pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] very slow script for distance calculation

[andrea s. <and...@gm...>]

Hi all,
is it normal that a script in pymol runs very very slow. In my case I am 
just selecting a residue of a protein and calculating the distance from 
the ligand atoms. I am doing this in a loop over 100 molecule. It took 
ca. 6 hours...!
My memory is 50% free (1Gb total). I am using this script in shell 
without gui.

thanks in advance

Regards,

andrea

Re: [PyMOL] Plugins

[Jerome P. <j.p...@pa...>]

Le Mardi 25 Octobre 2005 08:15, Tjaart de Beer a =E9crit=A0:
> Hi
>
> We are looking at possibly writing some plugins to extend the
> functionality of PyMOL. How would we go about this? Is there some
> documentation on the general process?
>
> Any help would be greatly appreciated!!

Hi,

Here is a usefull resource :
http://www.pymolwiki.org/index.php/Category:Plugins_Tutorial

Jerome Pansanel

[PyMOL] Plugins

[Tjaart de B. <tj...@tu...>]

Hi

We are looking at possibly writing some plugins to extend the 
functionality of PyMOL. How would we go about this? Is there some 
documentation on the general process?

Any help would be greatly appreciated!!


-- 
Tjaart de Beer
Bioinformatics and Computational Biology Unit
University of Pretoria
South Africa

---------
The software required "Windows XP or better" ... so I installed Linux

[PyMOL] launching PyMol from a python function

[Dmitriy I. B. <bry...@ms...>]

I'm trying to start PyMol from another python program.
After the 0_99beta17 it is possible to start it from the __main__ part of a 
code. But when I start PyMol from a function 'pymol.finish_launching()' goes 
in an endless loop. 

Here goes an example:
 ---------------------------------------------------------------
def funct():
   import __main__
   __main__.pymol_argv = [ 'pymol', '-qx' ]
   import pymol
   pymol.finish_launching()
   print "finished" 

if __name__ == '__main__':
   funct()
 ---------------------------------------------------------------
In this case PyMol window starts, but program never reaches 'print 
"finished"'. 

The same time
 ---------------------------------------------------------------
if __name__ == '__main__':
   import __main__
   __main__.pymol_argv = [ 'pymol', '-qx' ]
   import pymol
   pymol.finish_launching()
   print "finished"
 ---------------------------------------------------------------
works fineand prints "finshed" 

after getting into PyMol's finish_launching()  (inside __init__.py)
while not hasattr(__main__,'pymol'):
   e.wait(0.01)
Goes in an endless loop.
I've tried   print dir(__main__)   just before this loop. When PyMol is 
launched not from a function, __main__ indeed have attributes '__main__' and 
'pymol'.  Launched from a function, there are no '__main__' or 'pymol', but 
'funct'. 

I'll really appreciate any help or hints how make it possible to launch 
PyMol from a function or from a method of some class. 

  Dmitriy

[PyMOL] rTools

[matthew h. <Mat...@uv...>]

Another rTools question!

With the following script I get png files written for frames 1-11 and 
for 22-33, but none for the morphing part of the script. In fact, I 
cannot get any output images when running mv_morph in any context, 
either alone or with other commands. But the images displayed in Pymol 
while the mv_morph is running are exactly what I've been looking for.

Is there a way to get mv_morph to write png files for every step of the 
morph? All I get now is a single png written at the end of the morph.

I'm using rTools 0.7 with PymolX11Hybrid on OSX 10.3

Thanks again,

matt

mv_clear
mv_set 1-11, stick_transparency, 0, 1, dTTP
mv_cmd 11, disable dTTP
mv_morph 12-21, pre_chem, post_chem, morph_script.pml
mv_set 22-33, stick_transparency, 1, 0, post_chem_bond
movie f_morph

Re: [PyMOL] question about ray after alter and rebuild

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

Hi Pete,

Check on the sections "clipped_by" and "bounded_by" in the povray
documentation. You can clip with a defined plane, and can actually do so
using different planes for different objects. Alternatively you can use
other objects to clip. Another possibility is to use CSG difference or
intersection. Especially the latter will be painfully slow with surfaces an=
d
such, unfortunately. Come to think of it, it may be possible to directly
include this in the conversion to povray. Maybe if I have a moment, I'll ad=
d
it to the scripts I have and post the link... :)

