RE: [PyMOL] nmr ensemble alignment

2004-01-26 Thread Warren L. DeLano
Doug,

As far as I know there isn't any resource online, so I'll try to
answer your questions here:

PyMOL does not automatically align structures.

intra_fit is presumably the command you're looking for to do this, since
you're placing models are in one object.

intra_fit name ca, 1

would for example align all of the models to the first model using
alpha-carbon coordinates.

intra_fit resi 10-15, 1

would align all models to the coordinates of atoms in residues 10-15.

As far as RMS statistics go, PyMOL may be the best tool for this yet,
since it doesn't current have the ability to generate statistics for the
ensemble.

What statistics in particular would you like it to provide?  

Also note that if you have you ensemble in a multiple-model pdb file
(with MODEL and ENDMDL records), you can just load it in one command

load ens.pdb

Cheers,
Warren


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

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Douglas Kojetin
 Sent: Monday, January 26, 2004 11:22 AM
 To: pymol
 Subject: [PyMOL] nmr ensemble alignment
 
 Hi All-
 
 Will reading in a structural ensemble 
 
 load pdb01.pdb, ens
 load pdb02.pdb, ens
 ...
 
 ... automagically align the structures?  If not, do I need to run
 another command, such as ' intra_fit (name ca) ' ?  Or should I use
 normal 'fit'?
 
 Also, what is the best method for determining the RMS of the ensemble?
 There are a few commands in the reference manual (rms, rms_cur,
 intra_rms, intra_rms_cur), and I'm confused as to which is best for
 structural ensembles.
 
 Or, to save typing, is there a current web resource for using PyMOL
 with NMR models (with hints, scripts, etc.)?  One thing I /miss/ from
 MOLMOL is the 'sausage' display -- has anyone implemented this in
PyMOL
 yet?
 
 Thanks,
 Doug
 
 
 
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RE: [PyMOL] How to send pymol command to pymol by python interpreter

2004-01-22 Thread Warren L. DeLano
Takefumi,

You only need to worry about this if you're using an external Python
interpreter with a modular build of PyMOL.  For example, after
installing a late-model linux PyMOL RPM, you run

python script.py

Where script.py contains the following sequence:

import pymol
pymol.finish_launching()

which is needed to insure that PyMOL's API in the parallel thread is
defined ready to receive messages.

The problem is that PyMOL can't launch until import pymol completes
and returns and __main__.pymol is defined.  However, that means that the
next command in your script will need to be executed before PYMOL has
had a chance to initialize itself.  So the current approach is to launch
the PyMOL thread, and then call a function which blocks until PyMOL is
all ready to go...

Cheers,
Warren

[PS If there's anyone out there with a more elegant alternative for
launching the PyMOL thread from a standalone Python script, I'd sure
like to hear it : )].

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

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Takefumi Sora
 Sent: Wednesday, January 21, 2004 10:57 PM
 To: pymol-users@lists.sourceforge.net
 Subject: RE: [PyMOL] How to send pymol command to pymol by python
 interpreter
 
 
 Hi.
 
 I appreciate your answer, Warren.
 Thank you.
 
 Please let me ask one more question.
 
 You said I need two lines first:
 import pymol
 pymol.finish_launching()
 
 As long as I use,I can't the role of
 pymol.finish_launching()
 if I don't call this, what troubles will happen ?
 
 Takefumi SORA
 
 
 
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RE: [PyMOL] Ray Tracing Crash

2004-01-21 Thread Warren L. DeLano
Morri,

The RH9 Patch is described and published on: 

https://rhn.redhat.com/errata/RHBA-2003-136.html

I would not expect Debian to suffer from the same crash.  If it does,
then we may be dealing with a genuine bug in PyMOL (assuming that you're
not simply running out of RAM).

With respect to Debian, in order to debug the problem, you might want to
send me a PyMOL session file which crashes on your system when the next
command issued is ray.  

