pymol-users Mailing List for PyMOL Molecular Graphics System

Dear all,
  How can I use the color from the  Setting menu.The ranges of color is more.I first select the region  which I have to make boron color,I used the color boron in setting-color menu,But it failed.Any suggestions are welcome.Thanx in advance.
  Shivesh kumar


shivesh
       
---------------------------------
Be a better Globetrotter. Get better travel answers from someone who knows.
Yahoo! Answers - Check it out.

To all you colouring aficionados,

I've updated the color_b.py script on my web page to include Mark Wall's
addition of user-defined, 3-colour, gradients.  Now you can type on the
command line something like:

  color_b selection, gradient=user, user_rgb=(0.,.3,1.,.8,.8,.8,1.,.8,0.)

to get colours that range from a light blue (0, .3, 1) , through grey 
(.8, .8, .8) to orange (1, 0.8, 0). Or you can use integer values between 0
and 255 like so:

  color_b selection, gradient=user,
user_rgb=(0.,77,255,204,204,204,255,204,0.)

If any one value is larger than 1, then it is assumed that all values are
between 0 and 255.  

You can find it in: 

  http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821            Fax: 613-533-2497
<rob...@qu...>    http://pldserver1.biochem.queensu.ca/~rlc

Has anyone gotten pocketpicker to work with version 1.0?  I installed it
and fixed the paths in the modules to reflect the install location
(including fixing the number of pathname separators), but when I start
it from the plugins menu, it just sits there. It should pop up the
control panel, but nothing happens, no matter how long I let it sit.

Suggestions?

Thanks,
	Andy

On Monday 16 July 2007 03:14:32 Martin H=F6fling wrote:
> Am Freitag, 13. Juli 2007 schrieb Joris Beld:
>
> Gruezi Boris,
>
> > I do not want to start a linux distribution war but we are curious under
> > which distribution pymol is developed/tested and what people generally
> > are using to run pymol (with 3D capability!)??
> > Thanks a lot for the info.
>
> Every recent distribution should give you good 3D performance if drivers
> are set up correctly. I can share OpenSUSE  packages (slightly older) than
> the officially available deb's for ubuntu (in gutsy). They should also
> work/be available for Debian as well.

I've never had problems at all with Mandriva.=20

praedor

=2D-=20
Reichstag fire is to Hitler as 9/11 is to Bush

Am Freitag, 13. Juli 2007 schrieb Joris Beld:

Gruezi Boris,

> I do not want to start a linux distribution war but we are curious under
> which distribution pymol is developed/tested and what people generally
> are using to run pymol (with 3D capability!)??
> Thanks a lot for the info.

Every recent distribution should give you good 3D performance if drivers ar=
e=20
set up correctly. I can share OpenSUSE  packages (slightly older) than the=
=20
officially available deb's for ubuntu (in gutsy). They should also work/be=
=20
available for Debian as well.=20

Best
	Martin

=2D-=20
=46alls dir die Antwort zu ungenau erscheint, k=F6nnte es an der
=46ragestellung liegen. (Daniel Fass in de.org.ccc)

Joris,
 
Given that the vast majority of PyMOL downloads logged are not for Linux
(nearly 10 to 1 against), given the recently splintering of the Linux
desktop market, and given the importance of maintaining backward
compatibility with older Linux distributions, we must take a simple
lowest-common denominator approach toward our precompiled Linux binaries.  
 
Thus, our 32-bit Linux builds are currently prepared in a glibc-2.3
environment using GCC3.  These builds deliver reasonable performance and
compatibility on a wide set of distributions.  Obviously, we cannot prepare
optimized builds for each member of the diverse combinatorial population of
systems (DISTRO x VERSION x RUNTIME x GPU x DRIVER) where it needs to run.
Based on PyMOL usage alone, nearly 90% of our platform-specific effort
should be directed at Windows and Mac, not Linux.  Supporting one Linux
binary out of three total is already an over-allotment of effort.
 
Practically speaking, the only way to achieve top PyMOL performance on Linux
is to build from source code using libraries and compilers optimal for your
specific hardware and distribution.  That is one of the reasons why the
PyMOL open-source code is targeted at Linux 8-)!
 