Cheers,

Tsjerk

On 10/24/05, Peter Adrian Meyer <pa...@co...> wrote:
>
>
> > Or you can dump to povray and render at whatever resolution you want,
> > but the image will not resemble exactly what is seen in the pymol viewe=
r
> > window.
> >
>
> I've noticed problems with the clipping planes (z axis) whenever I've
> tried this. Specifically, the near clipping plane is apparently not
> respected in pov-ray conversion (particularly for maps/isomeshes).
> I don't know if this has been fixed or not as of yet, but I wasn't able t=
o
> find a way to work around this. Your milage may vary...
>
> Pete
>
>
> Pete Meyer
> Fu Lab
> BMCB grad student
> Cornell University
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by the JBoss Inc.
> Get Certified Today * Register for a JBoss Training Course
> Free Certification Exam for All Training Attendees Through End of 2005
> Visit http://www.jboss.com/services/certification for more information
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>



--

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

Re: [PyMOL] question about ray after alter and rebuild

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

> Or you can dump to povray and render at whatever resolution you want,
> but the image will not resemble exactly what is seen in the pymol viewer
> window.
>

I've noticed problems with the clipping planes (z axis) whenever I've
tried this.  Specifically, the near clipping plane is apparently not
respected in pov-ray conversion (particularly for maps/isomeshes).
I don't know if this has been fixed or not as of yet, but I wasn't able to
find a way to work around this.  Your milage may vary...

Pete


Pete Meyer
Fu Lab
BMCB grad student
Cornell University

Re: [PyMOL] non-pdb coordinate help

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

Hi Kristl,

The pdb-file is column formatted. You can find a specification of the file
format at
http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html
The easiest is to write a python script to do the conversion.

