pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] pymol problems with python after FC4 update

[Stuart Endo-S. <stu...@du...>]

After running a routine update on my FC4 box that included updates to X11, 
launching Pymol causes one of two things:

1. X completely crashes and must be killed from a remote login to regain 
system control.

2. Pymol manages to launch with the following messages:


[stuart@localhost installs]$ pymol
/usr/lib/python2.2/site-packages/pymol/modules/pymol/__init__.py:326: 
RuntimeWarning: Python C API version mismatch for module _cmd: This Python 
has API version 1012, module _cmd has version 1011.
  import _cmd

 This PyMOL(TM) Incentive Product is Copyright (C) 2005 DeLano Scientific LLC.

 A current PyMOL Maintenance and/or Support Subscription may be required for
 legal usage of this Build beyond a finite honor-system evaluation period.
 Please visit http://www.pymol.org/funding.html for more information.

 This PyMOL Executable Build is based on Open-Source PyMOL version 0.98.
/usr/lib/python2.2/site-packages/pymol/modules/pymol/__init__.py:323: 
RuntimeWarning: Python C API version mismatch for module pcatch: This Python 
has API version 1012, module pcatch has version 1011.
  _cmd.runpymol() # only returns if we are running pretend GLUT
/usr/lib/python2.2/site-packages/pymol/modules/pymol/xray.py:16: 
RuntimeWarning: Python C API version mismatch for module sglite: This Python 
has API version 1012, module sglite has version 1011.
  import sglite
/usr/lib/python2.2/site-packages/pymol/modules/pymol/xray.py:16: 
RuntimeWarning: Python C API version mismatch for module ExtensionClass: This 
Python has API version 1012, module ExtensionClass has version 1011.
  import sglite
 OpenGL-based graphics engine:
  GL_VENDOR: NVIDIA Corporation
  GL_RENDERER: GeForce FX 5700LE/AGP/SSE2/3DNOW!
  GL_VERSION: 1.2 (2.0.0 NVIDIA 76.67)
 Adapting to GeForce hardware...



I uninstalled/reinstalled pymol, both from the RH9.0 RPM and tarballs, updated 
to the latest stable python release and installed Pymol again, but no change 
in messages.  There was a similar listing back in 2003 on the mailing list, 
but no response was posted.  The messages suggest Pymol is looking for 
information in /usr/lib/python2.2, which is empty of pretty much anything at 
all now, I think the update cleaned it out when it updated to 2.4, but I 
can't figure out if I need to transfer files from the 2.4 directory to the 
2.2, or install 2.2 manually.

Any ideas anyone?

Thanks,
Stuart Endo-Streeter







____________________________________
Stuart Endo-Streeter
Structural Biology and Biophysics
Dept. Biochemistry
LSRC C266
Duke University
919-681-1668
stu...@du...

RE: [PyMOL] test in pymol scripting language

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

Use Python blocks!

> Something like that:
> 	if (count_atoms nt) =3D=3D 0
> 	then cmd.delete("nt")

if cmd.count_atoms("nt") =3D=3D 0: \
   cmd.delete("nt")

Note the explicit use of "continuation" lines via backslashes.   This =
ensures that PyMOL hands over both lines to the Python interpreter as a =
single block.

Cheers,
Warren

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

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

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Sebastien Moretti
> Sent: Thursday, September 29, 2005 8:43 AM
> To: pymol-users
> Subject: [PyMOL] test in pymol scripting language
>=20
> Hello,
> Is there a way to use test commands in pymol scripting language ?
>=20
> Something like that:
> 	if (count_atoms nt) =3D=3D 0
> 	then cmd.delete("nt")
>=20
> Thanks
>=20
> --
> S=E9bastien Moretti
> http://www.igs.cnrs-mrs.fr/
> CNRS - IGS
> 31 chemin Joseph Aiguier
> 13402 Marseille cedex
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by:
> Power Architecture Resource Center: Free content, downloads,=20
> discussions,
> and more. http://solutions.newsforge.com/ibmarch.tmpl
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

[PyMOL] test in pymol scripting language

[Sebastien M. <seb...@ig...>]

Hello,
Is there a way to use test commands in pymol scripting language ?

