pymol-users Mailing List for PyMOL Molecular Graphics System

Hi Colin,
> Does anyone have any experience in running pymol in 3D using a DLP
> projector? I have an Optoma EW610ST, running from a windows seven machine
> using a Geforce GT620 GPU. The computer and projector are connected via
> HDMI but at present I am not able to configure any 3D output.
>
GeForce cards are incapable of presenting windowed OpenGL 3D at 120 Hz. You
need a Quadro card. The NVidia 3D Vision (
http://www.nvidia.com/object/3d-vision-main.html) page should have all the
info you need.
Cheers,
-- Jason
-- 
Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.
(e) Jas...@sc...
(o) +1 (603) 374-7120

 
 
Dear pymol users,
I want to make a cross-section on a ion tunnel protein to cut it in half and observe the intenal characters of the tunnel. According to materials on web, I runed the following commands:
hide all
show surface
set ray_trace_mode, 0
set two_sided_lighting, off
set ray_interior_color, grey50
 
But I didn't see any obvious change on the structure except that the protein became dim. Could you help me with that?
Tnanks in advance!
 
Yeping Sun

Hi Gary & Jason,
two more things to add:
Optimized anaglyph is not available in immediate mode rendering.
You can reset all settings like this:
PyMOL> reinitialize settings
Cheers,
 Thomas
Jason Vertrees wrote, On 06/27/13 15:01:
> Hi Gary,
> 
> I think you misunderstood.
> 
> First, with a good video card, use Setting > Rendering > Modernize for
> the fastest and highest quality on screen rendering. In fact, it's
> essentially as good as ray tracing but without shadows. If your
> machine cannot handle this, the fallback is immediate mode rendering,
> which PyMOL has been using for years. Machines with older and lower
> quality video cards sometimes cannot handle this rendering technique:
> they're simply incapable of using such drawing techniques.
> 
>> Point 4 should now be:
>> 4) do not use 'ray' when trying to use anaglyph stereo. This is a shame because an anaglyph image for a slide or printout might be useful.
> 
> You have this backwards. The 'ray' command works just fine in anaglyph
> mode. I've made countless 3D images using 'ray' and anaglyph mode.
> 
>> Some irreversible colour changes are frustrating after working for hours on molecular structures, and then finding anaglyph does not work. That’s why I'd like to find a 'reset' command for the settings – edit all settings. Initialise wipes out all my hard work (molecules, objects, selections, maps, etc etc). Currently I just have to revert to the last saved pse file.
> 
> Since we do not have 'undo' for things like colors you have to save
> keep saving your session files so you don't lose any color changes.
> 
>> Any idea why using modern shaders does not work with anaglyph and might this be improved later?
> 
> Again, modern shaders do indeed work with PyMOL–I use them all the
> time–your video card just has to be good enough and you need to be
> using PyMOL v1.5 or later.
> 
> Cheers,
> 
> -- Jason
-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Hi Gary,
I think you misunderstood.
First, with a good video card, use Setting > Rendering > Modernize for
the fastest and highest quality on screen rendering. In fact, it's
essentially as good as ray tracing but without shadows. If your
machine cannot handle this, the fallback is immediate mode rendering,
which PyMOL has been using for years. Machines with older and lower
quality video cards sometimes cannot handle this rendering technique:
they're simply incapable of using such drawing techniques.
> Point 4 should now be:
> 4) do not use 'ray' when trying to use anaglyph stereo. This is a shame because an anaglyph image for a slide or printout might be useful.
You have this backwards. The 'ray' command works just fine in anaglyph
mode. I've made countless 3D images using 'ray' and anaglyph mode.
> Some irreversible colour changes are frustrating after working for hours on molecular structures, and then finding anaglyph does not work. That’s why I'd like to find a 'reset' command for the settings – edit all settings. Initialise wipes out all my hard work (molecules, objects, selections, maps, etc etc). Currently I just have to revert to the last saved pse file.
Since we do not have 'undo' for things like colors you have to save
keep saving your session files so you don't lose any color changes.
> Any idea why using modern shaders does not work with anaglyph and might this be improved later?
Again, modern shaders do indeed work with PyMOL–I use them all the
time–your video card just has to be good enough and you need to be
using PyMOL v1.5 or later.
Cheers,
-- Jason
> From: Jason Vertrees <jas...@sc...>
> Date: Wednesday, 26 June 2013 21:53
> To: Gary Hunter <gar...@um...>
> Cc: Thomas Holder <tho...@sc...>, "pym...@li..." <pym...@li...>
> Subject: Re: [PyMOL] Anaglyph colours sorted (kind of)
>
> Hi Gary,
>
>
>> 1) do not use a black background
>
>
> Agreed. Something like gray works well in my experience. Don't forget in techniques like anaglyph and chromadepth color takes on another meaning–it encodes depth or separation. It's useful to keep this in mind.
>
>
>>
>> 2) do not use "setting > rendering > modernize"
>
>
> If you have a modern video card that supports shaders well, Setting > Rendering > Modernize will give you better performance and much prettier graphics. If, however, you're on a laptop with an old Intel graphics card, stick to immediate mode rendering ('set use_shaders, 0').
>
>
>>
>> 3) be careful with setting quality too high (especially on spheres)
>
>
> Again, using Setting > Rendering > Modernize will actually give you pixel perfect spheres drawn quickly. But, in immediate mode, you are correct.
>
>
> To create the highest-quality movies or images, make sure you ray trace your images. This can be done with the 'ray', and 'png' commands or as movie creation time if 'ray_trace_frames' is set.
>
>
> To reinitialize PyMOL just run the "reinitialize" command.
>
> Cheers,
>
> -- Jason
>
>
>>
>>
>> On 18/06/2013 09:59, "Thomas Holder" <tho...@sc...> wrote:
>>
>> >Hi Gary,
>> >
>> >actually PyMOL should be optimized for red/cyan and not green/magenta.
>> >There is no option to change the colors, sorry.
>> >
>> >In PyMOL 1.5 anaglyph has been improved and there are is an
>> >"anaglyph_mode" settings which defaults to 4 ("optimized anaglyph").
>> >Other reasonable values are 3 ("half-color") and 1 (gray).
>> >
>> >http://pymol.org/dsc/dokuwiki/doku.php?id=setting:anaglyph_mode
>> >
>> >If you really need to change the colors, you could take the open-source
>> >code and tweak the anaglyph_mode matrix in layer1/Scene.c
>> >
>> >Hope that helps.
>> >
>> >Cheers,
>> > Thomas
>> >
>> >Gary Hunter wrote, On 06/17/13 09:53:
>> >> Is there a way to customise the colours used in anaglyph stereo mode?
>> >> Anaglyph mode has been optimised for green/magenta glasses but I have
>> >> lots of red/cyan ones so I'd like to change the colours used if I can.
>> >> Gary
>> >>
>> >> Prof. Gary J. Hunter,
>> >> Department of Physiology and Biochemistry
>> >> University of Malta, Msida, MSD 2080, Malta.
>> >> phone: +356 2340 2917
>> >> phone: +356 21316655 (secretary), Fax: +356 21310577
>> >> http://www.um.edu.mt/ms/physbiochem
>> >
>> >--
>> >Thomas Holder
>> >PyMOL Developer
>> >Schrödinger Contractor
>> >
>> >--------------------------------------------------------------------------
>> >----
>> >This SF.net email is sponsored by Windows:
>> >
>> >Build for Windows Store.
>> >
>> >http://p.sf.net/sfu/windows-dev2dev
>> >_______________________________________________
>> >PyMOL-users mailing list (PyM...@li...)
>> >Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> >Archives: http://www.mail-archive.com/pym...@li...
>> >
>>
>>
>>
>> ------------------------------------------------------------------------------
>> This SF.net email is sponsored by Windows:
>>
>> Build for Windows Store.
>>
>> http://p.sf.net/sfu/windows-dev2dev
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>
>
>
>
> --
> Jason Vertrees, PhD
> Director of Core Modeling Products
> Schrödinger, Inc.
>
> (e) Jas...@sc...
> (o) +1 (603) 374-7120
--
Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.
(e) Jas...@sc...
(o) +1 (603) 374-7120