Hope it helps,

Tsjerk

On 10/24/05, Kristl Adams <kr...@ph...> wrote:
>
> I have several txt files of coordinates (mostly heme type compounds)
> that I'd like to format correctly for pymol to be able to read. I've
> tried several things looking at PDBs with hemes, but can't figure it out.
>
> Will someone with more experience please show me how this should be
> formatted for pymol to read properly.
>
> Thanks!
>
> This is one of the files: (This is a heme type molecule, TPP-NO)
>
> FE 0.000000 0.000000 0.300000
> N1 2.005000 0.000000 0.000000
> CA1 2.847000 1.093360 0.000000
> CB1 4.224580 0.677440 0.000000
> HB1 5.116370 1.304200 0.000000
> CB2 4.224580 -0.678560 -0.000000
> HB2 5.115270 -1.306870 -0.000000
> CA2 2.847000 -1.094470 -0.000000
> CM1 2.473030 -2.474910 -0.000000
> N2 0.000000 2.005000 -0.000000
> CA3 -1.093360 2.847000 -0.000000
> CB3 -0.677440 4.224580 -0.000000
> HB3 -1.304200 5.116370 -0.000000
> CB4 0.678560 4.224580 0.000000
> HB4 1.306870 5.115270 0.000000
> CA4 1.092590 2.847770 0.000000
> CM2 2.473030 2.473800 0.000000
> N3 -2.005000 0.000000 0.000000
> CA5 -2.847000 -1.093360 0.000000
> CB5 -4.224580 -0.677440 0.000000
> HB5 -5.116370 -1.304200 0.000000
> CB6 -4.224580 0.678560 -0.000000
> HB6 -5.115270 1.306870 -0.000000
> CA6 -2.847000 1.093360 -0.000000
> CM3 -2.472040 2.473520 -0.000000
> N4 0.000000 -2.005000 -0.000000
> CA7 1.092590 -2.848880 -0.000000
> CB7 0.674720 -4.225870 -0.000000
> HB7 1.300210 -5.118550 -0.000000
> CB8 -0.681280 -4.223950 0.000000
> HB8 -1.310860 -5.113740 0.000000
> CA8 -1.093360 -2.847000 0.000000
> CM4 -2.472890 -2.469800 0.000000
> C1 3.540060 -3.541940 0.000000
> C12 4.027960 -4.029840 -1.195110
> H12 3.642590 -3.644470 -2.139080
> C13 5.003770 -5.005650 -1.195110
> H13 5.389140 -5.391020 -2.139080
> C14 5.491670 -5.493550 0.000000
> H14 6.262420 -6.264300 0.000000
> C15 5.003770 -5.005650 1.195120
> H15 5.389140 -5.391020 2.139080
> C16 4.027960 -4.029840 1.195120
> H16 3.642590 -3.644470 2.139080
> C2 3.540050 3.540820 0.000000
> C22 4.027960 4.028730 -1.195120
> H22 3.642580 3.643350 -2.139080
> C23 5.003770 5.004540 -1.195120
> H23 5.389140 5.389910 -2.139080
> C24 5.491670 5.492440 0.000000
> H24 6.262420 6.263190 0.000000
> C25 5.003770 5.004540 1.195110
> H25 5.389140 5.389910 2.139080
> C26 4.027960 4.028730 1.195110
> H26 3.642590 3.643350 2.139080
> C3 -3.538280 3.541340 0.000000
> C32 -4.025820 4.029600 -1.195120
> H32 -3.640730 3.643940 -2.139080
> C33 -5.000900 5.006130 -1.195120
> H33 -5.385990 5.391790 -2.139080
> C34 -5.488440 5.494400 0.000000
> H34 -6.258620 6.265720 0.000000
> C35 -5.000900 5.006130 1.195110
> H35 -5.385990 5.391790 2.139080
> C36 -4.025820 4.029600 1.195110
> H36 -3.640730 3.643940 2.139080
> C4 -3.542500 -3.534230 0.000000
> C42 -4.031590 -4.020950 -1.195110
> H42 -3.645280 -3.636510 -2.139080
> C43 -5.009760 -4.994380 -1.195110
> H43 -5.396070 -5.378820 -2.139080
> C44 -5.498850 -5.481100 0.000000
> H44 -6.271460 -6.249970 0.000000
> C45 -5.009760 -4.994380 1.195120
> H45 -5.396070 -5.378820 2.139080
> C46 -4.031590 -4.020950 1.195120
> H46 -3.645280 -3.636510 2.139080
> N 0.135400 0.113610 1.981740
> O 0.660820 0.554490 2.898570
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by the JBoss Inc.
> Get Certified Today * Register for a JBoss Training Course
> Free Certification Exam for All Training Attendees Through End of 2005
> Visit http://www.jboss.com/services/certification for more information
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>



--

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

Re: [PyMOL] question about ray after alter and rebuild

[Sabuj P. <sab...@va...>]

Or you can dump to povray and render at whatever resolution you want,
but the image will not resemble exactly what is seen in the pymol viewer
window.

Peter Adrian Meyer wrote:
>>multiple structura alignment. I pointed out three structures for further
>>processing within all 12 structures. However, when I try to ray the
>>structural
>>resolution (only 3 of all 12 structures) to 2000x2000 with 'ray 2000,
>>2000', I
>>always received a low resolution (as screen resolution only) result. How
>>could
>>I do? Thanks a lot!
> 
> 
> 
> Pymol can't display a ray-traced image to higher resolution than your
> screen can show, but it can write it to a png file at that resolution (I'm
> assuming you're talking about pixel resolution, not diffraction resolution
> here).
> 
> ray 2000,2000 ; png HighRes.png
> 
> Pete
> 
> Pete Meyer
> Fu Lab
> BMCB grad student
> Cornell University

[PyMOL] non-pdb coordinate help

[Kristl A. <kr...@ph...>]

I have several txt files of coordinates (mostly heme type compounds) 
that I'd like to format correctly for pymol to be able to read.  I've 
tried several things looking at PDBs with hemes, but can't figure it out.

Will someone with more experience please show me how this should be 
formatted for pymol to read properly.

Thanks!

