pymol-users Mailing List for PyMOL Molecular Graphics System

You could also try to add sys.path.append(dllpath) to your python script,
where dllpath is the full path to the location of the pymol dll's.

Of course, this approach might run into problems with different python
versions; but depending on what you're trying to do it might be worth a
shot (if there's a python.exe that ships with the precompiled pymol
windows builds, then running your python script with that would be
probably be the easiest way).

Pete

> Yun,
>
> Precompiled PyMOL builds for Windows run inside their own Python
> interpreter.  Thus, to access PyMOL from Python, you need to run your
> script
> from within PyMOL. An easy way to do this is to give your script a ".pym"
> extension.
>
> Cheers,
> DeLano Scientific LLC
> Subscriber Support Services
> mailto:de...@de... <BLOCKED::mailto:de...@de...>
>
> "Not yet a PyMOL Subscriber, but want to support the project?  Email
> sa...@de... to quote your lab, school, or employer.  Thank you for
> sponsoring this open-source endeavor!" -WLD
>
>
>
>   _____
>
> From: pym...@li...
> [mailto:pym...@li...] On Behalf Of Li, Yun
> Sent: Tuesday, January 30, 2007 11:09 AM
> To: pym...@li...
> Subject: [PyMOL] ImportError: No module named _cmd
>
>
>
> Hi,
>
>
>
> I just installed the latest windows binary of PyMol on a PC. I tried to
> run
> PyMol from a Python script and run into the following error message:
> "ImportError: No module named _cmd"
>
>
>
> I remember running into the problem before. From somewhere I was able to
> find a _cmd.dll and solved the problem. But this time I could find a
> solution.
>
>
>
> Hope somebody could help me.
>
>
>
> Yun Li
>
>
>
> Assistant Professor of Chemistry
>
> Delaware Valley College
>
> 700 E. Butler Ave.,
>
> Doylestown, PA 18901
>
> (215) 489-2482
>
>
>
> -------------------------------------------------------------------------
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to share
> your
> opinions on IT & business topics through brief surveys - and earn cash
> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV_______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>


Pete Meyer
Fu Lab
BMCB grad student
Cornell University

Yun,
 
Precompiled PyMOL builds for Windows run inside their own Python
interpreter.  Thus, to access PyMOL from Python, you need to run your script
from within PyMOL. An easy way to do this is to give your script a ".pym"
extension.
 
Cheers,
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de... <BLOCKED::mailto:de...@de...> 
 
"Not yet a PyMOL Subscriber, but want to support the project?  Email
sa...@de... to quote your lab, school, or employer.  Thank you for
sponsoring this open-source endeavor!" -WLD
 


  _____  

From: pym...@li...
[mailto:pym...@li...] On Behalf Of Li, Yun
Sent: Tuesday, January 30, 2007 11:09 AM
To: pym...@li...
Subject: [PyMOL] ImportError: No module named _cmd



Hi,

 

I just installed the latest windows binary of PyMol on a PC. I tried to run
PyMol from a Python script and run into the following error message:
"ImportError: No module named _cmd"

 

I remember running into the problem before. From somewhere I was able to
find a _cmd.dll and solved the problem. But this time I could find a
solution.

 

Hope somebody could help me.

 

Yun Li

 

Assistant Professor of Chemistry

Delaware Valley College

700 E. Butler Ave.,

Doylestown, PA 18901

(215) 489-2482

 

Hi,

=20

I just installed the latest windows binary of PyMol on a PC. I tried to
run PyMol from a Python script and run into the following error message:
"ImportError: No module named _cmd"

=20

I remember running into the problem before. From somewhere I was able to
find a _cmd.dll and solved the problem. But this time I could find a
solution.

=20

Hope somebody could help me.

=20

Yun Li

=20

Assistant Professor of Chemistry

Delaware Valley College

700 E. Butler Ave.,

Doylestown, PA 18901

(215) 489-2482

=20

Folks, 
 
This is a reminder that Microsoft's new version of Windows, "Vista" has
serious issues with OpenGL-based software and should be avoided for the time
being.  
 
Only in the last few weeks have all of the major graphics card companies
finally begun to release Vista drivers with true OpenGL support.  Thus,
please allow a few months for the bugs to shake out before expecting PyMOL
(and other OpenGL-depedent programs) to run well on Vista.
 
If you buy a new Windows PC or laptop soon, be sure to check what operating
system comes installed -- you may need to specifically ask for Windows XP.
 