Something like that:
	if (count_atoms nt) =3D=3D 0
	then cmd.delete("nt")

Thanks

--=20
S=E9bastien Moretti
http://www.igs.cnrs-mrs.fr/
CNRS - IGS
31 chemin Joseph Aiguier
13402 Marseille cedex

[PyMOL] Need Help with Stereo L/R Confusion

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

Folks,

We are trying to track down and hopefully resolve a problem with the
left and right images getting confused in stereo mode with PyMOL.  I
think this problem is limited to nVidia Quadro cards, but need more
info.  So...

If (and only if) you use PyMOL in hardware stereo mode (with shutter
glasses), could you please send me a direct email response to the
following questions?  Please do so even if you don't have problems -- we
need a representative data set...

1) What OS are you running?  (Linux, Windows XP, IRIX, MacOS, ...)

2) What graphics brand and card/chip do you have?  (nVidia Quadro, ATI
FireGL, 3dLabs, ...)

3) When you run in Stereo, do the left and right images sometimes get
confused with PyMOL?  Are they always swapped or just randomly swapped?

4) Do any other graphics programs which suffer the same issue?  If so
which ones? (O, VMD, Quanta, etc.)

5) Do you have any other helpful comments or observations?

Thanks,
Warren

mailto:wa...@de...   =20

Sample response:

1. Linux Redhat 9.
2. nVidia Quadro FX 1100.
3. Yes, randomly swapped.
4. Haven't tried other software.
5. Never had this problem on SGI, only on Linux.

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

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

[PyMOL] Selective Clipping

[Dan K. <dw...@ma...>]

Anyone ever done this ?   For example if you had a surface 
representation in one object and a cartoon representation in another, 
could you clip the surface but not the cartoon ?

This would give you an alternative to fiddling with the transparency of 
the surface.

Thanks,
Dan

-- 
   Dan Kulp
   Biophysics Graduate Student @ UPenn
   dw...@ma...
   http://dwkulp.homelinux.net/tiki/tiki-index.php
--

[PyMOL] pymol -cp gives errors

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

Hi,

I have PyMOL version 0.99b14 installed on Linux .  I am running it  
interactively without the GUI using the command pymol -cp .  Whenever  
I accidentally type a return (null line) the PyMOL (or Python)  
interpreter crashes with this message:

Traceback (most recent call last):
   File "/opt/packages/pymol/ext/lib/python2.3/threading.py", line  
436, in __bootstrap
     self.run()
   File "/opt/packages/pymol/ext/lib/python2.3/threading.py", line  
416, in run
     self.__target(*self.__args, **self.__kwargs)
   File "/opt/packages/pymol/modules/pymol/parser.py", line 88, in  
stdin_reader
     cmd.do(l)
   File "/opt/packages/pymol/modules/pymol/commanding.py", line 247,  
in do
     if _raising(r): raise pymol.CmdException
CmdException: <pymol.CmdException instance at 0xb7d3b4ac>

What am I doing wrong?  The system has python 2.3.4 installed.

Mark

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

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

[PyMOL] Problem with alter command

[Soheila V. <so...@ch...>]

Dear Pymol Users,
=20
I have a simple question. I am trying to define the secondary structure =
of different loaded structures, using the "alter" command. I could do it =
easily for the structures that have the same SS but my problem is not =
all the loaded molecules have the same SS so I should be able to select =
different molecules and define the SS for each individually. My question =
is: How can I do that?
=20
In summary: How can I select a molecule and define the SS for that =
molecule only without changing it for other molecules.
=20
I really greatly appreciate any help suggestion,
=20
Soheila
=20
=20
=20
=20

[PyMOL] PyMol Movies Tutorial

[Sebastien G. <sge...@ma...>]

Are there any good tutorials for making movies with PyMol online? I have 
looked around and found some but I am wondering if there are any 
standouts and hopefully some that are aimed at linux users without using 
ImageMagick preferably as I am having trouble with it.
thanks,
Sebastien

Re: [PyMOL] From scenes to movies?

[Dirk K. <dir...@ps...>]

Hi Martin,

your script works beautifully!!! Thank you very much!!!
I would like to understand two commands that you use in your script, for 
which I couldn't find any infos, neither in the manual, nor in the 
reference nor in the WiKi. Could you please tell me:
- what does "set scene_animation,-1" mean?
- what do the "mview store" and "mview interpolate" commands mean?

Thanks again!!!

Best regards,

Dirk.

