pymol-users Mailing List for PyMOL Molecular Graphics System

Hello Folks,
I am trying to make triangles using cgo objects
Here is the code, this does not work
*********************************
from pymol.cgo import *
from pymol import cmd
obj =3D []
obj.extend( [ TRIANGLE,
	0.0, 0.0, 0.0, #vertex 1
	1.0, 0.0, 0.0, #vertex 2
	0.0, 0.0, 1.0, #vertex 3
	0,1,0, #normal 1
	0,1,0, #normal 2
	0,1,0, #normal 3
	1,1,1, #color vertex 1
	1,1,1, #color vertex 2
	1,1,1, #color vertex 3=09
	] )
cmd.load_cgo(obj,'my_triangle')
***********************************

But this one works
*************************
obj=3D[BEGIN, TRIANGLES,  =20
      VERTEX, 0.0, 0.0, 0.0,
      VERTEX, 4,4,4,
      VERTEX, 0.0, 0.0, 2.0,
      END ]
cmd.load_cgo(obj,'my_tri')
*******************************


I looked into cgo.h, cgo.c and manual it seemed vertices,normals and
colors is all that's needed for triangles
Please let me know what is missing/wrong.
Thanks for your time.

Regards
--Amit

PS: Chris your normalization code will come in handy when I get this
thing to work properly. Thanks!

Greetings PyMolers:

I have a couple of questions.  I am working on some figures and have 
found, at least for my particular protein,  the DSS in PyMol does a 
better job with secondary structure assignments than DSSP.  I have 
checked the assignments against the map and model in O.  Is there any 
way to output the assignments from PyMol?

Also I want to display surfaces and was wondering if anyone has an 
opinion on the reliability of PyMol vs. MSMS (or any other surface 
calculation programs).  Any input would be greatly appreciated.

Best regards,

Alex

Tsjerk,
Hope you are doing fine.
I was toying with your graph.py script.
I am trying to mod it to generate solid cube.( display triangles instead
of lines)
Could you toss an example how to add triangle inside your graph.py?=20
I could not find details in the docs. It appears pymol needs normals for
all vertex. This kind of strange as opposed to one for each triangle.
Thanks for you help!

--Amit
=20

-----Original Message-----
From: Tsjerk Wassenaar [mailto:t.a...@ch...]=20
Sent: Tuesday, May 25, 2004 1:04 AM
To: am...@sd...
Subject: Re: [PyMOL] 3d plotting in pymol


Hi Amit,

Well, that was my mistake.., I took adding the cmd.extend() a bit too
light-hearted, but I forgot to then parse the (string) elements on the
command line. So, for the size and radius these are trivial, but the
list arguments are a bit more extensive to parse in five minutes of
debugging ;) I have to do that later. You can for now try to use it as a
function graph(selection,shape,....etc) That should work.

I deliberately tried to progam it in such a way that it would be easy to
add new shapes and in a later stage also adapt coloring and such. I can
imagine it would be nice to be able to color according to coordinate,
b-factor, whatever.

But I hope this will do for now :)

Good luck,

Tsjerk

Amit Chourasia wrote:

>Tsjerk,
>This is what I tried
>
>1) load a small pdb files (10 atoms)
>2) run graph.py
>3) graph  all, star, 1, 0.10,[1,0,0],=20
>[0,0,1],[[1,0,0],[0,1,0],[0,0,1]],
>"graph"
>
>This is what I am getting
>*************************************
>Traceback (most recent call last):
>  File "C:\Program Files\PyMOL/modules\pymol\parser.py", line 139, in
parse
>    result=3Dapply(kw[nest][0],args[nest],kw_args[nest])
>  File "C:/Documents and Settings/amit/Desktop/graph.py", line 230, in=20
>graph
>
>obj.extend(shapefunctions[shape](sel.atom[i].coord,size,r,rgb1,rgb2,mtx
>))
>  File "C:/Documents and Settings/amit/Desktop/graph.py", line 58, in
star
>    i[0] =3D mvmult(mtx,i[0])
>  File "C:/Documents and Settings/amit/Desktop/graph.py", line 7, in
mvmult
>    return [ a[0][0]*b[0]+a[0][1]*b[1]+a[0][2]*b[2],
>TypeError: can't multiply sequence to non-int
>*************************************
>
>Is this something to do with the end of line? Need to use special=20
>character for line continuation when line is broken into several lines?
>
>Please let me know
>
>Thanks
>--Amit
>
>
> =20
>