This is one of the files:  (This is a heme type molecule, TPP-NO)

FE   0.000000   0.000000   0.300000
N1   2.005000   0.000000   0.000000
CA1   2.847000   1.093360   0.000000
CB1   4.224580   0.677440   0.000000
HB1   5.116370   1.304200   0.000000
CB2   4.224580   -0.678560   -0.000000
HB2   5.115270   -1.306870   -0.000000
CA2   2.847000   -1.094470   -0.000000
CM1   2.473030   -2.474910   -0.000000
N2   0.000000   2.005000   -0.000000
CA3   -1.093360   2.847000   -0.000000
CB3   -0.677440   4.224580   -0.000000
HB3   -1.304200   5.116370   -0.000000
CB4   0.678560   4.224580   0.000000
HB4   1.306870   5.115270   0.000000
CA4   1.092590   2.847770   0.000000
CM2   2.473030   2.473800   0.000000
N3   -2.005000   0.000000   0.000000
CA5   -2.847000   -1.093360   0.000000
CB5   -4.224580   -0.677440   0.000000
HB5   -5.116370   -1.304200   0.000000
CB6   -4.224580   0.678560   -0.000000
HB6   -5.115270   1.306870   -0.000000
CA6   -2.847000   1.093360   -0.000000
CM3   -2.472040   2.473520   -0.000000
N4   0.000000   -2.005000   -0.000000
CA7   1.092590   -2.848880   -0.000000
CB7   0.674720   -4.225870   -0.000000
HB7   1.300210   -5.118550   -0.000000
CB8   -0.681280   -4.223950   0.000000
HB8   -1.310860   -5.113740   0.000000
CA8   -1.093360   -2.847000   0.000000
CM4   -2.472890   -2.469800   0.000000
C1   3.540060   -3.541940   0.000000
C12   4.027960   -4.029840   -1.195110
H12   3.642590   -3.644470   -2.139080
C13   5.003770   -5.005650   -1.195110
H13   5.389140   -5.391020   -2.139080
C14   5.491670   -5.493550   0.000000
H14   6.262420   -6.264300   0.000000
C15   5.003770   -5.005650   1.195120
H15   5.389140   -5.391020   2.139080
C16   4.027960   -4.029840   1.195120
H16   3.642590   -3.644470   2.139080
C2   3.540050   3.540820   0.000000
C22   4.027960   4.028730   -1.195120
H22   3.642580   3.643350   -2.139080
C23   5.003770   5.004540   -1.195120
H23   5.389140   5.389910   -2.139080
C24   5.491670   5.492440   0.000000
H24   6.262420   6.263190   0.000000
C25   5.003770   5.004540   1.195110
H25   5.389140   5.389910   2.139080
C26   4.027960   4.028730   1.195110
H26   3.642590   3.643350   2.139080
C3   -3.538280   3.541340   0.000000
C32   -4.025820   4.029600   -1.195120
H32   -3.640730   3.643940   -2.139080
C33   -5.000900   5.006130   -1.195120
H33   -5.385990   5.391790   -2.139080
C34   -5.488440   5.494400   0.000000
H34   -6.258620   6.265720   0.000000
C35   -5.000900   5.006130   1.195110
H35   -5.385990   5.391790   2.139080
C36   -4.025820   4.029600   1.195110
H36   -3.640730   3.643940   2.139080
C4   -3.542500   -3.534230   0.000000
C42   -4.031590   -4.020950   -1.195110
H42   -3.645280   -3.636510   -2.139080
C43   -5.009760   -4.994380   -1.195110
H43   -5.396070   -5.378820   -2.139080
C44   -5.498850   -5.481100   0.000000
H44   -6.271460   -6.249970   0.000000
C45   -5.009760   -4.994380   1.195120
H45   -5.396070   -5.378820   2.139080
C46   -4.031590   -4.020950   1.195120
H46   -3.645280   -3.636510   2.139080
N   0.135400   0.113610   1.981740
O   0.660820   0.554490   2.898570

Re: [PyMOL] Adjust radius of sphere

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

Hi Anbang Li,

If you want to show the spheres in a relative size, you can use

set sphere_scale, 0.5

to scale down the size by half for example. To do this for a specific
object, use

set sphere_scale, 0.5, object

Otherwise, if you want to change the actual radius, you can use

alter selection, vdw=3Dnewradius

Possibly you have to use rebuild to update the scene afterwards.