Cheers,
Warren
 
--
DeLano Scientific LLC
Subscriber Support Services
 


  _____  

From: pym...@li...
[mailto:pym...@li...] On Behalf Of Joris Beld
Sent: Sunday, July 15, 2007 5:20 AM
Cc: pym...@li...
Subject: Re: [PyMOL] best linux distribution to run pymol


Dear all,

Thanks for all the input!
It seems like people do not notice any difference in speed between the
different linux distributions. Also not between KDE or Gnome. That is good
to know. 

Apparently I have some other problem (unrelated to pymol, probably
openGL/glx related) which causes the dramatic difference in speed between
our Redhat (5 fully patched) and Suse (10.2 fully patched). We are using the
latest nvidia drivers from the nvidia website.

Than, about Accelrys/Insight/Discovery Studio. We got Insight/Material
Studio (we do not have the license for DS1.6 or 1.7) to run under Fedora7.
Pymol also runs fine so probably I will switch both machines to Fedora7.
Anyway, thanks again!

Best wishes,

Joris Beld
Laboratory of Organic Chemistry
Swiss Federal Institute of Technology

Forlani Roberto wrote: 

 



  

-----Original Message-----

From: pym...@li... 

[mailto:pym...@li...] On Behalf 

Of Mathias W.

Sent: 13 July 2007 12:48

To: PyM...@li...

Subject: Re: [PyMOL] best linux distribution to run pymol



Joris Beld schrieb:

    

Dear all,

      

(unfortunately i cannot switch to Suse since i cannot get 

Insight/Discovery Studio to run under Suse).

      

This due to the ignorance of the accelrys developers. Even 

the newest version of DS (1.7) does not run on modern 

Distributions using glibc-2.4 or higher. They say that they 

only support RHEL4 which is real old (and uses glibc-2.3).

I guess it would have been no big deal to test DS on a 

glibc-2.4 system and to find the bug which is preventing it 

from running (I don't think they are still using 

linuxthreads). As of the time DS 1.7 was released glibc-2.4 

was already widely spread and so I call this ignorance. I got 

a test version of DS 1.7 and I don't want to use an old linux 

just because of this modelling program. As you pointed out 

you end up with the situation that you cannot run any other 

newer program (or only with great effort)...



--

Mad

    



 

Mathias,

granted that I am not getting money from accelrys ;) I think we should

differentiate between support to different distributions and

compatibility with different distribution.

I have an "unsupported" DS 1.7 running on RHEL 5 (with very nice native

support for nvidia graphics) and a week ago it was running "unsupported"

on a Kubuntu 7.04 (feisty fawn).

At the moment I can not say how pymol is performing on RHEL 5.



Regards,

Roberto





-------------------------------------------------------------------------

This SF.net email is sponsored by DB2 Express

Download DB2 Express C - the FREE version of DB2 express and take

control of your XML. No limits. Just data. Click to get it now.

http://sourceforge.net/powerbar/db2/

_______________________________________________

PyMOL-users mailing list

PyM...@li...

https://lists.sourceforge.net/lists/listinfo/pymol-users

  

Dear all,

Thanks for all the input!
It seems like people do not notice any difference in speed between the 
different linux distributions. Also not between KDE or Gnome. That is 
good to know.

Apparently I have some other problem (unrelated to pymol, probably 
openGL/glx related) which causes the dramatic difference in speed 
between our Redhat (5 fully patched) and Suse (10.2 fully patched). We 
are using the latest nvidia drivers from the nvidia website.

Than, about Accelrys/Insight/Discovery Studio. We got Insight/Material 
Studio (we do not have the license for DS1.6 or 1.7) to run under 
Fedora7. Pymol also runs fine so probably I will switch both machines to 
Fedora7. Anyway, thanks again!