--
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-- :)
-- :) 	Tsjerk A. Wassenaar, M.Sc.
-- :) 	Molecular Dynamics Group
-- :) 	Dept. of Biophysical Chemistry
-- :) 	University of Groningen
-- :) 	Nijenborgh 4
-- :) 	9747 AG Groningen
-- :) 	The Netherlands
-- :)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-- :)
-- :) 	Hi! I'm a .signature virus!
-- :) 	Copy me into your ~/.signature to help me spread!
-- :)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

> Why do you think pymol cannot be sold?  The copyright license 
> does not seem to imply this[1], and such a restriction would 
> render pymol not Open Source.

> Warren, can you tell us what you think on this?

Michael & Carly,

Yes, in my world, open-source means available to all people and for all
purposes, including for sale or resale.  
  
I don't have a problem with people placing different terms on parallel or
related efforts, but if their code or materials are to be distributed with
PyMOL, then their redistribution terms must be compatible with PyMOL's
terms, with no exceptions.  If not, then the author of the material must be
fully responsible for maintenance and distribution.  

Cheers,
Warren

--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020
  

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of 
> Michael Banck
> Sent: Monday, August 23, 2004 5:13 AM
> To: pym...@li...
> Subject: Re: [PyMOL] PyMOL tutorial (moved and slightly updated)
> 
> On Fri, Aug 20, 2004 at 09:37:00AM -0700, 
> chu...@in... wrote:
> > >In any case, you ask a useful question:  I too would like to know 
> > >what license, if any, is granted by the tutorial's authors.  If 
> > >released under an appropriate license, it could be modified for 
> > >Linux/Unix/MacOSX users, and used in course material, distributed 
> > >with PyMOL, etc.
> > 
> > I haven't really thought about licenses for releasing the tutorial 
> > under, I'm not familiar with the different types of 
> licenses. I would 
> > like to see the tutorial treated as the program
> 
> Having it under the same copyright license as pymol seems 
> like a good idea to me.
> 
> > where you can't sell it or claim you created it. 
> 
> Why do you think pymol cannot be sold? The copyright license 
> does not seem to imply this[1], and such a restriction would 
> render pymol not Open Source.
> 
> Warren, can you tell us what you think on this?
> 
> 
> Michael
> 
> [1] "Permission to use, copy, modify, distribute, and 
> distribute modified versions of this software and its 
> documentation for any purpose and without fee is hereby granted [...]"
> 
> 
> -------------------------------------------------------
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> 

Hi PyMOL-users,

I have taken a look into the archives and FAQs about making 300dpi images.
It seems straight forward on the surface, image size in inches * 300dpi
gives the number you put into the ray command.  However, there is mention
of correcting for aspect ratio, which is defined by the viewport.  This
brings me to my question.

Is the viewport aspect ratio dominant and which dimension is dominant?
Here is an example.  I have my viewport set to 800*600.  I want a figure
that is 6in wide at 300 dpi.  So, I render my image at ray 1800, 1800.
Does pymol create white space on the height of my image to maintain the
aspect ratio from the viewport or does it clip width? 

Of course, in this example I have given all the numbers.  I ask for those
times we resize our windows accidently, forget to set the viewport, etc.

Chris

Christopher L. Colbert, Ph.D.
Research Associate
Howard Hughes Medical Institute                   Phone: (214) 648 5002
University of Texas Southwestern Medical Center	  FAX:   (214) 648 5095
5323 Harry Hines Boulevard
Dallas, TX 75390

Is it possible to get pymol to simply print a list of selected distances
from a command such as:

distance foo =3D (name P), (chain B and name ca), 8

This command shows the distances nicely in the gui, but I would like a =
table
of the atoms and their respective distances.

Thanks,
Bob

Hi,

With the old wizard interface, I could capture selection actions with the
do_select method.  Is there a similary way with the Plugins?  (I'm willing
to write more code, I just don't know quite where to start.)