Cheers,

Tsjerk

On 10/24/05, Li Anbang <lia...@gm...> wrote:
>
> Hi all,
>
> I have a question about radius of sphere: I select a atom, show its
> sphere, then I want to increase the radius of sphere. How to do this?
>
> Thanks for answers.
> Anbang Li
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by the JBoss Inc.
> Get Certified Today * Register for a JBoss Training Course
> Free Certification Exam for All Training Attendees Through End of 2005
> Visit http://www.jboss.com/services/certification for more information
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>



--

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

Re: [PyMOL] question about ray after alter and rebuild

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

> multiple structura alignment. I pointed out three structures for further
> processing within all 12 structures. However, when I try to ray the
> structural
> resolution (only 3 of all 12 structures) to 2000x2000 with 'ray 2000,
> 2000', I
> always received a low resolution (as screen resolution only) result. How
> could
> I do? Thanks a lot!


Pymol can't display a ray-traced image to higher resolution than your
screen can show, but it can write it to a png file at that resolution (I'm
assuming you're talking about pixel resolution, not diffraction resolution
here).

ray 2000,2000 ; png HighRes.png

Pete

Pete Meyer
Fu Lab
BMCB grad student
Cornell University

[PyMOL] Adjust radius of sphere

[Li A. <lia...@gm...>]

Hi all,

I have a question about radius of sphere: I select a atom, show its
sphere, then I want to increase the radius of sphere. How to do this?

Thanks for answers.
Anbang Li

Re: [PyMOL] question about ray after alter and rebuild

[Kristian R. <k_r...@ya...>]

--- Chung-Ming Yu <yu...@ga...> wrote:

> Dear all:
> 
> I changed the topology of secondary structures with
> 'alter' commands and then
> I used 'rebuild' command to show the new topology of
> secondary structures in
> multiple structura alignment. I pointed out three
> structures for further
> processing within all 12 structures. However, when I
> try to ray the structural
> resolution (only 3 of all 12 structures) to
> 2000x2000 with 'ray 2000, 2000', I
> always received a low resolution (as screen
> resolution only) result. How could
> I do? Thanks a lot!
> 
> Fisher C.-M. Yu
> 
> yu...@ga...
> 
> 
> 
>
-------------------------------------------------------
> This SF.Net email is sponsored by the JBoss Inc.
> Get Certified Today * Register for a JBoss Training
> Course
> Free Certification Exam for All Training Attendees
> Through End of 2005
> Visit http://www.jboss.com/services/certification
> for more information
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
>
https://lists.sourceforge.net/lists/listinfo/pymol-users
> 



	
		
__________________________________ 
Yahoo! Mail - PC Magazine Editors' Choice 2005 
http://mail.yahoo.com

[PyMOL] question about ray after alter and rebuild

[Chung-Ming Y. <yu...@ga...>]

Dear all:

I changed the topology of secondary structures with 'alter' commands and then
I used 'rebuild' command to show the new topology of secondary structures in
multiple structura alignment. I pointed out three structures for further
processing within all 12 structures. However, when I try to ray the structural
resolution (only 3 of all 12 structures) to 2000x2000 with 'ray 2000, 2000', I
always received a low resolution (as screen resolution only) result. How could
I do? Thanks a lot!

Fisher C.-M. Yu

yu...@ga...

[PyMOL] MacPyMOL 0.99b19

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

I started using the new MacPyMOL beta and have discovered that it  
does not support keyboard qualifiers to emulate a multibutton mouse.   
This was very useful on my Powerbook as I could do most operations  
without plugging in a 3-button mouse.  Has anyone also noted this?
_________________________________
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry
Biophysics Research Division, University of Michigan
sa...@um...        (734) 764-3353        fax (734) 764-3323
http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html

[PyMOL] rTools and states

[matthew h. <Mat...@uv...>]

Hi all,

I've been trying to make my first "real" movie in Pymol with rTools 0.7 
and PymolX11Hybrid (0.98) on OSX 10.3. So far rTools does what I want 
it to (mv_morph is awesome!) but I cannot get rTools to cycle through 
the states of a morph I've made. I can get individual states to show up

mv_rot 1-100:1, x, 360, mov

will rotate state 1, and

mv_rot 1-100:10, x, 360, mov

will rotate state 10, but

mv_rot 1-100:1-10, x, 360, mov

does not cycle through the states as is suggested in the rTools 
documentation. Is there a way to make rTools cycle through the states 
of an object while doing other things? Is there a way to make it cycle 
through states at all? I've tried mixing some mset and mplay commands 
(which work on their own) with the rTools commands but without success.