I've found that all recent versions (1.5, 1.6, non-incentive) of Pymol 
on my laptop running updated Fedora 18 (nvidia drivers) don't allow me 
to use the control or shift keys for selection or editing in the gui. I 
dug out an older version (1.4.1) and it behaved properly. It appears to 
be pymol specific as coot and other programs work fine. Has anyone seen 
this before?
Thanks,
--paul
-- 
Paul Paukstelis, Ph.D
Assistant Professor
University of Maryland
Chemistry & Biochemistry Dept.
Center for Biomolecular Structure & Organization
pau...@um...
301-405-9933

Hello,
Does anyone have any experience in running pymol in 3D using a DLP projector? I have an Optoma EW610ST, running from a windows seven machine using a Geforce GT620 GPU. The computer and projector are connected via HDMI but at present I am not able to configure any 3D output.
Many thanks,
Colin
Manchester
Protein
Structure
Facility
Dr. Colin W. Levy
MIB G034
Tel. 0161 275 5090
Mob.07786 197 554
c....@ma...<mailto:c....@ma...>

Thanks again for a prompt reply.
 I usually use LCD shutter glasses but they are starting to fail. Anaglyph
is a useful alternative and works on any monitor of course.
I'm also keen to use it for seminars with projected anaglyph images and
movies.
Not sure if I should keep ranting on about anaglyph here? Is the wiki an
alternative?
Just to recap of what to avoid after loading and working on your molecules:
1) do not use a black background
2) do not use "setting > rendering > modernize"
3) be careful with setting quality too high (especially on spheres)
Point 4 should now be:
4) do not use 'ray' when trying to use anaglyph stereo. This is a shame
because an anaglyph image for a slide or printout might be useful.
Some irreversible colour changes are frustrating after working for hours on
molecular structures, and then finding anaglyph does not work. That1s why
I'd like to find a 'reset' command for the settings ­ edit all settings.
Initialise wipes out all my hard work (molecules, objects, selections, maps,
etc etc). Currently I just have to revert to the last saved pse file.
Any idea why using modern shaders does not work with anaglyph and might this
be improved later?
Gary
 Prof. Gary J. Hunter,
 Department of Physiology and Biochemistry
 University of Malta, Msida, MSD 2080, Malta.
 phone: +356 2340 2917
 phone: +356 21316655 (secretary), Fax: +356 21310577
 http://www.um.edu.mt/ms/physbiochem
From: Jason Vertrees <jas...@sc...>
Date: Wednesday, 26 June 2013 21:53
To: Gary Hunter <gar...@um...>
Cc: Thomas Holder <tho...@sc...>,
"pym...@li..." <pym...@li...>
Subject: Re: [PyMOL] Anaglyph colours sorted (kind of)
Hi Gary,
> 1) do not use a black background
Agreed. Something like gray works well in my experience. Don't forget in
techniques like anaglyph and chromadepth color takes on another meaning­it
encodes depth or separation. It's useful to keep this in mind.
 
> 2) do not use "setting > rendering > modernize"
If you have a modern video card that supports shaders well, Setting >
Rendering > Modernize will give you better performance and much prettier
graphics. If, however, you're on a laptop with an old Intel graphics card,
stick to immediate mode rendering ('set use_shaders, 0').
 