Cheers,
Warren
 
--
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...
 
 

Hi Xavier-
=20
To show ligands coming into a protein binding site I generally use some =
sort of morphing approach rather than translating the ligand.  The reason =
is that slerpy, even if it could cope with translate, would not interpolate=
 the ligand position from one view to the next so you'll end up with =
sudden jerky movements of the ligand. =20
=20
On the other hand, if you generate a multistate model using morphing =
(either lsqman, rigimol, or http://www.molmovdb.org/molmovdb/morph/) then =
you can use smorph in slerpy to incorporate the morph into your movie.  =
See also http://ginsberg.med.virginia.edu/~dcoop/Help/morph.html for hints =
on setting up a morph.
=20
I've been working on a slerpy demo page that includes some morphing but =
it's not done yet.
=20
I've never tried using the translate command in a slerpy action.  I'll =
have a look at that tonight.
=20
Thanks,
=20
Joel

>>> "HANOULLE Xavier" <xav...@un...> 1/29/2007 1:11 PM =
>>>

Hello all ! I am trying to use Slerpy to make a movie and I get some =
trouble. I would like to show a ligand coming and binding to my protein*  =
So, following the Slerpy instructions, I stored all my orientations then I =
tried to apply actions to the different views. But when I typed this =
command:            sgo 2            saction =93translate [0,20,0], =
ligand=94 I got the following error: =93Error: too many arguments for =
add_action_current; 1 expected, 2 found.Usage: add_action_current cmd=94 I =
have an object named =93ligand=94 in Pymol and the command =93translate =
[0,20,0], ligand=94 works pretty well in Pymol (without using Slerpy)*Does =
anyone know how to solve the problem? Thanks! Xavier. Xavier HANOULLE, =
Ph.D.
UMR 8576 CNRS=20
RMN biologique
Universit=E9 des Sciences et Technologies de Lille - France=20

Hello all !

=20

I am trying to use Slerpy to make a movie and I get some trouble. I =
would
like to show a ligand coming and binding to my protein=85=20

=20

So, following the Slerpy instructions, I stored all my orientations then =
I
tried to apply actions to the different views. But when I typed this
command:

            sgo 2

            saction =93translate [0,20,0], ligand=94

=20

I got the following error:

 =93Error: too many arguments for add_action_current; 1 expected, 2 =
found.

Usage: add_action_current cmd=94

=20

I have an object named =93ligand=94 in Pymol and the command =
=93translate
[0,20,0], ligand=94 works pretty well in Pymol (without using Slerpy)=85

Does anyone know how to solve the problem?

=20

Thanks!

=20

Xavier.

=20

Xavier HANOULLE, Ph.D.

UMR 8576 CNRS=20
RMN biologique
Universit=E9 des Sciences et Technologies de Lille - France

=20

Frank,
 
We no longer have access to Sharp3D equipment, but here is the last PyMOL
build known to work with that monitor:  http://delsci.com/sharp3d/
 
The general feedback from from demos was that these small low-resolution
monitors are not sufficient to meet molecular graphics needs.  However, the
Sharp3D technology might be viable at higher display resolutions, such as
1600x1200 or 1920x1080, if such products were ever introduced.  
 
Dimension technologies http://www.dti3d.com/ has a 1280x1024
auto-stereoscopic 3D display which uses a related technology, which, from
what I understand, does not require customized software builds to drive it.
 
Cheers,
Warren
 
--
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...
 
"Not yet a PyMOL Subscriber, but want to support the project?  Email
sa...@de... to quote your lab, school, or employer.  Thank you for
sponsoring this open-source endeavor!" -WLD
 


  _____  

From: pym...@li...
[mailto:pym...@li...] On Behalf Of S. Frank Yan
Sent: Thursday, January 25, 2007 5:11 PM
To: pym...@li...
Subject: [PyMOL] Stereo on Sharp LCD



Hi,

 

I'm testing the Sharp 3D LCD monitor (LL-151-3D) using PyMOL 0.99rc6.  By
simply pressing the "3D" button on the monitor without enabling any stereo
in PyMOL, it appears to show somewhat enhanced depth.  However, if I enable
the quad-buffered stereo in PyMOL, the picture is just smeared.  I was
wondering if special version of PyMOL is needed, as well as specific graphic
cards.  If so, is such version of PyMOL available for purchase or download.
Or, this is just the best the monitor can do.  

 

Thank you very much.