Thanks,

-michael

--
This isn't a democracy;|                        _  |Michael Lerner
 it's a cheer-ocracy.  | ASCII ribbon campaign ( ) |   Michigan
-Torrence,  Bring It On|  - against HTML email  X  |  Biophysics
                       |                       / \ | mlerner@umich

Hi all,
	Does anyone know if it is possible to display tube thickness 
as a function of the B-factor?  The cartoon_tube_radius function 
doesn't seem to have the capability to make this sort of alteration. 
Could this be accomplished using one of the 'flag' commands?

Any help would be appreciated.

Thanks,
Brian Kelch

Hello everybody.
Thanks to Darrel Duffy, it is possible to import easely PDB and MOL =
files to 3Dmax.
http://www.windyweather.net/WW/max/molecule/index.html
Ciao
Eli

Dear Marcelo,

* castilho <cas...@if...> [2004-08-23 17:02] wrote:
> My name is Marcelo and I am a basic-level pymol user. I work with docking
> programs and I am trying to make pymol our default program for analysing
> docking results...this brings me to some questions:
> 
> Is it possible to colour protein surface according to Hydrogen
> donor/acceptor properties in pymol ?

I guess that depends on whether you can define what constitutes a donor
or acceptor easily enough.  I think with sufficient logical operations
you could.  For example:

  select donor, name N or (resn ASN and elem N) or (resn GLN and elem N)
  etc.

Then you could colour the "donor" selection as you like.

> Does Pymol computes a ligand-protein interface (for example just the contact
> area between the ligand and the protein)? is it possible to see just this
> surface area according to the previous question schema ?

If you have the ligand and protein in separate objects, let's call them
ligand and protein, you can do this:

  show surf, ligand within 3. of protein
  show surf, protein within 3. of ligand

where it will show the surface only for atoms within 3 Angstroms of the
other molecule.  You could also include the "byres" keyword which might
remove some holes in the surface if desired:

  show surf, byres ligand within 3. of protein

If the structure file you read in contains both, then you can create
separate objects from the single initial object:
 
  create protein, initial and chain A
  create ligand, initial and chain B

where I'm assuming that the protein has the "A" chain identifier and the
ligand has the "B" chain identifier and the initial object was called
"initial".

> Does pymol read grid (Goodford's grids) ? in case not, how can I convert
> GRID maps into something pymol can read ?

It appears that you can convert Goodfords grid format to other map
formats (e.g. Brix and CCP4) using the Bsoft program package:

http://www.niams.nih.gov/rcn/labbranch/lsbr/software/bsoft/bsoft.html

The software contains the code for reading and writing GRID files, so
perhaps that could be incorporated into PyMOL.  (I couldn't find any
license file, though I suppose the author could be contacted directly.)

Hope this helps.

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.                         <rl...@po...>
Senior Research Associate                            phone: 613-533-6821
Dept. of Biochemistry, Queen's University,             fax: 613-533-2497
Kingston, ON K7L 3N6  Canada       http://adelie.biochem.queensu.ca/~rlc
    PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2

Hi all,

Is there a way to display the header record from a pdb file after reading it in t=
o PyMOL? Or is that lost?
Preferentially I would like to be able to keep the whole header whilst working an=
d be able to write it out together with the coordinates, perhaps with an extra re=
mark saying something like "PyMOL was=20=
here!"


If it is difficult to implement, at a minimum I would like to see in the PyMOL-lo=
g the HEADER and TITLE cards, after reading a pdb-file, (to be I sure typed in th=
e correct pdb-code in that nice=20=
pdb-loader plug-in, for example=2E=2E=2E)

Just a thought=2E=2E=2E



Bj=F6rn Kauppi

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This was a very helpful answer.  If anyone would like to see equivalent c 
code, I'd be happy to post it.


--------------------------------------------
From Chris:


hi Josh-

I'm no programmer but I used this to pipe some output to pymol from perl:

$pid=open(PYMOL,"| $pymol_path -qpxif 0");

where $pymol_path was the path to the executable, this opens pymol in a 
viewer only mode.
one of those options allows pymol to listen to STDIN for input.

also perl needs:

PYMOL->autoflush(1);


HTH
Chris

_________________________________________________________________
Don’t just search. Find. Check out the new MSN Search! 
http://search.msn.click-url.com/go/onm00200636ave/direct/01/