Cheers,
Warren

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

 -Original Message-
 From: Morri Feldman [mailto:morrifeld...@yahoo.com]
 Sent: Tuesday, January 20, 2004 10:36 PM
 To: Warren L. DeLano; 'Matt Franklin'; 'Morri Feldman'
 Cc: 'pymol-users'
 Subject: RE: [PyMOL] Ray Tracing Crash
 
 Warren and Matt,
 
 Thanks so much for your help.  I must be using the
 stock glibc because set max_threads, 1 allows me to
 ray trace without crashing.  I will tell my system
 administrator to patch glibc.  Do you know where I
 should look for the patch?
 
 My debian/testing system at home also has trouble ray
 tracing especially sticks.  When it fails I get a
 segmentation fault.  Is my problem at home also due to
 an unpatched glibc?
 
 The error message is:
 /usr/bin/pymol: line 7: 32460 Segmentation fault
 python
 /usr/lib/python2.3/site-packages/pymol/__init__.py $*
 
 Thanks for creating such a great program,
 Morri
 
 --- Warren L. DeLano war...@delanoscientific.com
 wrote:
  Morri,
 
  (First, thanks Matt for the great diagnostic
  advice!)
 
  This sounds to me like a potential threading
  deadlock, possible
  due to the broken threading in RedHat 9.  Are you
  using the stock
  version or have you patched glibc?
 
  If you haven't patched your RedHat 9, then one way
  to be sure
  this is the problem is to set max_threads, 1
  before issuing the ray
  command.  If PyMOL doesn't hang, then you've found
  the culprit.
 
  If have already patched your RH9, then let's do
  some more work
  to determine what's going on...
 
  Cheers,
  Warren
 
  --
  mailto:war...@delanoscientific.com
  Warren L. DeLano, Ph.D.
  Principal Scientist
  DeLano Scientific LLC
  Voice (650)-346-1154
  Fax   (650)-593-4020
 
   -Original Message-
   From: pymol-users-ad...@lists.sourceforge.net
  [mailto:pymol-users-
   ad...@lists.sourceforge.net] On Behalf Of Matt
  Franklin
   Sent: Tuesday, January 20, 2004 6:25 PM
   To: Morri Feldman
   Cc: pymol-users
   Subject: Re: [PyMOL] Ray Tracing Crash
  
   Morri Feldman wrote:
I am running pymol .93.  When I try to ray trace
  a scene, the gui
  shows
   a
white status bar that moves halfway across the
  screen and then
  freezes.
After this the GUI is frozen and must be killed.
   No error messages
  are
shown.  The computer is running RedHat 9 and has
  4 processors.  Has
anyone else experienced this problem?  Do you
  have any solutions?
   
This message may double post because I
  accidentally tried to post it
   from
my other email account.  Sorry
   
Thanks, Morri
   
Morri Feldman
   
  
   Hi Morri -
  
   The progress bar for raytracing doesn't move
  linearly - the first half
   of the bar is covered fairly quickly, then more
  slowly, then very
   slowly, then the last fifth is usually covered in
  one jump.  Are you
   sure you just aren't being impatient?  Try
  raytracing a very simple
   scene, like a single amino acid in spheres mode,
  to see if it hangs
   then.  Also try raytracing parts of your scene in
  case some funny bit
  of
   your molecule is causing this problem.  Finally,
  try reducing the
   complexity of your surfaces and/or spheres: set
  surface_quality, -1
  (0
   is the default).
  
   Feel free to contact me directly - I'm local!
  (Although Warren will
  be
   more helpful...)
  
   - Matt
  
  
   --
   Matthew FranklinPhone:(650)225-4596
   Postdoctoral Researcher   Fax:(650)225-3734
   Genentech, Inc.
   1 DNA Way, South San Francisco, CA 94080
  
  
  
  
 
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RE: [PyMOL] Ray Tracing Crash

2004-01-20 Thread Warren L. DeLano
Morri,

(First, thanks Matt for the great diagnostic advice!)

This sounds to me like a potential threading deadlock, possible
due to the broken threading in RedHat 9.  Are you using the stock
version or have you patched glibc?