> 3) be careful with setting quality too high (especially on spheres)
Again, using Setting > Rendering > Modernize will actually give you pixel
perfect spheres drawn quickly. But, in immediate mode, you are correct.
To create the highest-quality movies or images, make sure you ray trace your
images. This can be done with the 'ray', and 'png' commands or as movie
creation time if 'ray_trace_frames' is set.
To reinitialize PyMOL just run the "reinitialize" command.
Cheers,
-- Jason
 
> 
> On 18/06/2013 09:59, "Thomas Holder" <tho...@sc...> wrote:
> 
>> >Hi Gary,
>> >
>> >actually PyMOL should be optimized for red/cyan and not green/magenta.
>> >There is no option to change the colors, sorry.
>> >
>> >In PyMOL 1.5 anaglyph has been improved and there are is an
>> >"anaglyph_mode" settings which defaults to 4 ("optimized anaglyph").
>> >Other reasonable values are 3 ("half-color") and 1 (gray).
>> >
>> >http://pymol.org/dsc/dokuwiki/doku.php?id=setting:anaglyph_mode
>> >
>> >If you really need to change the colors, you could take the open-source
>> >code and tweak the anaglyph_mode matrix in layer1/Scene.c
>> >
>> >Hope that helps.
>> >
>> >Cheers,
>> > Thomas
>> >
>> >Gary Hunter wrote, On 06/17/13 09:53:
>>> >> Is there a way to customise the colours used in anaglyph stereo mode?
>>> >> Anaglyph mode has been optimised for green/magenta glasses but I have
>>> >> lots of red/cyan ones so I'd like to change the colours used if I can.
>>> >> Gary
>>> >>
>>> >> Prof. Gary J. Hunter,
>>> >> Department of Physiology and Biochemistry
>>> >> University of Malta, Msida, MSD 2080, Malta.
>>> >> phone: +356 2340 2917 <tel:%2B356%202340%202917>
>>> >> phone: +356 21316655 <tel:%2B356%2021316655> (secretary), Fax: +356
>>> 21310577 <tel:%2B356%2021310577>
>>> >> http://www.um.edu.mt/ms/physbiochem
>> >
>> >--
>> >Thomas Holder
>> >PyMOL Developer
>> >Schrödinger Contractor
>> >
>> >--------------------------------------------------------------------------
>> >----
>> >This SF.net email is sponsored by Windows:
>> >
>> >Build for Windows Store.
>> >
>> >http://p.sf.net/sfu/windows-dev2dev
>> >_______________________________________________
>> >PyMOL-users mailing list (PyM...@li...)
>> >Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> >Archives: http://www.mail-archive.com/pym...@li...
>> >
> 
> 
> 
> ------------------------------------------------------------------------------
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> 
> Build for Windows Store.
> 
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> Archives: http://www.mail-archive.com/pym...@li...
-- 
Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.
(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi Marshall,
To unsubscribe you'll have to go to
https://lists.sourceforge.net/lists/listinfo/pymol-users and do it yourself.
Hope it helps,
Tsjerk
On Thu, Jun 27, 2013 at 6:00 AM, Pope, Marshall R
<mar...@ui...>wrote:
>
>
> Warm regards,
> R. Marshall Pope
> www.medicine.uiowa.edu/proteomics
>
>
> ________________________________
> Notice: This UI Health Care e-mail (including attachments) is covered by
> the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is
> confidential and may be legally privileged. If you are not the intended
> recipient, you are hereby notified that any retention, dissemination,
> distribution, or copying of this communication is strictly prohibited.
> Please reply to the sender that you have received the message in error,
> then delete it. Thank you.
> ________________________________
>
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Windows:
>
> Build for Windows Store.
>
> http://p.sf.net/sfu/windows-dev2dev
> _______________________________________________
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
-- 
Tsjerk A. Wassenaar, Ph.D.

Warm regards,
R. Marshall Pope
www.medicine.uiowa.edu/proteomics
________________________________
Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you.
________________________________

Dear all,
I'm trying to write a script to perform mutagenesis on a pdb
coordinate file via the command line. When I run the script, it
produces the expected output on the terminal and even creates the
desired output PDB file, but the output file is exactly identical to
the input file other than the name.
I am running the PyMOL 1.3 educational version on Windows 7 64 bit. My
working directory contains the PyMOL.exe executable, my mutate.py
script, and my digly.pdb coordinate file of a simple GLY-GLY peptide.
The mutate.py script appears as follows:
from pymol import cmd
import sys
pdb = sys.argv[1]
name = sys.argv[2]
selection = sys.argv[3]
mutant = sys.argv[4]
print "pdb: " + pdb
print "name: " + name
print "selection: " + selection
print "mutant: " + mutant
cmd.load(pdb)
cmd.wizard("mutagenesis")
cmd.refresh_wizard()
cmd.get_wizard().do_select(selection)
cmd.get_wizard().set_mode(mutant)
cmd.get_wizard().apply()
cmd.set_wizard()
cmd.save("%s_m.pdb" % name, name)
I launch the script via the command line from the working directory
using the following command:
PyMOL.exe -qc mutate.py -- digly.pdb digly A/2 ASN
This produces the following output:
pdb: digly.pdb
name: digly
selection: A/2/
mutant: ASN
It also creates the digly_m.pdb file in the working directory.
However, this file is exactly identical to the digly.pdb file.
Could someone please point out the mistake in my script? I have
attached the diglycine peptide to this message. Thanks a lot for any
help.
-Dan