Ideally what I'd like to do is mv_trans OBJ1 and dock it onto OBJ2 
while OBJ2 stays in state 1. Then I'd like to mv_rot OBJ1 while, at the 
same time, cycling through the morphed states of OBJ2. Is something 
like this even possible?

Thanks,

Matt

[PyMOL] drawing CGO cones

[Andrew W. <sen...@gm...>]

Hey all,
Is there a way to create CGO cones in pymol?

Cheers

Andrew Wollacott

[PyMOL] drawing CGO cones

[Andrew W. <sen...@gm...>]

Hi all,
Is there a way to draw CGO cones in pymol?

Cheers

Andrew Wollacott

[PyMOL] Independent frames

[<mar...@at...>]

Hi PYMOLers,

is it somehow possible to treat each frame of multiple-frame-object ind=
ependently to the intent that atomic connectivity is considered indepen=
dently and not according to the first frame? I would like to visualise =
reaction (bond breaking and formation) but what I get is that, visually=
, there is bond between atoms distant by 3=2E3 angstroms and the newly =
formed bond is not visible=2E

Thanks,

martink

[PyMOL] How to label atoms by partial charge?

[<mar...@at...>]

Hi PYMOLers,

I have troubles with labeling atoms by partial charge=2E I can assign o=
ccupancy and b-factors but column with charges in my PDB file is not re=
cognized=2E It seems to me that both occupancy- and b-factor-containing=
 columns must be placed at certain position; how is it with charges?

thanks,

martink

RE: [PyMOL] Re: Apple's tk and pymol

[William S. <wg...@ch...>]

Hi Warren:

The display window is actually X so I assume it must be fink/X11 glut.
Sorry I omitted that.

Bill


>
> Are you using Framework GLUT or Fink/Xll GLUT?  The latter might work
>

RE: [PyMOL] Re: Apple's tk and pymol

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

Bill,

Are you using Framework GLUT or Fink/Xll GLUT?  The latter might work
because X11 actually runs as a separate process and has its own event
queue which feeds into GLUT.  If the former is working for you, then
please provide some more specifics regarding OS version, 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
> William Scott
> Sent: Thursday, October 20, 2005 4:28 PM
> To: pym...@li...
> Subject: [PyMOL] Re: Apple's tk and pymol
>=20
> I just fired up pymol installed via fink using Python=20
> compiled against a Framework build of Python that in turn is=20
> build against the TCL TK framework.
>=20
> > your either get interaction with the GLUT GUI, or the Tcl/Tk user=20
> > interface, but not both : (.
>=20
> I can't reproduce the problem, i.e., both guis work ok for me.
>=20
> Sorry if I am missing something obvious.  Otherwise, it might work.
>=20
> Bill
>=20
>=20
> William G. Scott
>=20
> Associate Professor
> Department of Chemistry and Biochemistry and The Center for=20
> the Molecular Biology of RNA Sinsheimer Laboratories=20
> University of California at Santa Cruz Santa Cruz, California=20
> 95064 USA
>=20
> phone:  +1-831-459-5367 (office)
>                 +1-831-459-5292 (lab)
> fax:         +1-831-4593139  (fax)
> url:          http://chemistry.ucsc.edu/~wgscott/
>=20
>=20
>=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] Re: Apple's tk and pymol

[William S. <wg...@ch...>]

I just fired up pymol installed via fink using Python compiled  
against a Framework build of Python that in turn is build against the  
TCL TK framework.

> your either get interaction with the GLUT GUI, or the Tcl/Tk user
> interface, but not both : (.