Best wishes,

Joris Beld
Laboratory of Organic Chemistry
Swiss Federal Institute of Technology

Forlani Roberto wrote:
>  
>
>   
>> -----Original Message-----
>> From: pym...@li... 
>> [mailto:pym...@li...] On Behalf 
>> Of Mathias W.
>> Sent: 13 July 2007 12:48
>> To: PyM...@li...
>> Subject: Re: [PyMOL] best linux distribution to run pymol
>>
>> Joris Beld schrieb:
>>     
>>> Dear all,
>>>       
>>> (unfortunately i cannot switch to Suse since i cannot get 
>>> Insight/Discovery Studio to run under Suse).
>>>       
>> This due to the ignorance of the accelrys developers. Even 
>> the newest version of DS (1.7) does not run on modern 
>> Distributions using glibc-2.4 or higher. They say that they 
>> only support RHEL4 which is real old (and uses glibc-2.3).
>> I guess it would have been no big deal to test DS on a 
>> glibc-2.4 system and to find the bug which is preventing it 
>> from running (I don't think they are still using 
>> linuxthreads). As of the time DS 1.7 was released glibc-2.4 
>> was already widely spread and so I call this ignorance. I got 
>> a test version of DS 1.7 and I don't want to use an old linux 
>> just because of this modelling program. As you pointed out 
>> you end up with the situation that you cannot run any other 
>> newer program (or only with great effort)...
>>
>> --
>> Mad
>>     
>
>  
> Mathias,
> granted that I am not getting money from accelrys ;) I think we should
> differentiate between support to different distributions and
> compatibility with different distribution.
> I have an "unsupported" DS 1.7 running on RHEL 5 (with very nice native
> support for nvidia graphics) and a week ago it was running "unsupported"
> on a Kubuntu 7.04 (feisty fawn).
> At the moment I can not say how pymol is performing on RHEL 5.
>
> Regards,
> Roberto
>
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by DB2 Express
> Download DB2 Express C - the FREE version of DB2 express and take
> control of your XML. No limits. Just data. Click to get it now.
> http://sourceforge.net/powerbar/db2/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>   

Hi List!

OK, I got Pymol working on my Mac intel (thanks again Warren!)

But, you know, python with aqua-based tkinter is pretty cool (no
offense to pymol with original tkinter!).

So I tried "Gratuitous Eye-Candy Tweaks" from
http://www.pymolwiki.org/index.php/MAC_Install, with 2 important
modifications.

1- I compiled my pymol from SVN with Fink python 2.5.1. pymol-py25
from Fink fails for me (X11 problems)
2- I followed this receipt for python:
  wget -c http://www.python.org/ftp/python/2.5.1/Python-2.5.1.tar.bz2
  tar xvfj Python-2.5.1.tar.bz2
  cd Python-2.5.1
  export PATH=/usr/bin:$PATH
  ./configure --enable-framework --enable-universalsdk
  make
  sudo make frameworkinstall

(others versions of python below 2.4.4 failed on my mac intel, even
hacking Makefile).

So, following the receipt "Gratuitous Eye-Candy Tweaks" I got it when
running pymol:

2007-07-13 15:24:55.364 Python[7656] *** _NSAutoreleaseNoPool():
Object 0x18737c20 of class NSCarbonWindowContentView autoreleased with
no pool in place - just leaking

and a frozen pymol menu, although "PyMOL Viewer" window functional and
even accepting command lines.

OK if I cannot get pymol with aqua-based tkinter but I would like to
listen from others if they would be able to have it.

Besides, any tip abou the issue above would be ver appreciate.

Many thanks in advance.
Alan
-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<

=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf=20
> Of Mathias W.
> Sent: 13 July 2007 12:48
> To: PyM...@li...
> Subject: Re: [PyMOL] best linux distribution to run pymol
>=20
> Joris Beld schrieb:
> > Dear all,
>=20
> > (unfortunately i cannot switch to Suse since i cannot get=20
> > Insight/Discovery Studio to run under Suse).
>=20
> This due to the ignorance of the accelrys developers. Even=20
> the newest version of DS (1.7) does not run on modern=20
> Distributions using glibc-2.4 or higher. They say that they=20
> only support RHEL4 which is real old (and uses glibc-2.3).
> I guess it would have been no big deal to test DS on a=20
> glibc-2.4 system and to find the bug which is preventing it=20
> from running (I don't think they are still using=20
> linuxthreads). As of the time DS 1.7 was released glibc-2.4=20
> was already widely spread and so I call this ignorance. I got=20
> a test version of DS 1.7 and I don't want to use an old linux=20
> just because of this modelling program. As you pointed out=20
> you end up with the situation that you cannot run any other=20
> newer program (or only with great effort)...
>=20
> --
> Mad

=20
Mathias,
granted that I am not getting money from accelrys ;) I think we should
differentiate between support to different distributions and
compatibility with different distribution.
I have an "unsupported" DS 1.7 running on RHEL 5 (with very nice native
support for nvidia graphics) and a week ago it was running "unsupported"
on a Kubuntu 7.04 (feisty fawn).
At the moment I can not say how pymol is performing on RHEL 5.