If you haven't patched your RedHat 9, then one way to be sure
this is the problem is to set max_threads, 1 before issuing the ray
command.  If PyMOL doesn't hang, then you've found the culprit.

If have already patched your RH9, then let's do some more work
to determine what's going on... 

Cheers,
Warren

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

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Matt Franklin
 Sent: Tuesday, January 20, 2004 6:25 PM
 To: Morri Feldman
 Cc: pymol-users
 Subject: Re: [PyMOL] Ray Tracing Crash
 
 Morri Feldman wrote:
  I am running pymol .93.  When I try to ray trace a scene, the gui
shows
 a
  white status bar that moves halfway across the screen and then
freezes.
  After this the GUI is frozen and must be killed.  No error messages
are
  shown.  The computer is running RedHat 9 and has 4 processors.  Has
  anyone else experienced this problem?  Do you have any solutions?
 
  This message may double post because I accidentally tried to post it
 from
  my other email account.  Sorry
 
  Thanks, Morri
 
  Morri Feldman
 
 
 Hi Morri -
 
 The progress bar for raytracing doesn't move linearly - the first half
 of the bar is covered fairly quickly, then more slowly, then very
 slowly, then the last fifth is usually covered in one jump.  Are you
 sure you just aren't being impatient?  Try raytracing a very simple
 scene, like a single amino acid in spheres mode, to see if it hangs
 then.  Also try raytracing parts of your scene in case some funny bit
of
 your molecule is causing this problem.  Finally, try reducing the
 complexity of your surfaces and/or spheres: set surface_quality, -1
(0
 is the default).
 
 Feel free to contact me directly - I'm local!  (Although Warren will
be
 more helpful...)
 
 - Matt
 
 
 --
 Matthew FranklinPhone:(650)225-4596
 Postdoctoral Researcher   Fax:(650)225-3734
 Genentech, Inc.
 1 DNA Way, South San Francisco, CA 94080
 
 
 
 ---
 The SF.Net email is sponsored by EclipseCon 2004
 Premiere Conference on Open Tools Development and Integration
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RE: [PyMOL] homologous alignments?

2004-01-19 Thread Warren L. DeLano
Camille,

If I understand your question, you're looking for the setting
which creates a discrete color transition at the edges of helices and
strands, instead of blending.  It is:

set cartoon_discrete_colors, on

For example

color grey, name ca
color yellow, ss s and name ca
color red, ss h and name ca
set cartoon_discrete_colors, on

Cheers,
Warren

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

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- 
 ad...@lists.sourceforge.net] On Behalf Of cami...@mrc-lmb.cam.ac.uk
 Sent: Monday, January 19, 2004 7:37 AM
 To: Warren L. DeLano
 Cc: 'Michael Bovee'; pymol-users@lists.sourceforge.net
 Subject: Re: [PyMOL] homologous alignments?
 
 Hello,
I am unable to read the archive at the moment so can anyone
tell
 me the command that allows colouring of the edge of helices and
strands
 (usually grey). I think this was posted recently but I don't have it
in
 any of my saved scripts.
 
 Many thanks,
   Camille
 
 Dr Camille Shammas
 Medical Research Council Laboratory of Molecular Biology Hills Road, 
 Cambridge CB2 2QH, UK.
 Tel: +44 (0)1223 402407
 Mobile: 07812035842
 E-mail: cami...@mrc-lmb.cam.ac.uk
 
 
 
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RE: [PyMOL] working directory

2004-01-19 Thread Warren L. DeLano
Lesley,

If you always want PyMOL to start in a different directory, you
can create a .pymolrc file in you home directory with a command like

cd /users/lesley/scripts

Which will be executed every time you start PyMOL.

Cheers,
Warren

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

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Lesley Debono
 Sent: Sunday, January 18, 2004 11:56 PM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] working directory
 
 i have pymol installed on an OSX machine. When I begin pymol i am in
 the root (\) directory. My scripts are in a different directory. Is
 there a way I can begin in another directory when starting Pymol?
 
 cheers
 Lesley
 
 
 
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RE: [PyMOL] mouse

2004-01-16 Thread Warren L. DeLano
Thierry,

This behavior could be the symptom of either malfunctioning OpenGL, or a
screen with two few colors to support color-encoded picking (which is
what PyMOL uses behind the scenes).