Hi Gary,
1) do not use a black background
>
Agreed. Something like gray works well in my experience. Don't forget in
techniques like anaglyph and chromadepth color takes on another meaning–it
encodes depth or separation. It's useful to keep this in mind.
> 2) do not use "setting > rendering > modernize"
>
If you have a modern video card that supports shaders well, Setting >
Rendering > Modernize will give you better performance and much prettier
graphics. If, however, you're on a laptop with an old Intel graphics card,
stick to immediate mode rendering ('set use_shaders, 0').
> 3) be careful with setting quality too high (especially on spheres)
>
Again, using Setting > Rendering > Modernize will actually give you pixel
perfect spheres drawn quickly. But, in immediate mode, you are correct.
To create the highest-quality movies or images, make sure you ray trace
your images. This can be done with the 'ray', and 'png' commands or as
movie creation time if 'ray_trace_frames' is set.
To reinitialize PyMOL just run the "reinitialize" command.
Cheers,
-- Jason
>
> On 18/06/2013 09:59, "Thomas Holder" <tho...@sc...>
> wrote:
>
> >Hi Gary,
> >
> >actually PyMOL should be optimized for red/cyan and not green/magenta.
> >There is no option to change the colors, sorry.
> >
> >In PyMOL 1.5 anaglyph has been improved and there are is an
> >"anaglyph_mode" settings which defaults to 4 ("optimized anaglyph").
> >Other reasonable values are 3 ("half-color") and 1 (gray).
> >
> >http://pymol.org/dsc/dokuwiki/doku.php?id=setting:anaglyph_mode
> >
> >If you really need to change the colors, you could take the open-source
> >code and tweak the anaglyph_mode matrix in layer1/Scene.c
> >
> >Hope that helps.
> >
> >Cheers,
> > Thomas
> >
> >Gary Hunter wrote, On 06/17/13 09:53:
> >> Is there a way to customise the colours used in anaglyph stereo mode?
> >> Anaglyph mode has been optimised for green/magenta glasses but I have
> >> lots of red/cyan ones so I'd like to change the colours used if I can.
> >> Gary
> >>
> >> Prof. Gary J. Hunter,
> >> Department of Physiology and Biochemistry
> >> University of Malta, Msida, MSD 2080, Malta.
> >> phone: +356 2340 2917
> >> phone: +356 21316655 (secretary), Fax: +356 21310577
> >> http://www.um.edu.mt/ms/physbiochem
> >
> >--
> >Thomas Holder
> >PyMOL Developer
> >Schrödinger Contractor
> >
> >--------------------------------------------------------------------------
> >----
> >This SF.net email is sponsored by Windows:
> >
> >Build for Windows Store.
> >
> >http://p.sf.net/sfu/windows-dev2dev
> >_______________________________________________
> >PyMOL-users mailing list (PyM...@li...)
> >Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> >Archives: http://www.mail-archive.com/pym...@li...
> >
>
>
>
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Windows:
>
> Build for Windows Store.
>
> http://p.sf.net/sfu/windows-dev2dev
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
-- 
Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.
(e) Jas...@sc...
(o) +1 (603) 374-7120

Thanks for the reply.
Of course you are correct that anaglyph in Pymol is 'optimised' for
red/cyan glasses, despite the fact that the Pymol wiki says stereo mode 10
is for green/magenta ones (which is where I got the idea when it all went
wrong for me).
I have a learned a few things not to do in Pymol to use anaglyph, and I
have not found this info documented anywhere so here are a couple of
problems. My big mistake was starting with point 1 ;-)
1) do not use a black background
2) do not use "setting > rendering > modernize"
3) be careful with setting quality too high (especially on spheres)
There are probably other things for me to find not to do. I used point (2)
as a quick way to get a nice rendering, without knowing exactly what it
does. It does change all the colours so that anglyph no longer works. Is
there a way to reset it?
And a way to reset all edited settings back to default?
Gary
 Prof. Gary J. Hunter,
 Department of Physiology and Biochemistry
 University of Malta, Msida, MSD 2080, Malta.
 phone: +356 2340 2917
 phone: +356 21316655 (secretary), Fax: +356 21310577
 http://www.um.edu.mt/ms/physbiochem
On 18/06/2013 09:59, "Thomas Holder" <tho...@sc...> wrote:
>Hi Gary,
>
>actually PyMOL should be optimized for red/cyan and not green/magenta.
>There is no option to change the colors, sorry.
>
>In PyMOL 1.5 anaglyph has been improved and there are is an
>"anaglyph_mode" settings which defaults to 4 ("optimized anaglyph").
>Other reasonable values are 3 ("half-color") and 1 (gray).
>
>http://pymol.org/dsc/dokuwiki/doku.php?id=setting:anaglyph_mode
>
>If you really need to change the colors, you could take the open-source
>code and tweak the anaglyph_mode matrix in layer1/Scene.c
>
>Hope that helps.
>
>Cheers,
> Thomas
>
>Gary Hunter wrote, On 06/17/13 09:53:
>> Is there a way to customise the colours used in anaglyph stereo mode?
>> Anaglyph mode has been optimised for green/magenta glasses but I have
>> lots of red/cyan ones so I'd like to change the colours used if I can.
>> Gary
>> 
>> Prof. Gary J. Hunter,
>> Department of Physiology and Biochemistry
>> University of Malta, Msida, MSD 2080, Malta.
>> phone: +356 2340 2917
>> phone: +356 21316655 (secretary), Fax: +356 21310577
>> http://www.um.edu.mt/ms/physbiochem
>
>-- 
>Thomas Holder
>PyMOL Developer
>Schrödinger Contractor
>
>--------------------------------------------------------------------------
>----
>This SF.net email is sponsored by Windows:
>
>Build for Windows Store.
>
>http://p.sf.net/sfu/windows-dev2dev
>_______________________________________________
>PyMOL-users mailing list (PyM...@li...)
>Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>Archives: http://www.mail-archive.com/pym...@li...
>

It seems the difference I was looking for was 
pymol something.pml -- arg1 arg2 arg3
I was missing the --
Thanks
Jordan
On Jun 26, 2013, at 4:21 AM, lie...@vu... wrote:
> On Wednesday 26 June 2013 08:52:39 Jordan Willis wrote:
>> I'm looking to pass a .pml file, do some stuff, and then save it as a
>> session. Pymol -c My.pml looks like a good option. I'm trying to write
>> hundreds of sessions each with different arguments. I was wondering if its
>> possible to pass command line arguments that can then be seen by the python
>> interpreter inside a .pml
>> 
>> While I'm at it, is it easy to pass objects, i.e. variable names, between
>> the python enviroment and the pml enviroment inside a .pml script? Is
>> cmd.extend the best option? Is there a way to go backwards (from the .pml
>> to the python interpreter)?
> 
> This .pml sequence works for me:
> 
> stored.a = 5
> python
> import sys
> print sys.argv
> print stored.a
> stored.a = 10
> python end
> print stored.a
> 
> Cheers,
> 
> -- 
> Lieven Buts, Postdoctoral Fellow
> Structural Biology Brussels, Vrije Universiteit Brussel
> Department of Structural Biology, VIB
> 
> 
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Windows:
> 
> Build for Windows Store.
> 
> http://p.sf.net/sfu/windows-dev2dev
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> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