Regards,
Roberto

Joris Beld schrieb:
> Dear all,

> (unfortunately i cannot switch to Suse since i cannot get 
> Insight/Discovery Studio to run under Suse).

This due to the ignorance of the accelrys developers. Even the newest version of DS (1.7) does not run on modern 
Distributions using glibc-2.4 or higher. They say that they only support RHEL4 which is real old (and uses glibc-2.3).
I guess it would have been no big deal to test DS on a glibc-2.4 system and to find the bug which is preventing it from 
running (I don't think they are still using linuxthreads). As of the time DS 1.7 was released glibc-2.4 was already 
widely spread and so I call this ignorance. I got a test version of DS 1.7 and I don't want to use an old linux just 
because of this modelling program. As you pointed out you end up with the situation that you cannot run any other newer 
program (or only with great effort)...

-- 
Mad

I accidentaly sent my reply to your private address first -- sorry.
Resending to the list.

2007/7/13, Joris Beld <be...@or...>:
> We have two molecular modeling PCs with 3D emitters (and CRT monitors).
> One runs the linux distribution Redhat (Gnome) and the other one Suse
> (KDE). It seems to us that the one running Suse/KDE is much faster than
> the one running Redhat/Gnome. Faster in the sense of rotating big
> surface rendered hexamers, 60mers. These are equivalent machines with
> one year old Athlon64, 4GB RAM and Nvidia Fx1400 graphic cards.
> (unfortunately i cannot switch to Suse since i cannot get
> Insight/Discovery Studio to run under Suse).

Try to check if both machines have the same drivers for NVidia video cards
(paste output of `glxinfo' command at terminal if you are unable to
figure it out).
NVidia company's drivers that give best performance and utilize 3D acceleration
are closed-source, so distributions which have religious approach to Free
Software tend not to include it and use less efficient free/open source drivers
(as in vanilla Debian, or as I would expect from Red Hat -- at least from freely
available Red Hat that I remember, and from currently available Fedora, I'm not
sure about Red Hat Enterprise).  Distributions that are focused more on user
experience than on ideology (such as Ubuntu or as I would expect from SuSE)
include rather closed-source NVidia's drivers.

If your RH box uses open-source drivers, try to download drivers from nvidia.com
and install them manually.  Their installation script is automated and usually
works right out of the box.

Also, please send distribution versions so that I can comment on it -- Red Hat
Enterprise, as far as I know, tends to use old versions of packages since they
are tested and stable.

I personally use PyMOL (not that I use it much) on PLD Linux Distribution
(http://www.pld-linux.org/) which I also co-develop, but this is a very specific
distribution tailored for power users and experienced administrators.  There is
repared .spec file for PyMOL in distro's CVS repository so that users
can compile
open-source line of PyMOL in automated way and install results in their system
as an RPM package, which makes managing system much easier.

Regards,
Maciek

-- 
-><- This signature intentionally left blank. -><-

Dear all,

We have two molecular modeling PCs with 3D emitters (and CRT monitors). 
One runs the linux distribution Redhat (Gnome) and the other one Suse 
(KDE). It seems to us that the one running Suse/KDE is much faster than 
the one running Redhat/Gnome. Faster in the sense of rotating big 
surface rendered hexamers, 60mers. These are equivalent machines with 
one year old Athlon64, 4GB RAM and Nvidia Fx1400 graphic cards. 
(unfortunately i cannot switch to Suse since i cannot get 
Insight/Discovery Studio to run under Suse).

I do not want to start a linux distribution war but we are curious under 
which distribution pymol is developed/tested and what people generally 
are using to run pymol (with 3D capability!)??
Thanks a lot for the info.