 

Frank

 

 

Hi,

=20

I'm testing the Sharp 3D LCD monitor (LL-151-3D) using PyMOL 0.99rc6.
By simply pressing the "3D" button on the monitor without enabling any
stereo in PyMOL, it appears to show somewhat enhanced depth.  However,
if I enable the quad-buffered stereo in PyMOL, the picture is just
smeared.  I was wondering if special version of PyMOL is needed, as well
as specific graphic cards.  If so, is such version of PyMOL available
for purchase or download.  Or, this is just the best the monitor can do.


=20

Thank you very much.

=20

Frank

=20

=20

PyMOLers,

I updated CE Align to fix a slight annoyance.  Before, I would translate both 
molecules to the center and align them.  Now, I just move one molecule on top 
of the other.  This allows one to do a poor-man's multiple alignment.  For 
example:
  cealign 1A15, 1DON
  cealign 1A15, 1EOT
  cealign 1A15, 1ESR
  cealign 1A15, 1HA6
will align 1DON, 1EOT, 1ESR, and 1HA6 on top of 1A15, assuming of course 
you've already loaded all the proteins.  Note, that my syntax is:
  cealign MASTER, TARGET
where the MASTER protein never moves -- this is backwards from PyMOL's align 
command.  The new source code is on the wiki.

As for help, I think it would benefit the community if we could get someone to 
make a Windows package for us.  So, if you can make one, please grab the 
source code from the wiki and give it a shot!  

Also, a big thanks to Luca Jovine for the help with the Macs!  He reports that 
it does indeed work.  Details are also on the Wiki.

Thanks,

-- Jason

-- 

Jason Vertrees (jav...@ut...)
Doctoral Student
Biophysical, Structural & Computational Biology Program
University of Texas Medical Branch 
Galveston, Texas

http://www.best.utmb.edu/
http://www.pymolwiki.org/

David,

This does not exist at present, but thank you for suggesting it.

Cheers,

DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...
 
"Not yet a PyMOL Subscriber, but want to support the project?  Email
sa...@de... to quote your lab, school, or employer.  Thank you for
sponsoring this open-source endeavor!" -WLD
 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of David F Burke
> Sent: Thursday, January 25, 2007 8:32 AM
> To: pym...@li...
> Subject: [PyMOL] Side by side views
> 
> Pymol users,
> 
> I wish to compare several protein structures and was 
> wondering how or if, in pymol, one can view two structures 
> side by side and rotate each structure around their own 
> centre of gravity. This is a bit like stereo view but with 
> different structures in the left and right views. Many thanks David
> --
> David Burke PhD
> Department of Zoology, University of Cambridge, Downing 
> Street, Cambridge, CB2 3EJ Email:df...@ca...
> Tel: 01223 330933
> 
> --------------------------------------------------------------
> -----------
> Take Surveys. Earn Cash. Influence the Future of IT Join 
> SourceForge.net's Techsay panel and you'll get the chance to 
> share your opinions on IT & business topics through brief 
> surveys - and earn cash 
> http://www.techsay.com/default.php?page=join.php&p=sourceforge
> &CID=DEVDEV
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Warren helped me with a similar problem a while ago (I can't find the link
in the mailing list archive), and this might do the job for you:

If you download and run my script at
http://www-personal.umich.edu/~mlerner/Pymol/mg_pymol_utils.py
you can start up two PyMOL sessions.  You then type send_view in one of
them, receive_view in the other one, and the "receive_view" one will follow
along.

I don't know how to get that all working in one window, but you can always
just paste the images together.

I find this really useful for comparing structures with different ligands
bound, different parts of a dynamics run, etc.

In your case, you might need to align all of the structures to one reference
structure first, so that the views are similar.

Hope this helps,

-Michael Lerner

On 25 Jan 2007 16:32:21 +0000, David F Burke <df...@ca...> wrote:
>
> Pymol users,
>
> I wish to compare several protein structures and was wondering how or if,
> in pymol, one can view two structures
> side by side and rotate each structure around their own centre of gravity.
> This is a bit like stereo view but with
> different structures in the left and right views. Many thanks David
> --
> David Burke PhD
> Department of Zoology, University of Cambridge,
> Downing Street, Cambridge, CB2 3EJ
> Email:df...@ca...
> Tel: 01223 330933
>
> -------------------------------------------------------------------------
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to share
> your
> opinions on IT & business topics through brief surveys - and earn cash
> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>



-- 
Biophysics Graduate Student
Carlson Lab, University of Michigan
http://www.umich.edu/~mlerner http://lernerclan.net

Pymol users,

I wish to compare several protein structures and was wondering how or if, in pymol, one can view two structures 
side by side and rotate each structure around their own centre of gravity. This is a bit like stereo view but with 
different structures in the left and right views. Many thanks David
-- 
David Burke PhD 
Department of Zoology, University of Cambridge,
Downing Street, Cambridge, CB2 3EJ
Email:df...@ca...
Tel: 01223 330933

Hello all !