Hi Paul,
I have the same problem. I am using Fedora 18 and PyMOL v.1.5 (from
the repository).
It is annoying. Right now I have to use another computer if I want to
use the more 'advanced' functions of PyMOL.
I found one other person with the same problem who posted to the
Fedora forum, and got no response:
http://www.forum.fedoraforum.org/showthread.php?t=287005
No explanations here.
Adam
On Wed, Jun 26, 2013 at 3:08 AM, Paul Paukstelis
<sho...@gm...> wrote:
> I've found that all recent versions (1.5, 1.6, non-incentive) of Pymol
> on my laptop running updated Fedora 18 (nvidia drivers) don't allow me
> to use the control or shift keys for selection or editing in the gui. I
> dug out an older version (1.4.1) and it behaved properly. It appears to
> be pymol specific as coot and other programs work fine. Has anyone seen
> this before or have some sort of explanation?
>
> Thanks,
>
> --paul
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Windows:
>
> Build for Windows Store.
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> _______________________________________________
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Hey :)
You don't even need the python block, as the pymol interpreter is a python
interpreter with just some added extras. Single lines of python code are
never a problem. This works nicely for me
File test-argv.pml:
================
print sys.argv
for i in sys.argv[1:]: print i
Run pymol:
================
pymol test-argv.pml -- bla bla bla
Output:
================
PyMOL>print sys.argv
['/martini/tsjerk/Programs/pymol-1.5.0.4/pymol.exe', 'bla', 'bla', 'bla']
PyMOL>for i in sys.argv[1:]: print i
bla
bla
bla
Enjoy!
Tsjerk
On Wed, Jun 26, 2013 at 11:21 AM, <lie...@vu...> wrote:
> On Wednesday 26 June 2013 08:52:39 Jordan Willis wrote:
> > I'm looking to pass a .pml file, do some stuff, and then save it as a
> > session. Pymol -c My.pml looks like a good option. I'm trying to write
> > hundreds of sessions each with different arguments. I was wondering if
> its
> > possible to pass command line arguments that can then be seen by the
> python
> > interpreter inside a .pml
> >
> > While I'm at it, is it easy to pass objects, i.e. variable names, between
> > the python enviroment and the pml enviroment inside a .pml script? Is
> > cmd.extend the best option? Is there a way to go backwards (from the .pml
> > to the python interpreter)?
>
> This .pml sequence works for me:
>
> stored.a = 5
> python
> import sys
> print sys.argv
> print stored.a
> stored.a = 10
> python end
> print stored.a
>
> Cheers,
>
> --
> Lieven Buts, Postdoctoral Fellow
> Structural Biology Brussels, Vrije Universiteit Brussel
> Department of Structural Biology, VIB
>
>
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Windows:
>
> Build for Windows Store.
>
> http://p.sf.net/sfu/windows-dev2dev
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
-- 
Tsjerk A. Wassenaar, Ph.D.

On Wednesday 26 June 2013 08:52:39 Jordan Willis wrote:
> I'm looking to pass a .pml file, do some stuff, and then save it as a
> session. Pymol -c My.pml looks like a good option. I'm trying to write
> hundreds of sessions each with different arguments. I was wondering if its
> possible to pass command line arguments that can then be seen by the python
> interpreter inside a .pml
>
> While I'm at it, is it easy to pass objects, i.e. variable names, between
> the python enviroment and the pml enviroment inside a .pml script? Is
> cmd.extend the best option? Is there a way to go backwards (from the .pml
> to the python interpreter)?
This .pml sequence works for me:
stored.a = 5
python
import sys
print sys.argv
print stored.a
stored.a = 10
python end
print stored.a
Cheers,
-- 
Lieven Buts, Postdoctoral Fellow
Structural Biology Brussels, Vrije Universiteit Brussel
Department of Structural Biology, VIB

Hello,
I'm looking to pass a .pml file, do some stuff, and then save it as a session. Pymol -c My.pml looks like a good option. I'm trying to write hundreds of sessions each with different arguments. I was wondering if its possible to pass command line arguments that can then be seen by the python interpreter inside a .pml
So it would be like:
My.pml
<
python
argument1 = sys.argv[0] #except sys.argv doesn't work
#do something with argument
python end
do some stuff in the pml
save('somefile')
>
I'd also be willing to just write a pure python script and use the API provided I can still write session files and save them with ease. I don't know how to do that without passing it to Pymol first and using it's interpreter. 
While I'm at it, is it easy to pass objects, i.e. variable names, between the python enviroment and the pml enviroment inside a .pml script? Is cmd.extend the best option? Is there a way to go backwards (from the .pml to the python interpreter)?
Jordan

post to pymol mail list
Thank you very much!