Martin Nervall wrote:

> Dirk,
>
>  Actually there is a way to render a movie from predefined scenes. I 
> created a .pse-file with my desired scenes and then made a movie from 
> the extrapolations between the scenes. It will look pretty much as an 
> ordinary scene_animation in Pymol. From the movie I rendered lots of 
> .png-files which I finally merged into a .mpg or .avi movie. It's time 
> consuming but it works.
>
> Here is a sample script that will render a 50 frame movie from two 
> scenes stored in movie.pse:
>
> ********************************''
> load movie.pse
> set scene_animation,-1
> set scene_animation_duration,0
>
> mset 1 x50
> scene F1
> mview store, 1
>
> scene F2
> mview store, 30
> mview store, 35
>
> scene F1
> mview store, 50
>
> mview interpolate
>
> set ray_trace_frames = 1
> mpng movie
> ********************************''
>
> Hope this is to some help.
>
> cheers
>
> /Martin
>
> At 09:49 2005-09-26, Dirk Kostrewa wrote:
>
>> Hi Warren,
>>
>> the scenes feature in PyMOL is _really_ nice! By choosing appropriate 
>> scenes, it does exactly what I would like to show in a movie 
>> describing a protein structure. Is there a way in PyMOL to export the 
>> individual frames for a movie from scenes? If not, this would be my 
>> most desired missing feature in 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
>> ****************************************
>>
>>
>>
>> -------------------------------------------------------
>> SF.Net email is sponsored by:
>> Tame your development challenges with Apache's Geronimo App Server. 
>> Download it for free - -and be entered to win a 42" plasma tv or your 
>> very
>> own Sony(tm)PSP.  Click here to play: 
>> http://sourceforge.net/geronimo.php
>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
>
> ____________________________________
> Martin Nervall
> Molecular Biotechnology Program
> Dept. of Cell & Molecular Biology
> Biomedical Center
> Box 596
> SE-751 24 Uppsala
> Sweden
> Phone +46 (0)18 471 5058
> http://xray.bmc.uu.se/~aqwww/
>
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by:
> Tame your development challenges with Apache's Geronimo App Server. 
> Download it for free - -and be entered to win a 42" plasma tv or your 
> very
> own Sony(tm)PSP.  Click here to play: http://sourceforge.net/geronimo.php
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users



-- 

****************************************
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
****************************************

Re: [PyMOL] From scenes to movies?

[Martin N. <ne...@xr...>]

Dirk,

  Actually there is a way to render a movie from predefined scenes. I 
created a .pse-file with my desired scenes and then made a movie from the 
extrapolations between the scenes. It will look pretty much as an ordinary 
scene_animation in Pymol. From the movie I rendered lots of .png-files 
which I finally merged into a .mpg or .avi movie. It's time consuming but 
it works.

Here is a sample script that will render a 50 frame movie from two scenes 
stored in movie.pse:

********************************''
load movie.pse
set scene_animation,-1
set scene_animation_duration,0

mset 1 x50
scene F1
mview store, 1

scene F2
mview store, 30
mview store, 35

scene F1
mview store, 50

mview interpolate

set ray_trace_frames = 1
mpng movie
********************************''

Hope this is to some help.

cheers

/Martin

At 09:49 2005-09-26, Dirk Kostrewa wrote:
>Hi Warren,
>
>the scenes feature in PyMOL is _really_ nice! By choosing appropriate 
>scenes, it does exactly what I would like to show in a movie describing a 
>protein structure. Is there a way in PyMOL to export the individual frames 
>for a movie from scenes? If not, this would be my most desired missing 
>feature in 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
>****************************************
>
>
>
>-------------------------------------------------------
>SF.Net email is sponsored by:
>Tame your development challenges with Apache's Geronimo App Server. 
>Download it for free - -and be entered to win a 42" plasma tv or your very
>own Sony(tm)PSP.  Click here to play: http://sourceforge.net/geronimo.php
>_______________________________________________
>PyMOL-users mailing list
>PyM...@li...
>https://lists.sourceforge.net/lists/listinfo/pymol-users


____________________________________
Martin Nervall
Molecular Biotechnology Program
Dept. of Cell & Molecular Biology
Biomedical Center
Box 596
SE-751 24 Uppsala
Sweden
Phone +46 (0)18 471 5058
http://xray.bmc.uu.se/~aqwww/

Re: [PyMOL] From scenes to movies?