I would like to employ pymol to perform some mutagenesis.

At present there is the mutagenesis wizard. Is it possible to execute
this from the command line ?

i.e.

sel resi X
set mutant to CYS
mutate(x) 
save strucutre


Cheers Mitch

JP,

> According to the manual, it is also supposed to be 
> constrained to the origin as well but doesn't appear to do 
> so, at least not in my hands Are its constraints possibly 
> overridden by such commands as center, orient, origin?

origin position=[0,0,0]
turn axis,angle

can change the origin, but x,y,z are always in the camera frame of reference
with the turn and move commmands.

> Reason for asking this is that it would be very nice (at 
> least for me) to be able to perform "local" transformations 
> (i.e. about local object axes, be it the camera or other) 
> that are bound to locally-defined axes
> - that are independent of the "global" or viewport orientation.

For this, use the rotate command.

# atomic coordinate based (geometry must be recomputed)

rotate x,90,

# object matrix based (geometry remains valid, but causes other problems)

rotate x,90,object=object-name

Note that the optional "camera" option (0,1) can control whether global or
camera frame of reference applies, and that the current global origin is
always the center.

origin object-name-or-selection

to change it

Don't mix the two types of rotations or PyMOL will get confused.

Cheers,
Warren

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of Cartailler, Jean-Philippe
> Sent: Tuesday, January 23, 2007 1:19 PM
> To: pym...@li...
> Subject: [PyMOL] Command:turn
> 
> Greetings,
> 
> Does anyone know if the camera commands (turn & move) can be 
> constrained to the reference (global) axes?  I would imagine 
> that the turn command
> (http://pymol.sourceforge.net/newman/ref/S1000comref.html#2_16
> 6) would cause a camera of 45 degrees about the reference axis:
> 
> PyMOL> turn x, 45
> 
> However, it appears to turn the camera about the viewport 
> "orientation", i.e. about the (horizonal) x-axis axis of the 
> viewport.  Note - this is pretty clear if you use Robert 
> Campbell's axes_cyl.py to visualize the reference axis.
> 
> According to the manual, it is also supposed to be 
> constrained to the origin as well but doesn't appear to do 
> so, at least not in my hands Are its constraints possibly 
> overridden by such commands as center, orient, origin?
> 
> Reason for asking this is that it would be very nice (at 
> least for me) to be able to perform "local" transformations 
> (i.e. about local object axes, be it the camera or other) 
> that are bound to locally-defined axes
> - that are independent of the "global" or viewport orientation.
> 
> Using winXP/Pymol 0.98.
> 
> Thanks!
> 
> JP Cartailler
> 
> --------------------------------------------------------------
> -----------
> Take Surveys. Earn Cash. Influence the Future of IT Join 
> SourceForge.net's Techsay panel and you'll get the chance to 
> share your opinions on IT & business topics through brief 
> surveys - and earn cash 
> http://www.techsay.com/default.php?page=join.php&p=sourceforge
> &CID=DEVDEV
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Greetings,

Does anyone know if the camera commands (turn & move) can be constrained
to the reference (global) axes?  I would imagine that the turn command
(http://pymol.sourceforge.net/newman/ref/S1000comref.html#2_166) would
cause a camera of 45 degrees about the reference axis:

PyMOL> turn x, 45

However, it appears to turn the camera about the viewport "orientation",
i.e. about the (horizonal) x-axis axis of the viewport.  Note - this is
pretty clear if you use Robert Campbell's axes_cyl.py to visualize the
reference axis.

According to the manual, it is also supposed to be constrained to the
origin as well but doesn't appear to do so, at least not in my hands
Are its constraints possibly overridden by such commands as center,
orient, origin?

Reason for asking this is that it would be very nice (at least for me)
to be able to perform "local" transformations (i.e. about local object
axes, be it the camera or other) that are bound to locally-defined axes
- that are independent of the "global" or viewport orientation.