I've found that all recent versions (1.5, 1.6, non-incentive) of Pymol 
on my laptop running updated Fedora 18 (nvidia drivers) don't allow me 
to use the control or shift keys for selection or editing in the gui. I 
dug out an older version (1.4.1) and it behaved properly. It appears to 
be pymol specific as coot and other programs work fine. Has anyone seen 
this before or have some sort of explanation?
Thanks,
--paul

On 2013年6月25日 09:47:19 -0400
Robert Campbell <rob...@qu...> wrote:
> Hi Stephen,
> 
> On Tue, 2013年06月25日 09:16 EDT, "Stephen P. Molnar"
> <s.m...@sb...> wrote:
> 
> > I have just installed the 64 bit Debian Testing distribution in an
> > Oracle VM on my laptop as a test bed.
> > 
> > I successfully compiled v 1.6.0.0 in my 6 bit Debian Wheezy
> > production OS.
> > 
> > I didn't get any error messages from my laptop installation during
> > the compilation process. However when run pymol only the viewer
> > window opens!
> > 
> > Here are the messages:
> > 
> > > Traceback (most recent call last):
> > > File
> > > "/home/computation/Apps/pymol/lib/python/pymol/__init__.py", line
> > > 448, in launch_gui __import__(self.invocation.options.gui) File
> > > "/home/computation/Apps/pymol/lib/python/pmg_tk/__init__.py",
> > > line 22, in <module> from PMGApp import * File
> > > "/home/computation/Apps/pymol/lib/python/pmg_tk/PMGApp.py", line
> > > 31, in <module> import Pmw ImportError: No module named Pmw
> > > Detected 4 CPU cores. Enabled multithreaded rendering.
> > > OpenGL Warning: No pincher, please call
> > > crStateSetCurrentPointers() in your SPU
> > 
> > Unfortunately, I don't have the faintest idea as to what is missing.
> > Any assistance will be appreciated. Thanks in advance. 
> 
> I would appear that you are just missing the python-pmw package on
> this machine, whereas it must have been present on your Wheezy
> version.
> 
> Cheers,
> Rob
Rob
Thanks for the suggestion. You were quite correct. Although, when I
check with Synaptic python-pmw was installed???? I reinstalled it and
the compilation worked correctly this time.
Many thanks
	Steve
-- 
Stephen P. Molnar, Ph.D.		Life is a fuzzy set
Foundation for Chemistry		Stochastic and multivariate
www.FoundationForChemistry.com
(614)312-7528 (c)
Skype: smolnar1

Hi Stephen,
On Tue, 2013年06月25日 09:16 EDT, "Stephen P. Molnar"
<s.m...@sb...> wrote:
> I have just installed the 64 bit Debian Testing distribution in an
> Oracle VM on my laptop as a test bed.
> 
> I successfully compiled v 1.6.0.0 in my 6 bit Debian Wheezy production
> OS.
> 
> I didn't get any error messages from my laptop installation during the
> compilation process. However when run pymol only the viewer window
> opens!
> 
> Here are the messages:
> 
> > Traceback (most recent call last):
> > File "/home/computation/Apps/pymol/lib/python/pymol/__init__.py",
> > line 448, in launch_gui __import__(self.invocation.options.gui)
> > File "/home/computation/Apps/pymol/lib/python/pmg_tk/__init__.py",
> > line 22, in <module> from PMGApp import *
> > File "/home/computation/Apps/pymol/lib/python/pmg_tk/PMGApp.py",
> > line 31, in <module> import Pmw
> > ImportError: No module named Pmw
> > Detected 4 CPU cores. Enabled multithreaded rendering.
> > OpenGL Warning: No pincher, please call crStateSetCurrentPointers()
> > in your SPU
> 
> Unfortunately, I don't have the faintest idea as to what is missing.
> Any assistance will be appreciated. Thanks in advance. 
I would appear that you are just missing the python-pmw package on this
machine, whereas it must have been present on your Wheezy version.
Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Dept. of Biomedical & Molecular Sciences
Botterell Hall Rm 644
Queen's University, 
Kingston, ON K7L 3N6 Canada
Tel: 613-533-6821
<rob...@qu...> http://pldserver1.biochem.queensu.ca/~rlc

I have just installed the 64 bit Debian Testing distribution in an
Oracle VM on my laptop as a test bed.
I successfully compiled v 1.6.0.0 in my 6 bit Debian Wheezy production
OS.
I didn't get any error messages from my laptop installation during the
compilation process. However when run pymol only the viewer window
opens!
Here are the messages:
> computation@inga:~/Apps/pymol/bin$ ./pymol
> PyMOL(TM) Molecular Graphics System, Version 1.6.0.0.
> Copyright (c) Schrodinger, LLC.
> All Rights Reserved.
> 
> Created by Warren L. DeLano, Ph.D. 
> 
> PyMOL is user-supported open-source software. Although some
> versions are freely available, PyMOL is not in the public domain.
> 
> If PyMOL is helpful in your work or study, then please volunteer 
> support for our ongoing efforts to create open and affordable
> scientific software by purchasing a PyMOL Maintenance and/or Support
> subscription.
> 
> More information can be found at "http://www.pymol.org".
> 
> Enter "help" for a list of commands.
> Enter "help <command-name>" for information on a specific command.
> 
> Hit ESC anytime to toggle between text and graphics.
> 
> Detected OpenGL version 2.0 or greater. Shaders available.
> Detected GLSL version 1.40.
> OpenGL Warning: No pincher, please call crStateSetCurrentPointers()
> in your SPU OpenGL graphics engine:
> GL_VENDOR: Humper
> GL_RENDERER: Chromium
> GL_VERSION: 2.1 Chromium 1.9
> Traceback (most recent call last):
> File "/home/computation/Apps/pymol/lib/python/pymol/__init__.py",
> line 448, in launch_gui __import__(self.invocation.options.gui)
> File "/home/computation/Apps/pymol/lib/python/pmg_tk/__init__.py",
> line 22, in <module> from PMGApp import *
> File "/home/computation/Apps/pymol/lib/python/pmg_tk/PMGApp.py",
> line 31, in <module> import Pmw
> ImportError: No module named Pmw
> Detected 4 CPU cores. Enabled multithreaded rendering.
> OpenGL Warning: No pincher, please call crStateSetCurrentPointers()
> in your SPU
Unfortunately, I don't have the faintest idea as to what is missing.
Any assistance will be appreciated. Thanks in advance. 
-- 
Stephen P. Molnar, Ph.D.		Life is a fuzzy set
Foundation for Chemistry		Stochastic and multivariate
www.FoundationForChemistry.com
(614)312-7528 (c)
Skype: smolnar1