[Dirk K. <dir...@ps...>]

Hi Warren & Pete,

Warren DeLano wrote:

>Pete & Dirk,
>
>Actually, I think Dirk is looking for something to convert the automatic
>scene-to-scene camera interpolation into movies...the immediate answer
>is no -- it isn't yet trivial to do, but we will be working on making
>that easier before the next release.
>
>  
>
yes, Warren is right - this is exactly what I would like to have. I'm 
looking forward to getting this feature!

Cheers,

Dirk.

>Cheers,
>Warren
>
>--
>Warren L. DeLano, Ph.D.                     
>Principal Scientist
>
>. DeLano Scientific LLC  
>. 400 Oyster Point Blvd., Suite 213           
>. South San Francisco, CA 94080 USA   
>. Biz:(650)-872-0942  Tech:(650)-872-0834     
>. Fax:(650)-872-0273  Cell:(650)-346-1154
>. mailto:wa...@de...      
> 
>
>  
>
>>-----Original Message-----
>>From: pym...@li... 
>>[mailto:pym...@li...] On Behalf Of 
>>Peter Adrian Meyer
>>Sent: Monday, September 26, 2005 2:25 PM
>>To: Dirk Kostrewa
>>Cc: pym...@li...
>>Subject: Re: [PyMOL] From scenes to movies?
>>
>>Hi Dirk,
>>
>>    
>>
>>>a protein structure. Is there a way in PyMOL to export the 
>>>      
>>>
>>individual
>>frames for a movie from scenes? If not, this would be my most 
>>desired missing feature in PyMOL!
>>
>>Yes.  What I do is to use a script to step through each frame 
>>of the movie (rotation by 1 degree, zoom in slightly, change 
>>transparency slightly, etc), ray-trace (optional), and dump 
>>the png.  From there, ffmpeg will combine all of these into a 
>>single movie file (memcoder is supposed to do this as well).
>>
>>I'm not entirely sure what you mean by frames from scenes, though.
>>
>>Hope this helps,
>>
>>Pete
>>
>>
>>Pete Meyer
>>Fu Lab
>>BMCB grad student
>>Cornell University
>>
>>
>>
>>
>>
>>
>>-------------------------------------------------------
>>SF.Net email is sponsored by:
>>Tame your development challenges with Apache's Geronimo App Server. 
>>Download it for free - -and be entered to win a 42" plasma tv 
>>or your very own Sony(tm)PSP.  Click here to play: 
>>http://sourceforge.net/geronimo.php
>>_______________________________________________
>>PyMOL-users mailing list
>>PyM...@li...
>>https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>>
>>
>>
>>    
>>


-- 

****************************************
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
****************************************

RE: [PyMOL] Hardware Stereo OSX Tiger 10.4

[Moriarty, D. <dmo...@si...>]

I've had the same problem as well.  I'm using a dual G5 with a Radeon =
9800 Pro using  the CrystalEyes system.  I've also tried getting it work =
on several different systems running 10.4, and full screen stereo will =
not work on any of them.  If I boot the G5 into 10.3.9, full screen =
stereo works fine.  I can also run full screen stereo on the G5 running =
10.4 using Nanasaur 2 (heck of a way to test full screen stereo!).


Dan
---
Dr. Daniel Moriarty
Dept. of Chemistry & Biochemistry
Siena College
515 Loudon Road
Loudonville, NY 12211
(518) 783-2472
http://www.siena.edu/chemistry/


-----Original Message-----
From: pym...@li... on behalf of Stephen =
Dunham
Sent: Tue 9/27/2005 12:15 AM
To: pym...@li...
Subject: [PyMOL] Hardware Stereo OSX Tiger 10.4
=20
Hi

Can anyone lend support on getting full screen stereo to work with=20
either MacPymol 0.98 or the latest beta 0.99.

I am running Mac OS X version 10.4.2 on a dual G5 system with an ATI=20
Radeon 9650 graphics card and a Monitor Z-screen 2000i.

I have been able to run the GLUTStereo demo from the apple site, so I=20
believe the hardware is working correctly.  =20
http://developer.apple.com/samplecode/GLUTStereo/GLUTStereo.html


Any suggestions would be appreciated.  thanks,  Steve
--=20
********************************************
Stephen U. Dunham          TEL 610 625-7103
Department of Chemistry    FAX 610 625-7918
Moravian College         =20
1200 Main Street
Bethlehem, PA 18018

www.biochem.moravian.edu/biochemmain.html
********************************************

[PyMOL] Hardware Stereo OSX Tiger 10.4

[Stephen D. <ste...@mo...>]

Hi

Can anyone lend support on getting full screen stereo to work with 
either MacPymol 0.98 or the latest beta 0.99.