I can't reproduce the problem, i.e., both guis work ok for me.

Sorry if I am missing something obvious.  Otherwise, it might work.

Bill


William G. Scott

Associate Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA

phone:  +1-831-459-5367 (office)
                +1-831-459-5292 (lab)
fax:         +1-831-4593139  (fax)
url:          http://chemistry.ucsc.edu/~wgscott/

RE: [PyMOL] PyMol with MacOS 10.4

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

Konrad,

Heads up:  there are fundamental threading flaws inherent in Aqua/Tcl/Tk
that currently preclude use of PyMOL with them.  Basically, MacOS X
can't feed events to multiple threads -- just a single thread.

So, your either get interaction with the GLUT GUI, or the Tcl/Tk user
interface, but not both : (.

The only solution I can think of is embedding PyMOL into a Tcl/Tk
widget...not something that is possible yet.

By the way, you should be able to build current PyMOL CVS source code
directly agaist MacOS frameworks without MacPython.  But, like I
mentioned above, the end-result isn't optimal -- you get either OpenGL
or Tcl/Tk, but not both. =20

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
> kh...@ce...
> Sent: Thursday, October 20, 2005 5:02 AM
> To: pymol-users
> Subject: [PyMOL] PyMol with MacOS 10.4
>=20
> Are there other people out there who compile their own PyMol=20
> on the Mac and who have succeeded with MacOS 10.4 (Tiger)?
>=20
> After updating my Mac to Tiger, my PyMol installation doesn't work
> anymore:
>=20
> ~> pymol
> Traceback (most recent call last):
>    File "/usr/local/lib/pymol/modules/pymol/__init__.py",=20
> line 90, in ?
>      import pymol
>    File "/usr/local/lib/pymol/modules/pymol/__init__.py",=20
> line 306, in ?
>      import _cmd
> ImportError: Failure linking new module: /usr/local/lib/pymol/modules/
> pymol/_cmd.so: Symbol not found: _gluCylinder
>    Referenced from: /sw/lib/libglut.3.dylib
>    Expected in: /usr/X11R6/lib/libGL.1.dylib
>=20
>=20
> I guess that something has changed in Apple's OpenGL libraries. My =20
> first reaction was to reinstall PyMol from sources in the=20
> same way as =20
> before (i.e. using the Distutils installation method and Fink's =20
> installation of Python 2.3). This fails pretty quickly due to some =20
> problem with the GLUT headers:
>=20
> In file included from layer0/os_gl.h:95,
>                   from layer2/RepNonbondedSphere.c:19:
> /sw/include/GL/glut.h:432: error: parse error before "layer"
> /sw/include/GL/glut.h:432: warning: function declaration isn't a =20
> prototype
> /sw/include/GL/glut.h:490: error: parse error before "GLfloat"
> /sw/include/GL/glut.h:490: warning: function declaration isn't a =20
> prototype
> ...
>=20
> This is perhaps not so surprising, because I didn't update=20
> Fink after =20
> updating to 10.4 - because that didn't work either. In fact, I am =20
> sufficiently fed up with the fragility of Fink that I would like to =20
> get rid of it entirely.
>=20
> So I thought I should try to use MacPython 2.4.1 (my everyday Python =20
> on the Mac) and Apple's OpenGL and GLUT frameworks. That required a =20
> few patches to the PyMol sources (the includes need to be changed =20
> from GL/... to OpenGL/...) and a bit of tweaking setup.py plus some =20
> manual intervention (Distutils doesn't handle -framework=20
> parameters), =20
> but I got an error-free compile pretty quickly. I can then=20
> even start =20
> PyMol, but it messes up my screen to the point that I need to go to =20
> sleep mode and then restart to get the Finder redrawn. And I am not =20
> even sure that my approach is reasonable, given that with=20
> MacPython I =20
> also use Aqua-Tk, and thus no X11 at all. Window handling=20
> ought to be =20
> different then.
>=20
> Does anyone have more ideas for getting this to work? I don't care =20
> which Python and which Tk I use, as long as I can add my own Python =20
> modules and get PyMol with NumPy support.
>=20
> Konrad.
>=20
>=20
>=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