Please confirm that your display is running in 24 or 32 bit color.  If
that is the case and picking still fails, then please try saving a png
file of what you see on the screen (png filename.png).  If that PNG
file exhibits any distortion or artifacts, then that's the cause of the
problems.  Otherwise, PyMOL may have a bug...

Cheers,
Warren


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

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Thierry Granier
 Sent: Friday, January 16, 2004 12:52 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] mouse
 
 Good morning,
 
 I am trying to use pymol on a PC linux RedHat 9.0 using
 the software summit 2.2 of Xig, and I run into the following
 problem:
 after loading a molecule, when I try to click on an atom, for
selection,
 using
 CTRL shif lb or CTRL shift lb, I get the message
 no atom found nearby
 
 I have tried all the mouse settings from the gui with no success.
 
 Any help will be appreciated,
 thank you
 
 Thierry Granier.
 
 
 
 
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RE: [PyMOL] Restrict surface transparency to limited region

2004-01-14 Thread Warren L. DeLano
Roger,

This isn’t possible right now.  The only way to do it is to
create two objects, surfacing different atoms in each object, and then
enabling transparency in just one of the two objects.  

Cheers,
Warren


--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax   (650)-593-4020 
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Roger Dodd
Sent: Wednesday, January 14, 2004 4:49 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Restrict surface transparency to limited region

Dear PyMOL users/devs,
 
I am trying to produce a figure with a molecular surface and would like
to make this surface transparent only covering certain residues. I have
tried creating a separate surface for these residues and the rest of the
protein and setting transparency for the object covering only those
residues, but this gives a very discontinuous looking surface
representation. Is it possible to just enable transparency on a limited
region of a surface?
 
Thanks
 
Roger
 
--
Roger Dodd
CIMR
University of Cambridge
Wellcome Trust / MRC Building
Addenbrooke's Hospital
Hills Road
Cambridge
CB2 2XY




RE: [PyMOL] build instructions

2004-01-13 Thread Warren L. DeLano
Steve,

Although static building isn't supported by us, and although we
make no guarantees that the static launch process won't change
drastically without warning and at any time, you may wish to consult
setup/Rules.linux-semistat-py22 for an example.  

The trick with static builds is that PyMOL needs to do a bunch
of magic to get the environment right before the Python interpreter gets
going and Tkinter starts up.  Also note that you need to provide static
builds of all of the external dependencies in order to generate a truly
portable static build.
 
Cheers,
Warren

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

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Steven F. Killen
 Sent: Tuesday, January 13, 2004 12:37 PM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] build instructions
 
 Greetings,
 
 I'm trying to build pymol statically (instead of as a Python module)
and
 the documentation doesn't seem to have the options listed for the
 variables in the Makefile.  Is there somewhere I may not be looking?
 
 --
 Steve Killen skil...@umbc.edu
 
 
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[PyMOL] DeLano Scientific Closed Until Jan 7, 2004.

2003-12-20 Thread Warren L. DeLano
PyMOL Users,

This is the final reminder that I am now off-line and away from DeLano
Scientific (which will be closed) until January 7th.

Everyone please have a wonderful holiday and a Happy New Year!

Cheers,
Warren

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





RE: [PyMOL] Question

2003-12-19 Thread Warren L. DeLano
Avram,

set cartoon_highlight_color, red

Cheers,
Warren



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

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of slo...@mail.med.upenn.edu
 Sent: Friday, December 19, 2003 11:38 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Question
 
 Hi,
 
 does anyone know how to color the inside of helices a different color
 than the outsides?
 
 thanks
 
 Avram
 --
 Avram M. Slovic
 Biochemistry and Molecular Biophysics
 University of Pennsylvania
 420 Curie Blvd.
 1010 Stellar Chance Bldg.
 Philadelphia, PA 19104
 
 L:215-898-3496
 
 
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RE: [PyMOL] Display of electrostatic potential surfaces

2003-12-18 Thread Warren L. DeLano
Roger,
 
The problem with computing electrostatic maps in PyMOL
currently is that the Coulomb equation assumes a uniform dielectric and
thus doesn't give you correct potentials for macromolecules.  It is much
better to use an external tool such as Grasp, MEAD, APBS, or Delphi,
which can apply a different dielectric constant to the inside of the
protein than to the surrounding solvent.
 