I am running Mac OS X version 10.4.2 on a dual G5 system with an ATI 
Radeon 9650 graphics card and a Monitor Z-screen 2000i.

I have been able to run the GLUTStereo demo from the apple site, so I 
believe the hardware is working correctly.   
http://developer.apple.com/samplecode/GLUTStereo/GLUTStereo.html


Any suggestions would be appreciated.  thanks,  Steve
-- 
********************************************
Stephen U. Dunham          TEL 610 625-7103
Department of Chemistry    FAX 610 625-7918
Moravian College          
1200 Main Street
Bethlehem, PA 18018

www.biochem.moravian.edu/biochemmain.html
********************************************

RE: [PyMOL] transparency question

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

For various legacy reasons, the "transparency" setting only covers
surface transparency.  Try=20

set sphere_transparency, 0.5
set stick_transparency, 0.5

etc.

Cheers,
Warren


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

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

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Mark Mayer
> Sent: Monday, September 26, 2005 3:33 PM
> To: pym...@li...
> Subject: [PyMOL] transparency question
>=20
> Hi.
>=20
> Can anyone tell me how to get transparency to work? I'm using=20
> Open-Source PyMOL version 0.98 on Mac OS X 10.3.
> The command set transparency =3D 0.9
> does not generate errors in the text output window
> >  Setting: transparency set to 0.90000
> but nothing changes in the graphics window.
>=20
> I've tried command before as well as after drawing all my objects.
>=20
> I was planning to try and make transparent spheres around=20
> some selected side chains, with rest of molecule drawn as=20
> sticks and cartoons, so any advice (or example script) also=20
> appreciated.
>=20
> many thanks
> --
> Mark Mayer Ph.D.
> LCMN NICHD NIH DHHS
> Bldg 35, Room 3B 1002 MSC 3712
> 35 Lincoln Drive
> Bethesda MD 20892 3712
> Phone: 301-496-9346 (office); 301-496-9347 (lab); FAX=20
> 301-496-2396 Lab web site: http://mayerlab.nichd.nih.gov
>=20
> Send packages, Fedex and anything requiring a signature to:
>=20
> Bldg 35, Room 3B 1004
> 35 Lincoln Drive
> Bethesda MD 20892
>=20
>=20
>=20
> -------------------------------------------------------
> SF.Net email is sponsored by:
> Tame your development challenges with Apache's Geronimo App Server.=20
> Download it for free - -and be entered to win a 42" plasma tv=20
> or your very own Sony(tm)PSP.  Click here to play:=20
> http://sourceforge.net/geronimo.php
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

RE: [PyMOL] From scenes to movies?

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

Pete & Dirk,

Actually, I think Dirk is looking for something to convert the automatic
scene-to-scene camera interpolation into movies...the immediate answer
is no -- it isn't yet trivial to do, but we will be working on making
that easier before the next release.

Cheers,
Warren

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

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

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Peter Adrian Meyer
> Sent: Monday, September 26, 2005 2:25 PM
> To: Dirk Kostrewa
> Cc: pym...@li...
> Subject: Re: [PyMOL] From scenes to movies?
>=20
> Hi Dirk,
>=20
> > a protein structure. Is there a way in PyMOL to export the=20
> individual
> frames for a movie from scenes? If not, this would be my most=20
> desired missing feature in PyMOL!
>=20
> Yes.  What I do is to use a script to step through each frame=20
> of the movie (rotation by 1 degree, zoom in slightly, change=20
> transparency slightly, etc), ray-trace (optional), and dump=20
> the png.  From there, ffmpeg will combine all of these into a=20
> single movie file (memcoder is supposed to do this as well).
>=20
> I'm not entirely sure what you mean by frames from scenes, though.
>=20
> Hope this helps,
>=20
> Pete
>=20
>=20
> Pete Meyer
> Fu Lab
> BMCB grad student
> Cornell University
>=20
>=20
>=20
>=20
>=20
>=20
> -------------------------------------------------------
> SF.Net email is sponsored by:
> Tame your development challenges with Apache's Geronimo App Server.=20
> Download it for free - -and be entered to win a 42" plasma tv=20
> or your very own Sony(tm)PSP.  Click here to play:=20
> http://sourceforge.net/geronimo.php
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

Re: [PyMOL] From scenes to movies?