PyMOL comes with an XML-RPC server .. I don't know anything about it, but
I found this post on the MMTK list:

http://starship.python.net/pipermail/mmtk/2002/000435.html

-michael

--
This isn't a democracy;|                        _  |Michael Lerner
 it's a cheer-ocracy.  | ASCII ribbon campaign ( ) |   Michigan
-Torrence,  Bring It On|  - against HTML email  X  |  Biophysics
                       |                       / \ | mlerner@umich

On Thu, 26 Aug 2004, Joshua Tasman wrote:

>
> Has anyone had sucess running pymol "remotely", like from another program on
> the same system?
>
> I'd love to be able to dynamically display output of my C++ program through
> pymol.  Embedding the entire pymol interpreter in my program seems like an
> unwieldy solution.  I've tried starting pymol from my C++ code, with my
> program feeding into pymol via a standard UNIX pipe, but as pymol doesn't
> seem to use STDIN/STDOUT, this doesn't work.
>
> Thanks for any and all help,
>
> Josh
>
> (I'm using i86 Linux/Fedora core 1)
>
> _________________________________________________________________
> On the road to retirement? Check out MSN Life Events for advice on how to
> get there! http://lifeevents.msn.com/category.aspx?cid=Retirement
>
>
>
> -------------------------------------------------------
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>
>
>

At 03:11 AM 24/08/2004, Robert Lucas wrote:
>I have to admit though, once you raytrace the labels become almost unreadable
>and I think I will end up using them only to help me to position the final 
>labels
>in a picture editing program...

This has also been my conclusion.  If have settled on the following:

In pymol, make an additional set of ray traced stereo pictures, with the 
following additional commands:

set label_color, black
set label_font_id, 4
label name cb, ("...."+resi)    #shifts label away from under atom, dots 
connect it back to cb, to avoid confusion in if the picture is cluttered#

Then, in the picture editing program, I add text labels, based on the fuzzy 
grey ray traced labels, and then transfer them to the unlabelled ray traced 
pictures.


Anthony





----------------------------------------------------------------------
Anthony Duff
Postdoctoral Fellow
School of Molecular and Microbial Biosciences
Biochemistry Building, G08
University of Sydney, NSW 2006 Australia
Phone. 61-2-9351-3907   Fax. 61-2-9351-4726
----------------------------------------------------------------------

Has anyone had sucess running pymol "remotely", like from another program on 
the same system?

I'd love to be able to dynamically display output of my C++ program through 
pymol.  Embedding the entire pymol interpreter in my program seems like an 
unwieldy solution.  I've tried starting pymol from my C++ code, with my 
program feeding into pymol via a standard UNIX pipe, but as pymol doesn't 
seem to use STDIN/STDOUT, this doesn't work.

Thanks for any and all help,

Josh

(I'm using i86 Linux/Fedora core 1)

_________________________________________________________________
On the road to retirement? Check out MSN Life Events for advice on how to 
get there! http://lifeevents.msn.com/category.aspx?cid=Retirement

Hi!
I am trying to figure out how to make a movie with several panels,
i.e., one panel showing large protein structure domain movements, the
other on the same screen showing the corresponding detailed structural
changes at the domain interface. It would be nice to interlacing these
two together so one could show the highlight of either while keeping
the other on the screen. I saw the Feature demo movie in Pymol that
uses "wizard demo, reps" but have no clue how to create them. There are
also other demo files that I can't seem to open and see what's in them.
Any clues?

Xiao


		
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> I am having a problem with pymol on a Macintosh OS X
> system.  When I start the program, the viewer window
> comes up but I cannot see the external GUI....
>
> Do I need to re-install the program ?

Hi Rinku,

Which version of PyMOL are you using? If you are using the hybrid X11=20
version, you will first need to launch X11 in order to see the external=20=

GUI.

-Luca

  --------------------------------------------------------
  Luca Jovine, Ph.D.
  Brookdale Department of Molecular, Cell & Developmental Biology
  Mount Sinai School of Medicine
  Annenberg Building, Room 25-18
  One Gustave L. Levy Place, New York, NY 10029-6574, USA
  Voice: +1.212.241-8620=A0 FAX: +1.509.356-2832
  E-Mail: luc...@ma... - luc...@ms...
  W3: http://www.mssm.edu/students/jovinl02
  --------------------------------------------------------

Hi Everybody

I am having a problem with pymol on a Macintosh OS X
system.  When I start the program, the viewer window
comes up but I cannot see the external GUI....