Yes, PyMOL can compute a Coulombic map using the approach
you've outlined if partial charges have been assigned - but there isn't
a good way to do that in PyMOL just yet.
 
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax   (650)-593-4020 
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Roger Dodd
Sent: Thursday, December 18, 2003 3:53 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Display of electrostatic potential surfaces
 
Dear PyMOL users,
 
I would like to generate a figure of my protein where the surface
electrostatic potential is displayed. PyMOL now comes with a demo
function for display of such a surface. However, when I apply the
commands used in this demo, i.e.
 
cmd.set(coulomb_dielectric,80.0)
 cmd.map_new(e_pot,coulomb,1.0,pept,5)
 cmd.ramp_new(e_lvl,e_pot,[-3.6,-1.6,0.4])
 cmd.set(surface_color,e_lvl,pept)
 cmd.refresh()
 
to the model from my pdb file, I get a uniformly blue surface. I believe
this must be due to the lack of assignment of partial/formal charges to
the atoms in the pdb file. So, my questions are:
 
1. Is it possible to automatically assign the correct charges to atoms
within PyMOL
2. If not, is there a program that will do this and if so can the output
from this program be understood by PyMOL in some way.
 
Thanks for your help
 
Roger
 
--
Roger Dodd
CIMR
Addenbrooke's Hospital
Cambridge


[PyMOL] RE: 3-button mice

2003-12-18 Thread Warren L. DeLano
Chris,
 
I hereby nominate the Targus PAUM01U as the official 3-button mouse for
PyMOL users on the go.
 
http://www.targus.com/us/product_details.asp?sku=PAUM01U
 
They might be too small for some, but they work great for me, at home
and on the road!
 
(plus, they color-coordinate with Ti PowerBooks)
 
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax   (650)-593-4020 
-Original Message-
 
Sent: Thursday, December 18, 2003 5:45 AM
To: war...@delanoscientific.com
Subject: pymol
 
Hi,
I plan to update the website (http://www.macinchem.fsnet.co.uk) over the
Christmas Break and one question I'm often asked is which 3-button mouse
should I use for PYMOL under MacOSX?
Any suggestions?
Thanks
Chris


RE: [PyMOL] unsetting cartoon_colors

2003-12-18 Thread Warren L. DeLano
David,

For settings such as cartoon_color, surface_color, mesh_color,
the default value is -1.

set cartoon_color, -1

or

set cartoon_color, -1, object-name

will restore the color.

Thanks for pointing out that:

set cartoon_color, default

doesn't work!

Cheers,
Warren


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Warren L. DeLano, Ph.D.
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Voice (650)-346-1154
Fax   (650)-593-4020 
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of David A.
Horita
Sent: Thursday, December 18, 2003 10:50 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] unsetting cartoon_colors

Hi all,
I have a collection of molecules and want to color a particular helix
(in cartoon mode) a specific color different from other helices. 
Unfortunately, I had previously set cartoon_color from default to
another color, so now specifying a color for that helix (or even color
red, ss h) has no impact.  (it does change the color of the Calpha, but
not the cartoon itself).  
So, the question is, how do I unset the cartoon_color variable (without
wiping out my scene)?  The variable setting comes with the .pse file,
set cartoon_color, default gives an error about not knowing what color
default is.
Thanks,
Dave Horita
 
- 
David A. Horita, Ph.D.
Department of Biochemistry
Wake Forest University School of Medicine
Winston-Salem, NC 27157-1016 
Tel: 336 713-4194
Fax: 336 716-7671 
email:  dhor...@wfubmc.edu
web:  http://www.wfubmc.edu/biochem/faculty/Horita/
 




[PyMOL] RE: Stereo on G4 Laptop?