[Peter A. M. <pa...@co...>]

Hi Dirk,

> a protein structure. Is there a way in PyMOL to export the individual
frames for a movie from scenes? If not, this would be my most desired
missing feature in PyMOL!

Yes.  What I do is to use a script to step through each frame of the movie
(rotation by 1 degree, zoom in slightly, change transparency slightly,
etc), ray-trace (optional), and dump the png.  From there, ffmpeg will
combine all of these into a single movie file (memcoder is supposed to do
this as well).

I'm not entirely sure what you mean by frames from scenes, though.

Hope this helps,

Pete


Pete Meyer
Fu Lab
BMCB grad student
Cornell University

[PyMOL] From scenes to presentation

[<an...@bi...>]

Dirk is right.  Scenes are way nice.  What I am wondering is if there is =
a
way of incorporating them into powerpoint a little more smoothly than I
currently do.  As has been suggested by many, I use a hyperlink to the
.psw file.

Under XP, this fires up pymol, even if pymol is already running in the
background.  In other words, for a second or so, I see the empty pymol
window on top of the current slide of my presentation as pymol is
starting.  Is there a way to open the session with pymol that is already
running?

Under OSX, the session file is opened in a running pymol session
(pymolX11Hybrid), but the transition is even rougher than under XP.  The
current slide disappears and the Mac contemplates for a while before
opening the session.  The G5 is much slower than my XP notebook, but are
there any tricks to smoothen things up?

Has anyone tried this with StarOffice under linux?

Thanks


Andreas


> Hi Warren,
>
> the scenes feature in PyMOL is _really_ nice! By choosing appropriate
> scenes, it does exactly what I would like to show in a movie describing
> a protein structure. Is there a way in PyMOL to export the individual
> frames for a movie from scenes? If not, this would be my most desired
> missing feature in PyMOL!
>
> Best regards,
>
> Dirk.
>

--=20
   -->       Andreas F=F6rster       <--
 8 rue Doudart de Lagr=E9e, 38000 Grenoble
++33.(0)438.866201 and ++33.(0)456.452000
      www.biochem.utah.edu/~andreas

[PyMOL] From scenes to movies?

[Dirk K. <dir...@ps...>]

Hi Warren,

the scenes feature in PyMOL is _really_ nice! By choosing appropriate 
scenes, it does exactly what I would like to show in a movie describing 
a protein structure. Is there a way in PyMOL to export the individual 
frames for a movie from scenes? If not, this would be my most desired 
missing feature in 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
****************************************

RE: [PyMOL] (no subject)

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

Yes, the create command provide you with this ability, though at the end
of the process you end up with a new object.

create new_object, old_object1 | old_object2

In some cases, new_object can be the same name as either old_object1 or
old_object2:

create old_object1, old_object1 | old_object2

Also note that the vertical bar (the "or" operator) is optional in
recent betas, so

create old_object1, old_object1 old_object2

becomes legal.

Cheers,
Warren

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

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

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Joseph Fernandez
> Sent: Sunday, September 25, 2005 11:19 AM
> To: pym...@li...
> Subject: [PyMOL] (no subject)
>=20
> There is a very useful functionality in Sybyl, whereby the=20
> user can "merge" a residue from one molecular area, into=20
> another molecular area.  The residue then becomes a part of=20
> the latter moleculear area, without deleting it.  I wonder=20
> whether there is such a functionality in PyMol. =20
>=20
> As an example, I have created a new object, consisting of=20
> several residues that I have extracted from the active site=20
> of a protein (using the create command).=20
> I then deleted these residues from the original object=20
> (active site of protein).  I now want to merge an additional=20
> residue from the active site into the ligand object, and=20
> delete the residue from the active site, but without deleting=20
> the ligand object.
>=20
> Any assistance on this matter would be appreciated.
>=20
> Joe
>=20
>=20
> =09
> 	=09
> ______________________________________________________
> Yahoo! for Good
> Donate to the Hurricane Katrina relief effort.=20
> http://store.yahoo.com/redcross-donate3/=20
>=20
>=20
>=20
> -------------------------------------------------------
> SF.Net email is sponsored by:
> Tame your development challenges with Apache's Geronimo App Server.=20
> Download it for free - -and be entered to win a 42" plasma tv=20
> or your very own Sony(tm)PSP.  Click here to play:=20
> http://sourceforge.net/geronimo.php
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

[PyMOL] (no subject)

[Joseph F. <joe...@ya...>]

There is a very useful functionality in Sybyl, whereby
the user can "merge" a residue from one molecular
area, into another molecular area.  The residue then
becomes a part of the latter moleculear area, without
deleting it.  I wonder whether there is such a
functionality in PyMol.  