Best wishes,

Joris Beld

Laboratory of Organic Chemistry
Swiss Federal Institute of Technology Zürich
Switzerland

You need to install libGLU. My bet is that after you going to install
it pymol is going to ask you for another library (I don't recall the
name wright now).
Just go on Google and search the name of the missing library, get the
rpm and install it.

On 7/10/07, Kailee <kai...@go...> wrote:
> Dear all,
>
> I have downloaded Pymol0.99 for linux, and after following the instalation
> notes, I got error message: "pymol.exe: error while loading shared
> libraries: libGLU.so.1: cannot open shared object file: No such file or
> directory" when I tried to use pymol, can anyone suggest why does this
> happen?
>
> Also, as I am trying to look at the AMBER md trajectory files (.mdcrd) using
> PyMol, however after I installed PyMol windows version (successfully), in
> the "Open" tab, I can't find anywhere to load such files, can anyone suggest
> me how to do this please? thank you in advance!
>
> Regards,
> Kailee
> -------------------------------------------------------------------------
> This SF.net email is sponsored by DB2 Express
> Download DB2 Express C - the FREE version of DB2 express and take
> control of your XML. No limits. Just data. Click to get it now.
> http://sourceforge.net/powerbar/db2/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>

Hi all
I am interested to make a cartoon image file from a old PDB. This PDB
contains the coordinates of the only C-alpha atoms.
Is this is possible to create cartoon image through pymol.
can any on help me??
Thanks in advance

With Best Regards
Jhon Thomas

In the past, I've had some strange issues with loading AMBER
trajectories (they might all be fixed by now), but the following has
always worked for me:

1) Rename your files so that they have the same filename and the
extensions .top and .trj. For instance, if you're studying the protein
1YCR, you might name them 1YCR.top and 1YCR.trj.

2) Open up PyMOL and load the topology file ("load 1YCR.top")

3) Load the trajectory file ("load_traj 1YCR.trj")

After that, you may wish to align things with intra_fit.

-michael

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


On 7/10/07, Kailee <kai...@go...> wrote:
> Dear all,
>
> I have downloaded Pymol0.99 for linux, and after following the instalation
> notes, I got error message: "pymol.exe: error while loading shared
> libraries: libGLU.so.1: cannot open shared object file: No such file or
> directory" when I tried to use pymol, can anyone suggest why does this
> happen?
>
> Also, as I am trying to look at the AMBER md trajectory files (.mdcrd) using
> PyMol, however after I installed PyMol windows version (successfully), in
> the "Open" tab, I can't find anywhere to load such files, can anyone suggest
> me how to do this please? thank you in advance!
>
> Regards,
> Kailee
> -------------------------------------------------------------------------
> This SF.net email is sponsored by DB2 Express
> Download DB2 Express C - the FREE version of DB2 express and take
> control of your XML. No limits. Just data. Click to get it now.
> http://sourceforge.net/powerbar/db2/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>

Dear all,

I have downloaded Pymol0.99 for linux, and after following the instalation
notes, I got error message: "pymol.exe: error while loading shared
libraries: libGLU.so.1: cannot open shared object file: No such file or
directory" when I tried to use pymol, can anyone suggest why does this
happen?

Also, as I am trying to look at the AMBER md trajectory files (.mdcrd) using
PyMol, however after I installed PyMol windows version (successfully), in
the "Open" tab, I can't find anywhere to load such files, can anyone suggest
me how to do this please? thank you in advance!

Regards,
Kailee

Dear bb,

I recently ecountered an error which I cannot unambiguously trace and 
repair. It occurs whenever I want to start up pymol, o, coot, xdisp, ...