Using winXP/Pymol 0.98.

Thanks!

JP Cartailler

> Could someone please point me toward some information on the xmlrpc listener
> and how to communicate with pymol using this?

I am still actively maintaining/using the xmlrpc module (and really
should send Warren the most recent version so it can be included). I'm
happy to answer questions about it.

At the moment I'm not on the pymol mailing list (a situation I'm in
the process of remedying), so please CC me on followups.

-greg

I just looked at some old notes: If you try LIBGL_DEBUG=3Dverbose pymol in =
a terminal, you might get additional information whats wrong.=0A=0AEsben=0A=
=0A=0A=0A =0A______________________________________________________________=
______________________=0ADo you Yahoo!?=0AEveryone is raving about the all-=
new Yahoo! Mail beta.=0Ahttp://new.mail.yahoo.com

Hi=0A   How did you install the Nvidia-drivers? I Once had a similar proble=
m because I had used both the linux distribution package and installed manu=
ally with nvidias driver.  The old libraries were not properly removed by n=
vidias installer, giving rise to the partial working OpenGL. =0A=0ACheers,=
=0AEsben=0A=0A=0A=0A =0A___________________________________________________=
_________________________________=0ANever miss an email again!=0AYahoo! Too=
lbar alerts you the instant new Mail arrives.=0Ahttp://tools.search.yahoo.c=
om/toolbar/features/mail/

> | CGO labels are currently insufficient and need work.  Right 
> now, the 
> | only way to access high-quality labels (using scalable 
> TrueType fonts) 
> | is to create fake atoms and then label them.
> 
> What's the recommended way to do this? Can you just put them 
> anywhere you like, irrespective of any underlying physical 
> model?

Yes.  The open-source code & sponsor-only 1.x beta builds have a new
"pseudoatom" command that makes this particularly convenient.

pseudoatom my_lab, pos=[3.0,4.0,5.0], label=Custom Label Text

You can even drag the label around with the mouse (ctrl-left-click & drag).

> And then presumably make them zero radius, or give 
> them the background color, etc. so as not to see them?

No need -- simply:

as label, object-name

to hide any atomic representation.

Cheers,
Warren

Hi Warren

| CGO labels are currently insufficient and need work.  Right now, the only
| way to access high-quality labels (using scalable TrueType fonts) is to
| create fake atoms and then label them.

What's the recommended way to do this? Can you just put them anywhere you
like, irrespective of any underlying physical model? And then presumably
make them zero radius, or give them the background color, etc. so as not to
see them?

Terry

Richard,

Probably the easiest way to do this is with the "drag" command.  However,
all of the atoms to be drag must be contained within a single molecular
object.  It is not currently possible to move multiple objects at once using
the mouse.

drag object-name

Then move object with shift-(left or middle or right)-click-and-drag
actions.

Cheers,
Warren

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of Richard Gillilan
> Sent: Monday, January 22, 2007 1:48 PM
> To: pym...@li...
> Subject: [PyMOL] dock one protein into another?
> 
> 
> I'm having trouble figuring out how to use the edit mode in 
> PyMol. I would like to dock an entire protein (a homodimer 
> along with water) into another structure by rotating and 
> translating manually.
> 
> Is there a way to move multiple molecules like this as a group?
> 
> 
> Thanks
> 
> Richard Gillilan
> MacCHESS
> 
> --------------------------------------------------------------
> -----------
> Take Surveys. Earn Cash. Influence the Future of IT Join 
> SourceForge.net's Techsay panel and you'll get the chance to 
> share your opinions on IT & business topics through brief 
> surveys - and earn cash 
> http://www.techsay.com/default.php?page=join.php&p=sourceforge
> &CID=DEVDEV
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Ron,

CGO labels are currently insufficient and need work.  Right now, the only
way to access high-quality labels (using scalable TrueType fonts) is to
create fake atoms and then label them.

Cheers,
Warren

PS.  As a minor correction of fact, dashes aren't drawn with CGOs -- they're
hard-coded at the C level as measurement objects.

--
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...
 