As an example, I have created a new object, consisting
of several residues that I have extracted from the
active site of a protein (using the create command). 
I then deleted these residues from the original object
(active site of protein).  I now want to merge an
additional residue from the active site into the
ligand object, and delete the residue from the active
site, but without deleting the ligand object.

Any assistance on this matter would be appreciated.

Joe


	
		
______________________________________________________ 
Yahoo! for Good 
Donate to the Hurricane Katrina relief effort. 
http://store.yahoo.com/redcross-donate3/ 

[PyMOL] transparency question

[Mark M. <ma...@ma...>]

Hi.

Can anyone tell me how to get transparency to work? I'm using 
Open-Source PyMOL version 0.98 on Mac OS X 10.3.
The command set transparency = 0.9
does not generate errors in the text output window
>  Setting: transparency set to 0.90000
but nothing changes in the graphics window.

I've tried command before as well as after drawing all my objects.

I was planning to try and make transparent spheres around some 
selected side chains, with rest of molecule drawn as sticks and 
cartoons, so any advice (or example script) also appreciated.

many thanks
-- 
Mark Mayer Ph.D.
LCMN NICHD NIH DHHS
Bldg 35, Room 3B 1002 MSC 3712
35 Lincoln Drive
Bethesda MD 20892 3712
Phone: 301-496-9346 (office); 301-496-9347 (lab); FAX 301-496-2396
Lab web site: http://mayerlab.nichd.nih.gov

Send packages, Fedex and anything requiring a signature to:

Bldg 35, Room 3B 1004
35 Lincoln Drive
Bethesda MD 20892

RE: [PyMOL] How to change label size and font in pymol?

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

Xiang,

We're working on better fonts & label display.  In the meantime:

set label_font_id, 4

For the biggest and heaviest font PyMOL currently supports.

Cheers,
Warren


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

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

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of xiang li
> Sent: Friday, September 23, 2005 12:24 PM
> To: pym...@li...
> Subject: [PyMOL] How to change label size and font in pymol?
>=20
> I tried to search mail archive, but found no answer there,=20
> though some friends asked the same question.
>=20
> I found the size of lable is generally kind of small and not=20
> very easy to be visible.=20
>=20
> Thanks for any suggestions and help.
>=20
> --=20
>=20
> Li, Xiang (Sean)                     =20
> Dept of Bioengineering               =20
> University of Illinois at Chicago   =20
> Room 218 Science and Engineering Offices                     =20
> 851 S. Morgan St. (M/C 063)       =20
> Chicago, IL  60607-7052, USA  =20
> ph:   (312) 996-7467
> fax:  (312) 413-2018      =20
>=20
>=20
>=20
> -------------------------------------------------------
> SF.Net email is sponsored by:
> Tame your development challenges with Apache's Geronimo App Server.=20
> Download it for free - -and be entered to win a 42" plasma tv=20
> or your very own Sony(tm)PSP.  Click here to play:=20
> http://sourceforge.net/geronimo.php
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

[PyMOL] How to change label size and font in pymol?

[xiang li <xi...@gi...>]

I tried to search mail archive, but found no answer there, though some 
friends asked the same question.

I found the size of lable is generally kind of small and not very 
easy to be visible. 

Thanks for any suggestions and help.

-- 

Li, Xiang (Sean)                      
Dept of Bioengineering                
University of Illinois at Chicago    
Room 218 Science and Engineering Offices                      
851 S. Morgan St. (M/C 063)        
Chicago, IL  60607-7052, USA   
ph:   (312) 996-7467
fax:  (312) 413-2018       

RE: [PyMOL] alignment question

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

> is there any possibility to get a list of the pairs of atoms=20
> that are matched using the align command?

Not yet...sorry.  Alignment objects are coming, but post 1.0.