Our configuration is a CRT/LCD dual monitor using an Nvidia FX3500 under 
RHEL4. It was workin fine before I suddenly got this;

-------------------------------------------------------------------------
XDISP;

X Error of failed request:  BadValue (integer parameter out of range for 
operation)
   Major opcode of failed request:  78 (X_CreateColormap)
   Value in failed request:  0x0
   Serial number of failed request:  8
   Current serial number in output stream:  9
-------------------------------------------------------------------------
O;

X Error of failed request:  BadWindow (invalid Window parameter)
   Major opcode of failed request:  4 (X_DestroyWindow)
   Resource id in failed request:  0xdc
   Serial number of failed request:  16
   Current serial number in output stream:  19
-------------------------------------------------------------------------
PYMOL;

X Error of failed request:  BadValue (integer parameter out of range for 
operation)
   Major opcode of failed request:  78 (X_CreateColormap)
   Value in failed request:  0x0
   Serial number of failed request:  16
   Current serial number in output stream:  19
  PyMOL: abrupt program termination.
-------------------------------------------------------------------------

If more info is needed (e.g. Xorg.conf file), just let me know. Any help 
is greatly appreciated.

Jonathan Elegheert
Ghent University

hello

I want to change the ribbon radius of selected portion. I am superposing 2
molecules and I want to highlight the differences by making them in dot
lines. so I want to reduce the ribbon radius or make that portion as dotted
lines. Is there any option (r) script  in pymol.

Ethayathulla

Mathias,

PyMOL brute-forces a solution to this problem for molecular surfaces with
relatively evenly-spaced points.  The relevant source file is
layer0/Triangle.c.

Cheers,
Warren


> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of Mad
> Sent: Tuesday, July 03, 2007 11:05 PM
> To: pym...@li...
> Subject: [PyMOL] Generate Surfaces from a dot cloud
> 
> Hi,
> 
> I'm looking for a possibility to do a surface triangulation 
> for molecules, where I have basicly given only surface 
> points. Is this possible with pymol or can you point me some 
> sources for doing this. I did some searching through the 
> scientific world and came across several triangulation 
> algorithms and libraries but unfortunately I'm not a 
> mathematician nor a big programmer so that I didn't see the 
> possibility to easy use them for molecule surfaces.
> After some thinking I recognized that there are several 
> opensource molecular modelling programs out there and as I do 
> not want to reinvent the wheel I ask this here.
> 
> Mathias
> 
> --------------------------------------------------------------
> -----------
> This SF.net email is sponsored by DB2 Express Download DB2 
> Express C - the FREE version of DB2 express and take control 
> of your XML. No limits. Just data. Click to get it now.
> http://sourceforge.net/powerbar/db2/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Xuewu,
 
As far as I know, the GLUT library for Mac OS X does not (yet?) support the
scroll wheel.  However, you can use shift-right-click and drag to control
the clipping planes instead.
 
Cheers,
Warren



  _____  

From: pym...@li...
[mailto:pym...@li...] On Behalf Of Xuewu Zhang
Sent: Tuesday, July 03, 2007 7:05 PM
To: pym...@li...
Subject: [PyMOL] wheel slab doesn't work (pymol 1.0)


Hi,  
I compiled the svn pymol version 1.0 on a MacBook (using python in fink).
Everything worked perfectly, except that "wheel slab" of my three button USB
mouse doesn't work. It works fine in Macpymol, so the mouse itself it
functioning. Did I do something wrong or it is a bug? 
Thanks,
Xuewu

Hi Pymol-users,
I'm trying to install pymol from svn repository. After 
compiling ( python setup.py build, python setup.py install, 
     python setup2.py install) when I'm running pymol I have 
such an error

  OpenGL graphics engine:
   GL_VENDOR: NVIDIA Corporation
   GL_RENDERER: GeForce4 MX 440 with AGP8X/AGP/SSE/3DNOW!
   GL_VERSION: 1.5.8 NVIDIA 96.39
Traceback (most recent call last):
   File 
"/usr/lib/python2.4/site-packages/pymol/__init__.py", line 
254, in exec_deferred
     cmd.config_mouse(quiet=1)
   File 
"/usr/lib/python2.4/site-packages/pymol/__init__.py", line 
278, in adapt_to_hardware
     cmd.set('ribbon_smooth',0,quiet=1)
   File 
"/usr/lib/python2.4/site-packages/pymol/__init__.py", line 
364, in launch_gui
     __import__(self.invocation.options.gui)
   File 
"/usr/lib/python2.4/site-packages/pmg_tk/__init__.py", line 
22, in ?
     from PMGApp import *
   File "/usr/lib/python2.4/site-packages/pmg_tk/PMGApp.py", 
line 32, in ?
     class PMGApp(Pmw.MegaWidget):
AttributeError: 'module' object has no attribute 'MegaWidget'
  PyMOL: abrupt program termination.