2003-12-15 Thread Warren L. DeLano
Doug,

Yes, I just confirmed that PyMOL on a Mac 17 G4 PowerBook can
drive stereo using the StereoGraphics SVGA display adapter with an
external monitor.  I would expect any G4 PowerBook to be able to do
this.  The command line way to launch in stereo mode is given below.

/Applications/PyMOL.app/Contents/MacOS/PyMOL -BGS

Alternative, you could simply click on the PyMOL Stereo icon in the
Demos folder.

Cheers,
Warren


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

 -Original Message-
 Sent: Monday, December 15, 2003 11:16 AM
 To: war...@delanoscientific.com
 Subject: Stereo on G4 Laptop?
 
 Dear Warren,
 
 I am a crystallographer from the university of oregon.  I am
 considering purchasing a G4 laptop and was wondering if you had used
 the crystal eyes from Stereographics on a vga monitor plugged into one
 of these laptops.
 
 Thanks,
 Doug






RE: [PyMOL] expand to molecule (by connectivity)

2003-12-15 Thread Warren L. DeLano
Michal,

This capability is not in PyMOL yet as a selection operator, but
if you issue edit on a single atom, then the resulting pkchain
selection will contain that atom and all covalently attached atoms.  

edit 14/ca
color red, pkchain
unpick

Cheers,
Warren

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Voice (650)-346-1154 
Fax   (650)-593-4020

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Michal Bozon
 Sent: Saturday, December 13, 2003 7:25 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] expand to molecule (by connectivity)
 
 Dear pymol experts,
 
 I wonder if there's a simple way how to select a molecule (or expand
the
 selection to molecule) by connectivity.
 I mean the case there if there are more molecules in the object and I
want
 to select one of them and create a new object from it in order to
change
 it's properties.
 'Byres' and similar seleciton operators do not work.
 
 thanks,
 
 Michal Bozon
 
 
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RE: [PyMOL] Trying to plug APBS into PyMOL for electrostatics (not working yet)

2003-12-11 Thread Warren L. DeLano
Michael,

Impressive!  I think you're one of the few people to delve into
PyMOL's source like this.

Obviously I'd be the best person to look at your code, but I'm
crunched right now getting ready for this upcoming trip.  Also, if the
code is GPL-contaminated, then it can't be useful in the main version,
but perhaps we can rewrite this cleanly later on.  I can probably help
you in January.  What you've written sounds right...

One thing I'd suggest for debugging in the meantime is that you
use the isomesh or isosurface routines to explore what data is ending up
in the Map, before trying to use the color ramps.  There may also be
some code in the chempy brick stuff which could serve as an example for
populating the list.

Cheers,
Warren

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Voice (650)-346-1154 
Fax   (650)-593-4020





RE: [PyMOL] assign secondary structure?

2003-12-11 Thread Warren L. DeLano
Michael,

Unfortunately PYMOL/dss doesn't generate quite enough
information to recreate PDB SHEET and HELIX records.  PyMOL (like other
programs) simplifies the secondary structure concept down to a
per-residue property.  There is no such thing as a sheet or helix in
PYMOL, but merely sets of proximal residues with a secondary structure
property (ss) of 'H' or 'S'.  

load object-name.pdb
hide
show cartoon
dss object-name

Should be sufficient to get you a secondary structure representation for
any protein.

States represent multiple conformations -- you shouldn't need to worry
about them

Cheers,
Warren


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Voice (650)-346-1154 
Fax   (650)-593-4020

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Michael Bovee
 Sent: Thursday, December 11, 2003 1:38 PM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] assign secondary structure?
 
 Hi,
 I have a 'raw' pdb file of atom coordinates only, and I'm hoping to
use
 the dss command in pymol to get helix and strand designations that I
 can paste back into the header space of the pdb so that I can model
 fancy helices and strands and so forth to get a nice picture in pymol.
 Then I can superpose features with homologous proteins for which this
 header info is available. I just didnt want to modify or create this
 header info 'by hand' if I didn't have to...
 