Do I need to re-install the program ?

Thanks in Advance



		
_______________________________
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Win 1 of 4,000 free domain names from Yahoo! Enter now.
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Hi,
  I've tried the same thing on an ATI FireGL X1, but haven't had any
luck so far.  I've never gotten it to work yet.  I recommend sending
bug reports to ATI, I've done so but haven't heard back yet.  The more
the merrier. :)

  John Stone
  vm...@ks...

On Wed, Aug 25, 2004 at 11:44:24AM +0300, Dr. Daniel James White PhD wrot=
e:
> Hi
>=20
> has anyone had any luck getting quad buffered stereo with the new ATI=20
> linux drivers, fglrx 3.11
>=20
> I wondered if any one has a working XFree86 config file?
>=20
> my setup is
> ATI fglrx 3.11 drivers for Radeon 8500 LE  with linux 2.6 kernel=20
> (fedora core 2),
> trying to get quad buffered stereo on sony G520 monitor , stereo=20
> graphics enabler cable and e2 emitter box.
>=20
> or am I flogging a dead horse....
>=20
> cheers
>=20
> Dan
>=20
> Dr. Daniel James White BSc. (Hons.) PhD
> Cell Biology
> Department of biological and environmental science
> PO Box  35
> University of Jyv=E4skyl=E4
> Jyv=E4skyl=E4 FIN 40014
> Finland
> +358 14 260 4183 (work)
> +358 468102840 (new mobile)
> NEW PHONE NUMBER!!!
>=20
> http://www.chalkie.org.uk
> da...@ch...
> wh...@cc...

--=20
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: jo...@ks...                 Phone: 217-244-3349             =
=20
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078

Hi,
We have a cluster that I would like to use for making images and have
PBS running on there. Can you please share details about how you have
set it up?
Do you have pymol on all nodes? Is it parallelized or each frame (of the
movie) is rendered on individual nodes?

Thanks for any guidance.

Balaji

>=20
>    1. Re: Pymol and batch-queue jobs (Marc Saric)
>=20
> --__--__--
>=20
> Message: 1
> Date: Tue, 24 Aug 2004 09:02:14 +0200
> From: Marc Saric <mar...@gm...>
> To: Jason Thomas Maynes <ja...@bi...>,
>  pym...@li...
> Subject: Re: [PyMOL] Pymol and batch-queue jobs
>=20
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>=20
> Hi Jason,
>=20
> I have reposted your reply to the list, hope you don't mind.
>=20
> Jason Thomas Maynes wrote:
>=20
> | Hello:
> |
> | I run movie rendering through PBS but it's nothing fancy.
> | Essentially I have a perl script that takes a pymol movie script as
> | an argument and then sends customized (ie. render frames 40-50 etc)
> | pymol scripts as jobs to the queue.  Since pymol can't take a
command
> | line argument for what frames to render, I couldn't see a away
around
> | having customized scripts for each job.
>=20
> So an applet, which modifies a render-script on the fly (probably as a
> plugin ("remote-rendering" or something) from within Python might be
> usefull??
>=20
> I guess, this would be the way people do it -either interactively
> defining a script (probably with manual splitting/parameter-setting
for
> the job, or automatically if possible), which gets sent to a
> batch-queueing-system from a Tk-GUI or offline (save script for later
> execution).
>=20
>=20

Hi

has anyone had any luck getting quad buffered stereo with the new ATI=20
linux drivers, fglrx 3.11

I wondered if any one has a working XFree86 config file?

my setup is
ATI fglrx 3.11 drivers for Radeon 8500 LE  with linux 2.6 kernel=20
(fedora core 2),
trying to get quad buffered stereo on sony G520 monitor , stereo=20
graphics enabler cable and e2 emitter box.

or am I flogging a dead horse....

cheers

Dan

Dr. Daniel James White BSc. (Hons.) PhD
Cell Biology
Department of biological and environmental science
PO Box  35
University of Jyv=E4skyl=E4
Jyv=E4skyl=E4 FIN 40014
Finland
+358 14 260 4183 (work)
+358 468102840 (new mobile)
NEW PHONE NUMBER!!!

http://www.chalkie.org.uk
da...@ch...
wh...@cc...=

Hi List!	