I suppose this is due to errors in python Pmw installation?
Any ideas?
Many thanks in advance,
Max
-- 
Max Mayzel          mailto:ma...@nm...

Hi Louis,

* Clark, Louis <Lou...@co...> [2007-07-04 12:01] wrote:
> Dear user-group,
> 
>   I'm trying to learn how to use python commands inside pymol .pml
> scripts.  I seem to be missing some understanding about how the
> interface works.  Could somebody tell me how to fix this command below?
> 
>  
> 
> PyMOL>for x in range(10): cmd.label("(name ca and resi %d)" % x, "%s%s" 
> 
> PyMOL>% (resi, resn))
> 
> Traceback (most recent call last):
> 
>   File "/usr/local/pymol/modules/pymol/parser.py", line 232, in parse
> 
>     exec(com2[nest]+"\n",pymol_names,pymol_names)
> 
>   File "<string>", line 1, in ?
> 
> NameError: name 'resi' is not defined

You need quotes around the label expression '"%s%s" % (resi, resn)':

for x in range(10): cmd.label("(name ca and resi %d)" % x, '"%s%s" % (resi, resn)')

The expression has to be passed to pymol as a string to be interpreted
correctly.

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821            Fax: 613-533-2497
<rob...@qu...>    http://pldserver1.biochem.queensu.ca/~rlc

Hmmm.

With a little messing around, it seems that this works at the pymol prompt:

for x in range(10): cmd.label("(name ca and resi %d)" % x, '"%s%s\" %
(resi, resn)')

The only difference is in the quoting. Double quotes inside single quotes.

gilleain

On 7/4/07, Clark, Louis <Lou...@co...> wrote:
>
>
>
>
> Dear user-group,
>
>   I'm trying to learn how to use python commands inside pymol .pml scripts.
> I seem to be missing some understanding about how the interface works.
> Could somebody tell me how to fix this command below?
>
>
>
> PyMOL>for x in range(10): cmd.label("(name ca and resi %d)" % x, "%s%s"
>
> PyMOL>% (resi, resn))
>
> Traceback (most recent call last):
>
>   File "/usr/local/pymol/modules/pymol/parser.py", line
> 232, in parse
>
>     exec(com2[nest]+"\n",pymol_names,pymol_names)
>
>   File "<string>", line 1, in ?
>
> NameError: name 'resi' is not defined
>
>
>
> thanks much!!
>
>
>
> -Louis
>
>
>
> Louis Clark, Ph.D.
>
> lou...@co...
>
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by DB2 Express
> Download DB2 Express C - the FREE version of DB2 express and take
> control of your XML. No limits. Just data. Click to get it now.
> http://sourceforge.net/powerbar/db2/
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>

Dear user-group,

  I'm trying to learn how to use python commands inside pymol .pml
scripts.  I seem to be missing some understanding about how the
interface works.  Could somebody tell me how to fix this command below?

=20

PyMOL>for x in range(10): cmd.label("(name ca and resi %d)" % x, "%s%s"=20

PyMOL>% (resi, resn))

Traceback (most recent call last):

  File "/usr/local/pymol/modules/pymol/parser.py", line 232, in parse

    exec(com2[nest]+"\n",pymol_names,pymol_names)

  File "<string>", line 1, in ?

NameError: name 'resi' is not defined

=20

thanks much!!

=20

-Louis

=20

Louis Clark, Ph.D.

lou...@co... <mailto:lou...@co...>=20

=20

Hi,

I'm looking for a possibility to do a surface triangulation for molecules, where I have basicly given only surface 
points. Is this possible with pymol or can you point me some sources for doing this. I did some searching through the 
scientific world and came across several triangulation algorithms and libraries but unfortunately I'm not a 
mathematician nor a big programmer so that I didn't see the possibility to easy use them for molecule surfaces.
After some thinking I recognized that there are several opensource molecular modelling programs out there and as I do 
not want to reinvent the wheel I ask this here.

Mathias