 But, I can't get dss to work in pymol (even the refman warns that this
 algorithm has not been rigorously validated). The refman says USAGE is
 dss selection, state
 Does this mean I need to first make a selection that encompasses some
 part (or whole) of the molecule, or should this work on the entire
pdb?
   I don't know what 'states' are so I just opted for '0' which is
 supposed to mean 'all states'.
 
 Thanks,
 --Michael Bovee
 
 
 
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RE: [PyMOL] electron density settings

2003-12-10 Thread Warren L. DeLano
Robert,

If you're using version 0.93 or greater, set mesh_width, value
will adjust the mesh thickness in units of pixels.  Something in the
range of 1.5-2.5 usually works best.

set mesh_width,2.0
ray

If you're using an older version, you'll need to set mesh_radius
instead, which is in angstrom units.

To display the density around a ligand, create a mesh using the carve
option.

load map.ccp4
load protein.pdb
load ligand.pdb
isomesh m1, map, 1.0, ligand, carve=2.1

Cheers,
Warren

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Voice (650)-346-1154 
Fax   (650)-593-4020

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Robert
 Sent: Wednesday, December 10, 2003 2:55 PM
 To: 'Warren L. DeLano'
 Cc: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] electron density settings
 
 Hi there,
 
 1. How can I reduce the density-map line thickness in the ray-traced
 image?
 2. Is there a way to just display the density around a ligand
 
 many thanks
 robert
 
 Robert Schwarzenbacher, PhD
 The Joint Center for Structural Genomics
 phone: 858 822 3637
 
 
 
 
 
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[PyMOL] DeLano Scientific Downtime (Dec. 22-Jan 7)

2003-12-10 Thread Warren L. DeLano
PyMOL Sponsors and Users,

Please be advised that due to vacations, travel, and participation in
the CCP4 study weekend, DeLano Scientific LLC will be officially closed
from December 21st through January 7th.  

Sporadic email communication may be possible before Dec. 24th and after
Jan. 3rd, but essentially all other business functions (phone, fax,
quotes, invoices, receipts, etc.) will remain unavailable until after
the 7th.

During the break, please direct all PyMOL questions to the mailing list
where your peers may be able to assist you.  Also, please be sure to
have yourself a wonderful holiday season and a happy new year!

If there are any budgets out there with end of year money that simply
must be spent, DeLano Scientific would be glad to process your PyMOL
purchases and support subscription renewals prior to the 19th of
December.  

Cheers,
Warren

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Voice (650)-346-1154 
Fax   (650)-593-4020





RE: [PyMOL] Unable to read Gamess-US output

2003-12-06 Thread Warren L. DeLano
Jerome,

Generally speaking, PyMOL doesn’t read any GAMESS formats,
although there is some code in the chempy modules which at one time
could submit and retrieve output from a few simple GAMESS-US
calculations.  My advice would be to find another tool better suited for
Quantum chemistry applications.  But if you still want to use PyMOL,
then you'll need to convert your files into something like .mol or
.pdb...

Cheers,
Warren

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Voice (650)-346-1154 
Fax   (650)-593-4020

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Jerome Levesque
 Sent: Friday, December 05, 2003 8:37 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Unable to read Gamess-US output
 
 Hello,
 
 I am using GAMESS-US (not PC-GAMESS) on Linux to model very small
 molecules. When I try to load a GAMESS .dat file into PyMOL, it does
 not complain at all, but does not show anything either. There isn't
even
 a new object appearing in the right part of the PyMOL visualization
 window.
 
 I find this behaviour somewhat strange, since it seems to be specific
to
 my .dat files and do not even occur when I try to load silly files,
such
 as jpegs for example. Even in such silly cases, a new object will
 appears in the list (but not for my GAMESS .dat files!)
 
