-4.3.0
- GeForce2 Go graphic card (as well as three other types of cards)
Cheers,
St=E9phane
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D
St=E9phane M. Gagn=E9, Ph.D.
Professeur, biochimie et CREFSIP
3255 pavillon Marchand
Universit=E9 Laval, Qu=E9bec, Canada G1K 7P4
T=E9l=E9phone (bureau): (418) 656-7860
T=E9l=E9phone (labo): (418) 656-2131, poste 4530
T=E9l=E9copieur (Fax): (418) 656-7176
courrier =E9lectronique: sga...@rsvs.ulaval.ca
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=20
Yu Chen wrote:
> Hi, Peter
>
> What Linux are you using? Seems it's not a problem on RedHat linux,=
I=20
> am running both 7.3 and EL-AS, with 2.4.20 and 2.4.21 kernel=20
> respectively, and the exact same NVIDIA version without any problem=
at=20
> all.
> Although we are using python2.2, looks like you are using python2.3=
,=20
> maybe that's the problem?
>
> Best
> Chen
>
>
> On Wed, 13 Oct 2004 peter.du...@cellbio.unige.ch wrote:
>
>> Hello.
>>
>> I did a scan (albeit brief) of the mailing list for this issue, bu=
t=20
>> didn't find
>> it, so I decided to post it FYI.
>>
>> I wanted to mention a serious issue I just discovered after=20
>> installing the new
>> nvidia drivers for linux (specifically regarding the
>> "NVIDIA-Linux-x86-1.0-6111-pkg1.run" driver, though I imagine the=
=20
>> same is true
>> for all other 6111 drivers), on a 2.4.x kernel, as well as the=
=20
>> solution. It may
>> be important to make a note of this somewhere in the FAQ or instal=
lation
>> instructions (or perhaps it would be easy to fix in one of the pym=
ol=20
>> scripts).
>>
>>
>> PROBLEM:
>> =3D=3D=3D=3D=3D=3D=3D=3D
>>
>> Running Pymol gives the following message:
>>
>> Traceback (most recent call last):
>> File "/usr/lib/python2.3/site-packages/pymol/__init__.py", line 9=
0,=20
>> in ?
>> import pymol
>> File "/usr/lib/python2.3/site-packages/pymol/__init__.py", line 3=
06,=20
>> in ?
>> import _cmd
>> ImportError: libnvidia-tls.so.1: cannot handle TLS data
>>
>>
>> SOLUTIONS:
>> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
>>
>> There are 2 solutions to this problem.
>>
>> (1) either rename /usr/lib/tls to something else, or delete it=
=20
>> entirely. Pymol
>> then works perfectly ok. However, since this is akin to "If it hur=
ts,=20
>> cut it
>> off", it might break something down the line. Do note though, that=
=20
>> the files
>> contained within this dir are also in /usr/lib (not a symbolic lin=
k).
>>
>> (2) edit /etc/default/nvidia-glx (if it exists, for me it didn't),=
=20
>> and set
>> USE_TLS to 0. Reboot. Surely there must be another editable config=
file
>> somewhere with this option, but I haven't found it.
>>
>> According to a thread on PyKDE, "The tls (thread local storage) st=
uff=20
>> only
>> works if you are running a tls-enabled glibc on a 2.6 kernel, and =
when
>> installing nvidia-glx, you are normally asked by debconf on what t=
o=20
>> use."
>>
>> This suggests anyone running the new nvidia drivers on a 2.4.x ker=
nel=20
>> may
>> encounter this problem. Admittedly, I haven't tested them on a 2.6=
.x=20
>> kernel, so
>> I can't be sure the problem doesn't occur there either.
>>
>> Hope this helps someone.
>>
>> Cheers,
>> Peter
>>
>>
>> _.--'"`'--._ _.--'"`'--._ _.--'"`'--._ _
>> -:`.'|`|"':-. '-:`.'|`|"':-. '-:`.'|`|"':-. '.` :
>> '. | | | |'. '. | | | |'. '. | | | |'. '.:
>> '. '.| | | | '. '.| | | | '. '.| | | | '. '.
>> '. `.:_ | :_.' '. `.:_ | :_.' '. `.:_ | :_.' '. `.
>> `-..,..-' `-..,..-' `-..,..-' `
>>
>> Laboratory of Dr. Didier Picard
>> University of Geneva
>> Department of Cell Biology
>> Scinces III
>> 30, Quai Ernest-Ansermet
>> 1211 Geneva 4
>> Switzerland
>>
>> Tel: +41 22 379 3254
>> Fax: +41 22 379 6442
>>
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>> _.--'"`'--._ _.--'"`'--._ _.--'"`'--._ _
>> -:`.'|`|"':-. '-:`.'|`|"':-. '-:`.'|`|"':-. '.` :
>> '. | | | |'. '. | | | |'. '. | | | |'. '.:
>> '. '.| | | | '. '.| | | | '. '.| | | | '. '.
>> '. `.:_ | :_.' '. `.:_ | :_.' '. `.:_ | :_.' '. `.
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