"Not yet a PyMOL Subscriber, but want to support the project?  Email
sa...@de... to quote your lab, school, or employer.  Thank you for
sponsoring this open-source endeavor!" -WLD
 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of Ron Jacak
> Sent: Monday, January 22, 2007 10:42 AM
> To: pym...@li...
> Subject: [PyMOL] Labeling CGO objects
> 
> Label gurus,
> 
> I'm trying to label CGO objects with custom labels.  I found 
> the previous posts that explain how to create CGO text and 
> then the "painful" way of reorienting the labels when the 
> molecule is moved using cmd.rotate and cmd.translate.  I'm 
> curious if an easier way has been developed since the posts 
> in 2002.  I see that the "distance"  
> command draws in CGO cylinders (dashes) between two atom 
> selections and then labels them with the distance, meaning 
> that it is possible in PyMOL to have labels tied to a CGO 
> object.  I've tried to generate a selection (since cmd.label 
> requires a selection as the first param) from the CGO object 
> but I don't think it's possible and cmd.label won't take my 
> CGO object as the first param.
> 
> I've succeeded in getting something close to what I want by 
> labeling the closest atom to my CGO object with my custom 
> label, and then translating the label using the mouse.  But 
> this procedure is not possible to do in a script or plugin.  
> Is there a better way to label CGOs?
> 
> Thanks for any ideas.
> 
> -Ron
> 
> Ron Jacak
> Graduate Student
> University of North Carolina - Chapel Hill
> 
> --------------------------------------------------------------
> -----------
> Take Surveys. Earn Cash. Influence the Future of IT Join 
> SourceForge.net's Techsay panel and you'll get the chance to 
> share your opinions on IT & business topics through brief 
> surveys - and earn cash 
> http://www.techsay.com/default.php?page=join.php&p=sourceforge
&CID=DEVDEV
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

I'm having trouble figuring out how to use the edit mode in PyMol. I  
would like to dock an entire protein (a homodimer along with water)  
into another structure by rotating and translating manually.

Is there a way to move multiple molecules like this as a group?


Thanks

Richard Gillilan
MacCHESS

Label gurus,

I'm trying to label CGO objects with custom labels.  I found the  
previous posts that explain how to create CGO text and then the  
"painful" way of reorienting the labels when the molecule is moved  
using cmd.rotate and cmd.translate.  I'm curious if an easier way has  
been developed since the posts in 2002.  I see that the "distance"  
command draws in CGO cylinders (dashes) between two atom selections  
and then labels them with the distance, meaning that it is possible  
in PyMOL to have labels tied to a CGO object.  I've tried to generate  
a selection (since cmd.label requires a selection as the first param)  
from the CGO object but I don't think it's possible and cmd.label  
won't take my CGO object as the first param.

I've succeeded in getting something close to what I want by labeling  
the closest atom to my CGO object with my custom label, and then  
translating the label using the mouse.  But this procedure is not  
possible to do in a script or plugin.  Is there a better way to label  
CGOs?

Thanks for any ideas.

-Ron

Ron Jacak
Graduate Student
University of North Carolina - Chapel Hill

Dear all,
Thanks for all the suggestions.
- checked glxinfo and the startup log of pymol and it shows the loading =
of the propriety GL driver for our Nvidia FX1300 (see copy/paste below) =
and we're not running MESA.
- although...we also have this "freeglut (/usr/pymol/pymol.exe): unable =
to create..." error (but i never saw this since i (also) created =
shortcuts (in gnome) to pymol
- so the 'problem' is not fixed. And if i read the text below...maybe =
it's not possible to fix this.
- anyway...pymol shows a strange behavior: very slow startup of the =
tcl/tk window (but that's probably a problem of redhat/gnome...while on =
a Suse/KDE system i don't see this)
- and further, pymol always directly switches on the transmitter of the =
3D stereo...although not showing or using stereo.
- off topic: we bought this linux machine(s) to replace our old SGIs =
since Insight became available for Linux systems, saving ourselves a lot =
of money (SGIs are expensive).
Thanks for the help. Best,
Joris

./pymol
freeglut (/usr/pymol/pymol.exe): Unable to create direct context =
rendering for w indow 'PyMOL Viewer'
This may hurt performance.

 PyMOL(TM) Incentive Product - Copyright (C) 2006 DeLano Scientific LLC.

 A current PyMOL Maintenance and/or Support Subscription may be required
 for legal use 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 incorporates Open-Source PyMOL 0.99rc6.
 OpenGL graphics engine:
  GL_VENDOR: NVIDIA Corporation
  GL_RENDERER: Quadro FX 1300/PCI/SSE2/3DNOW!
  GL_VERSION: 1.2 (2.0.2 NVIDIA 87.74)
  Hardware stereo capability detected.
 Adapting to Quadro hardware.