When i try to set

Action > Preset > ligand_sites > transparent(better) for any protein, I 
get the following error:

Traceback (most recent call last):
   File "/soft/pymol/modules/pymol/parser.py", line 255, in parse
     exec(com2[nest]+"\n",pymol_names,pymol_names)
   File "<string>", line 1, in ?
AttributeError: 'module' object has no attribute 'ligand_sites_trans_hq'

What is wrong? How to fix it? Anybody else who faced this?

-- 
:-)
Ramesh K. Sistla

http://manmeram.blogspot.com

The Prayer of India:
--------------------
lOkAh samastAh suKhinO bhavantu -- Let the entire world be in peace!

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hi Jason,

I have reposted your reply to the list, hope you don't mind.

Jason Thomas Maynes wrote:

| Hello:
|
| I run movie rendering through PBS but it's nothing fancy.
| Essentially I have a perl script that takes a pymol movie script as
| an argument and then sends customized (ie. render frames 40-50 etc)
| pymol scripts as jobs to the queue.  Since pymol can't take a command
| line argument for what frames to render, I couldn't see a away around
| having customized scripts for each job.

So an applet, which modifies a render-script on the fly (probably as a
plugin ("remote-rendering" or something) from within Python might be
usefull??

I guess, this would be the way people do it -either interactively
defining a script (probably with manual splitting/parameter-setting for
the job, or automatically if possible), which gets sent to a
batch-queueing-system from a Tk-GUI or offline (save script for later
execution).


- --
Bye,
Marc Saric  http://www.marcsaric.de
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=SeXf
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Dear all,

My name is Marcelo and I am a basic-level pymol user. I work with docking
programs and I am trying to make pymol our default program for analysing
docking results...this brings me to some questions:

Is it possible to colour protein surface according to Hydrogen
donor/acceptor properties in pymol ?

Does Pymol computes a ligand-protein interface (for example just the contact
area between the ligand and the protein)? is it possible to see just this
surface area according to the previous question schema ?

Does pymol read grid (Goodford's grids) ? in case not, how can I convert
GRID maps into something pymol can read ?

Thanks a lot

Marcelo

What I did so that I could use the labels command was read the coordinates
in twice. One copy was used for display, the second copy had no atoms/representations
displays, but instead I attatched labels to the atoms on the second copy and
then moved these atoms around (and thusly the labels) till the label were
visible and well oriented.

I have to admit though, once you raytrace the labels become almost unreadable
and I think I will end up using them only to help me to position the final labels
in a picture editing program...

Robert

PS: Here is an example of what I mean:

#read in PDB file with dummy name to move around atom-labels
set label_color,black
load a.pdb,bbbb
label (/bbbb//A/GLN`112/CA) ,"  %s-%s" % (resn,resi)
translate [-1,0,0],/bbbb//A/GLN`112/CA


Ingo P. Korndoerfer:
>
>hello everybody,
>
>shouldn't it be possible to extract the proper rotation for the cgo
>labels
>from the view matrix ?
>
>i have been trying arount a few things, but was not so succesful so far.
>
>my idea was, to
>
>- extract the coordinates of the atom i want from the pdb file. either
>from within pymol or in an external python script.
>- put a label at those positions
>- move the label to the origin.
>- apply the inverse of the rotational part of the view matrix
>- move the label back to were it came from
>- and then adjust the wee little offsets for better image clarity
>manually (try and error, as in molscript).
>
>or is that not possible ?
>
>from what i have seen, i can not apply a matrix directly to the cgo
>objects,
>but would have to convert the matrix to three succesive rotations around
>x, y and z.
>
>also, moving the label to the origin, rotating and moving it back
>afterwards
>did not have quite the effect i was anticipating. i.e., it looked the
>same, as rotating in place.
>in particular, the label got moved a significant way off ...
>
>would anybody have any insights he would like to share ...
>
>putting in the labess in illustrator or gimp afterwards is way too
>cumbersome ...
>
>1000 thanks for your help
>
>ingo


_______________________________________________________________
Robert Lucas                      rl...@al...
Department of Biochemistry        Phone: (206) 616-4510
HHMI & Univ. of Washington        Fax:   (206) 685-7002
Health Science Bldg., Room K-428  Box 357742, Seattle, WA 98195
_______________________________________________________________