Thanks, thanks a lot Thomas it really helped
On Mon, Jun 24, 2013 at 2:12 PM,
<pym...@li...>wrote:
> Send PyMOL-users mailing list submissions to
> pym...@li...
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> or, via email, send a message with subject or body 'help' to
> pym...@li...
>
> You can reach the person managing the list at
> pym...@li...
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of PyMOL-users digest..."
>
>
> Today's Topics:
>
> 1. problem with "distance" (vincent Chaptal)
> 2. Re: problem with "distance" (Thomas Holder)
> 3. Re: Problems with Pymol v 1.6.0.0 (Thomas Holder)
> 4. Re: Problems with Pymol v 1.6.0.0 (Thomas Holder)
> 5. Averaging a pdb file (neshat haq)
> 6. Re: Averaging a pdb file (Thomas Holder)
> 7. Fixed width font in gui on OSX w/ PyMOL 1.6.0
> (Alexander D. Scouras)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: 2013年6月20日 17:09:06 +0200
> From: vincent Chaptal <vin...@ib...>
> Subject: [PyMOL] problem with "distance"
> To: pym...@li...
> Message-ID: <51C...@ib...>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
> I've just purchased v1.6 and installed it under MacOS 10.6.8.
> I have a problem with using "distance" from a script, as well as via the
> wizard.
>
> my pdb has 12 chains.
> when I type: distance d1, molA and chain a and resi 53 and name o, molA
> and chain d and resi 8 and name n
> the distance is drawn between: chain M and resi 7 and atom cg, and chain
> I and resi 53 and atom o.
>
> I don't understand the error. So I turned to the wizard ->measurement. I
> click on the atoms that are in front of me, and the distance is drawn
> again between chain M and resi 7 and atom cg, and chain I and resi 53
> and atom o.
> For a proof, I'm pasting the top screen where the names of the atoms I
> clicked is:
> You clicked /molA//A/SER`53/O
> Selector: selection "sele" defined with 1 atoms.
> You clicked /molA//D/GLY`8/N)
>
> I was previously under 1.3 and didn't have this problem.
> Can you help me?
> Vincent
>
>
> --
>
> Vincent Chaptal, PhD
>
> Institut de Biologie et Chimie des Prot?ines
>
> Drug-resistance modulation and mechanism Laboratory
>
> 7 passage du Vercors
>
> 69007 LYON
>
> FRANCE
>
> +33 4 37 65 29 01
>
> http://www.ibcp.fr
>
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
> Message: 2
> Date: 2013年6月20日 18:09:35 +0200
> From: Thomas Holder <tho...@sc...>
> Subject: Re: [PyMOL] problem with "distance"
> To: pym...@li...
> Message-ID: <51C...@sc...>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Vincent,
>
> we introduced dynamic_measures in PyMOL 1.4, which uses the atom ID and
> is not robust against duplicated IDs. So the workaround here is to
> switch dynamic_measures off:
>
> PyMOL> unset dynamic_measures
>
> Hope that helps.
>
> Cheers,
> Thomas
>
> vincent Chaptal wrote, On 06/20/13 17:09:
> > Hi,
> > I've just purchased v1.6 and installed it under MacOS 10.6.8.
> > I have a problem with using "distance" from a script, as well as via the
> > wizard.
> >
> > my pdb has 12 chains.
> > when I type: distance d1, molA and chain a and resi 53 and name o, molA
> > and chain d and resi 8 and name n
> > the distance is drawn between: chain M and resi 7 and atom cg, and chain
> > I and resi 53 and atom o.
> >
> > I don't understand the error. So I turned to the wizard ->measurement. I
> > click on the atoms that are in front of me, and the distance is drawn
> > again between chain M and resi 7 and atom cg, and chain I and resi 53
> > and atom o.
> > For a proof, I'm pasting the top screen where the names of the atoms I
> > clicked is:
> > You clicked /molA//A/SER`53/O
> > Selector: selection "sele" defined with 1 atoms.
> > You clicked /molA//D/GLY`8/N)
> >
> > I was previously under 1.3 and didn't have this problem.
> > Can you help me?
> > Vincent
>
> --
> Thomas Holder
> PyMOL Developer
> Schr?dinger Contractor
>
>
>
> ------------------------------
>
> Message: 3
> Date: 2013年6月21日 06:21:43 +0200
> From: Thomas Holder <tho...@sc...>
> Subject: Re: [PyMOL] Problems with Pymol v 1.6.0.0
> To: pym...@li...
> Message-ID: <51C...@sc...>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Matthew,
>
> thanks for the report. We fixed and pushed this to SVN today.
>
> Cheers,
> Thomas
>
> Matthew Baumgartner wrote, On 06/20/13 15:54:
> > Hi,
> > Adding to thread.
> >
> > I'm using pymol 1.6 (built from svn yesterday) on Ubuntu 13.04.
> > I've noticed that the selection indicators are not working properly.
> >
> > Steps to reproduce:
> > #launch ignoring the config file
> > pymol -k
> >
> > #in pymol
> >>fetch 1YCR
> >
> > Then open sequence viewer and select a range of residues. Only the first
> > residue is highlighed on the structure (pink squares).
> >
> > Is there some setting that I accidentally set somewhere?
> >
> > Thanks,
> > Matt
>
> --
> Thomas Holder
> PyMOL Developer
> Schr?dinger Contractor
>
>
>
> ------------------------------
>
> Message: 4
> Date: 2013年6月21日 07:13:10 +0200
> From: Thomas Holder <tho...@sc...>
> Subject: Re: [PyMOL] Problems with Pymol v 1.6.0.0
> To: pym...@li...
> Message-ID: <51C...@sc...>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Stephen,
>
> Stephen P. Molnar wrote, On 06/18/13 15:16:
> > Two minor, but annoying, problems with the new version in Debian 7.0 64
> bit/
> >