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

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

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Marc Bruning
> Sent: Tuesday, September 20, 2005 6:42 AM
> To: pym...@li...
> Subject: [PyMOL] alignment question
>=20
> hello,
>=20
> is there any possibility to get a list of the pairs of atoms=20
> that are matched using the align command?
>=20
> cheers,
> marc
>=20
>=20
> -------------------------------------------------------
> SF.Net email is sponsored by:
> Tame your development challenges with Apache's Geronimo App Server.=20
> Download it for free - -and be entered to win a 42" plasma tv=20
> or your very own Sony(tm)PSP.  Click here to play:=20
> http://sourceforge.net/geronimo.php
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

RE: [PyMOL] rot+trsl matrices

[Xavier S. <si...@qu...>]

Dear Warren (and others who might be interested - Zac, Robert ?):

Thank you for the cmd.get_object_matrix(object-name), this is what we
were looking for. Or almost, here are a few comments :

1) We were also looking for an equivalent "cmd_set_object_matrix" or
something like that, but could not find it. Does it exist somewhere ?

2) "reset" and "undo" do not seem to reinitialize the matrix

3) moving the molecule with the commands rotate/translate instead of
with the rotF/movF from the mouse, the matrix does not get updated.

4) We get some numerical instabilities. For example, using the following
function a few times (on a pdb file "mono") gives values which are
greater than 1 for the cos/sin of the rotation matrix, and then quickly
diverge :

   from Numeric import *
   print cmd.get_object_matrix('mono')
   cmd.transform_object('mono',[cos(1.57), 0, -sin(1.57), 0.0, 0, 1, 0,
   0.0, sin(1.57), 0, cos(1.57), 0.0, 0, 0, 0, 0.0])
   print cmd.get_object_matrix('mono')
   cmd.transform_object('mono',cmd.get_object_matrix('mono'),0,0,'',0,1)
   print cmd.get_object_matrix('mono')

Note that it diverges also but more slowly when replacing the second
transform line by :
   cmd.transform_object('mono',[cos(1.57), 0, sin(1.57), 0.0, 0, 1, 0,
   0.0, -sin(1.57), 0, cos(1.57), 0.0, 0, 0, 0, 0.0])

Can you help us with some of these issues ?
Thank you very much.
--Xavier (w/ Leandro and Stefano)

ps : thank you Zac & Robert for your help !

> Provided objects are moved in their entiretly, recent PyMOL betas may
> provide what you want via
>
> cmd.get_object_matrix(object-name)
>
> Cheers,
> Warren
>
> --
> Warren L. DeLano, Ph.D.
> Principal Scientist
>
> . DeLano Scientific LLC
> . 400 Oyster Point Blvd., Suite 213
> . South San Francisco, CA 94080 USA
> . Biz:(650)-872-0942  Tech:(650)-872-0834
> . Fax:(650)-872-0273  Cell:(650)-346-1154
> . mailto:wa...@de...
>
>
> > -----Original Message-----
> > From: pym...@li...
> > [mailto:pym...@li...] On Behalf Of
> > Xavier Siebert
> > Sent: Friday, September 16, 2005 10:01 AM
> > To: pym...@li...
> > Subject: [PyMOL] rot+trsl matrices
> >
> > 	Hello,
> >
> > I would like to dock several molecules into a map and display
> > a score in real time (i.e., as the molecules are moved around
> > with the mouse).
> >
> > For that I have to retrieve the rotation+translation matrix
> > for each molecule while it is being moved around, to feed it
> > into a scoring algorithm.
> >
> > Do you know how to get these matrices ?
> > Thank you !
> > --X.
> >
> > -------------------------------------------------
> > Xavier Siebert, Ph.D.
> > Laboratoire de Virologie Mole(c)culaire & Structurale UMR 2472
> CNRS-GIF
> > 1 Av. de la Terrasse, Bat. 14 B
> > 91198 Gif-sur-Yvette, FRANCE
> >
> > tel : (++33)-1-69.82.38.56
> > fax : (++33)-1-69.82.43.08
> >
> >
> > -------------------------------------------------------
> > SF.Net email is sponsored by:
> > Tame your development challenges with Apache's Geronimo App Server.
> > Download it for free - -and be entered to win a 42" plasma tv
> > or your very own Sony(tm)PSP.  Click here to play:
> > http://sourceforge.net/geronimo.php
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
> >
> >
> >
>