> > #1 The pull down menus in the graphics windows refuse to remain open
> > when clicked, unless I left click and hold. Is this normal behavior?
>
> this is not normal behavior. Unfortunately I can't reproduce it. I don't
> have a Debian system, but I tested on Ubuntu, Gentoo and CentOS. I'll
> test on Debian when I get the change.
>
> > #2. Caver 2.1.2 will not save the location of the Directory with the
> > plug-in .jar file. The work around is rather cumbersome.
>
> Caver is a third-party plugin and as far as I know will not save any
> settings to disk. The easiest workaround is to edit PYMOL_LOCATION in
> Caver2_1_2.py (the Plugin Manager can tell you where to find
> Caver2_1_2.py).
>
> Actually, a nice way to reorganize the Caver plugin would be:
>
> Caver2_1_2
> |-- Caver2_1.jar
> |-- __init__.py (was: Caver2_1_2.py)
> `-- lib
> |-- dt3d.jar
> |-- j3dcore.jar
> |-- j3dutils.jar
> |-- ujmp-complete-0.2.4.jar
> `-- vecmath.jar
>
> And in Caver2_1_2/__init__.py, change:
>
> PYMOL_LOCATION = sys.modules[__name__].__path__[0]
>
> Cheers,
> Thomas
>
> --
> Thomas Holder
> PyMOL Developer
> Schr?dinger Contractor
>
>
>
> ------------------------------
>
> Message: 5
> Date: 2013年6月23日 22:52:10 +0530
> From: neshat haq <nes...@gm...>
> Subject: [PyMOL] Averaging a pdb file
> To: pym...@li...
> Message-ID:
> <CAM3wsb1FiqVXXLK7Ea8R6xutztaC=
> 5UZ...@ma...>
> Content-Type: text/plain; charset="iso-8859-1"
>
> How can we convert a 10 structure in apdb file to an approximate average.
> Is there any plugin or tool?
> I once tried average3d.py from mura lab but that average structure is
> duplicate of the first structure we opt.
>
> Anyways any suggestion will be appriciated.
>
> --
> Best regards
> Neshatul Haque
> PhD, Dpt of Biotechnology
> university of hyderabad
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
> Message: 6
> Date: 2013年6月23日 22:15:14 +0200
> From: Thomas Holder <tho...@sc...>
> Subject: Re: [PyMOL] Averaging a pdb file
> To: pym...@li...
> Message-ID: <51C...@sc...>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Neshatul,
>
> try "spheroid":
>
> PyMOL> fetch 1nmr, async=0
> PyMOL> spheroid 1nmr
>
> To relax locally distorted structure, you can use sculpting:
>
> PyMOL> fetch 1nmr, async=0
> PyMOL> sculpt_activate 1nmr, 1
> PyMOL> spheroid 1nmr
> PyMOL> set sculpting, 1
> # ... until you like it
> PyMOL> set sculpting, 0
>
> Hope that helps.
>
> Cheers,
> Thomas
>
> neshat haq wrote, On 06/23/13 19:22:
> > How can we convert a 10 structure in apdb file to an approximate average.
> > Is there any plugin or tool?
> > I once tried average3d.py from mura lab but that average structure is
> > duplicate of the first structure we opt.
> >
> > Anyways any suggestion will be appriciated.
>
> --
> Thomas Holder
> PyMOL Developer
> Schr?dinger Contractor
>
>
>
> ------------------------------
>
> Message: 7
> Date: 2013年6月24日 01:41:47 -0700
> From: "Alexander D. Scouras" <sc...@be...>
> Subject: [PyMOL] Fixed width font in gui on OSX w/ PyMOL 1.6.0
> To: "pym...@li..."
> <pym...@li...>
> Message-ID: <A17...@be...>
> Content-Type: text/plain; charset="us-ascii"
>
> I'm wondering if it's possible to switch the MacPyMOL gui to use a fixed
> width font.
>
> I've seen Jason's suggestion for the external Tk GUI and the FAQ.
>
> http://www.mail-archive.com/pym...@li.../msg10847.html
> http://pymol.sourceforge.net/faq.html#FONT
>
> I've confirmed that they work fine if I launch the PyMOLX11Hybrid gui, but
> no luck with the OSX native one (_ext_gui = None), and haven't been able to
> introspect anything equivalent.
>
> Thanks,
>
> Alex Scouras
> Postdoctoral Scholar
> Alber Lab
> UC Berkeley
> -------------- next part --------------
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> ------------------------------
>
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Windows:
>
> Build for Windows Store.
>
> http://p.sf.net/sfu/windows-dev2dev
>
> ------------------------------
>
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
> End of PyMOL-users Digest, Vol 85, Issue 16
> *******************************************
>
-- 
Best regards
Neshatul Haque
PhD, Dpt of Biotechnology
university of hyderabad

Dear Pymol Users,
I have installed PyMOL 1.6 built from source code on Ubuntu and Windows on June 23, 2013.
I've noticed that the label of distance (or angle) is not shown properly.
I describe the steps to reproduce:
1. load a PDB file.
2. select two atoms by clicking the middle button on the PyMOL Viewer (pushing a wheel of a computer mouse).
3. type ">dist" to create a distance object (dist01).
Then, a yellow broken line was produced between the selected atoms.
However, the label of distance (i.e. 2.2 Å) was not shown though the older versions (including v1.6-beta2) correctly showed.
Label of angle is the same.
It is also ineffective to select "Show -> label" of object "dist01" from PyMOL Viewer.
Please help me.
Thanks,
Yoshitaka
-- 
**********************************************************
Yoshitaka Moriwaki
Dept. of Biotechnology, Grad. Sch. of Agri. and Life Sci.,
The Univ. of Tokyo
**********************************************************

Dear PyMol users,
The mutagenesis wizard does not seem to work if ignore_case is set to
0. I can reproduce this on an older incentive build and on the OS X
compiled version from svn revision 4007.
Thanks,
Marius