 Thanks in advance for any help,
 
 Jérôme Levesque
 
 --
 Jérôme Levesque, Ph.D. student
 
 Femtosecond Research Program
 National Research Council
 100 Sussex drive, room 2044
 Ottawa, ON
 K1A 0R6
 Canada
 
 tel.: 613-998-9468
 fax.: 613-991-3437
 
 
 
 
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[PyMOL] More on A Few Good MacPyMOL OS X Beta Testers

2003-12-02 Thread Warren L. DeLano
 and improve in
synchronization with the cross-platform open-source version.

The beta test remains open through January for those who meet the six
qualifications.  

Cheers,
Warren
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Voice (650)-346-1154 
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RE: [PyMOL] Object orientation matrices

2003-12-02 Thread Warren L. DeLano
Laurence,

Sort of.  Right now PyMOL doesn't fully support translations of
individual objects by independent matrices, but you can translate their
representations by a matrix for animation purposes using translate and
rotate with the object argument.   

However, you can cleanly transform the atoms in an object.  See

print cmd.transform_selection.__doc__

for details on the matrix used for that.

The object matrix system is just about due for an overhaul -- we
need more flexibility than is currently provided...

Cheers,
Warren

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Voice (650)-346-1154 
Fax   (650)-593-4020

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Laurence Pearl
 Sent: Tuesday, December 02, 2003 5:47 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Object orientation matrices
 
 Is there any way of accessing the matrices that define the orientation
 and position of an individual object relative to the world in PyMol in
 the same way that get_view and set_view do for the overall view matrix
?
 


 --
Laurence H. Pearl
 
Section of Structural Biology, Institute of Cancer Research
Chester Beatty Laboratories,  237 Fulham Road, London SW3 6JB, UK
 
Phone +44-207-970 6045 : Secretary +44-207-970 6046
FAX   +44-207-970 6051 : E-Mail laurence.pe...@icr.ac.uk


 --
 Live Simply and do Serious Things ..  - Dorothy Crowfoot Hodgkin


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RE: [PyMOL] cannot 'fit' a particular pdb file

2003-12-02 Thread Warren L. DeLano
Michael,

Try align...

Fit only works when all of the atom identifiers match.  Align
matches atoms through a 1D alignment and then performs some
optimization:

align TtHisRSca, EcHRSadeca
align SaHRSca, EcHRSadeca 

Cheers,
Warren

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Voice (650)-346-1154 
Fax   (650)-593-4020

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Michael Bovee
 Sent: Tuesday, December 02, 2003 11:17 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] cannot 'fit' a particular pdb file
 
 Hi,
 I have loaded 3 pdb files of homologous forms of an enzyme. The 'fit'
 command works for superimposing/aligning two of them, but the third
 file always gives a No Atoms Selected error. Is there something in the
 pdb file I can fix? As a general rule now, I Hide Everything at first
 and then Show Lines as I begin with a new PyMOL session. I can see all
 three molecules, just can't align the third one (EcHRSade) with the
 first two (TtHisRS and SaHRS).
 
 PyMOLfit TtHisRS, SaHRS
   Executive: RMS =4.222 (718 to 718 atoms)
 
 PyMOLfit TtHisRS, EcHRSade
 ExecutiveRMS-Error: No atoms selected.
 PyMOLfit EcHRSade, TtHisRS
 ExecutiveRMS-Error: No atoms selected.
 PyMOLfit EcHRSade, SaHRS
 ExecutiveRMS-Error: No atoms selected.
 
 Thanks,
 --Michael
 
 
 
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[PyMOL] Clarification on A Few Good MacPyMOL OS X Beta Testers

2003-12-02 Thread Warren L. DeLano
 with the cross-platform open-source version.

The beta test remains open through January for those who meet the six
qualifications.  

Cheers,
Warren
--
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Voice (650)-346-1154 
Fax   (650)-593-4020





RE: [PyMOL] Viewing homotetramers with PyMol

2003-12-02 Thread Warren L. DeLano
Rene,

The problem is that each biological unit copy in the PDB is
handled as a separate molecular state (i.e. a movie), which then become
distinct states in PyMOL.  Hit play to see what I mean.

To solve this, the most recent versions of PyMOL can split multi-state
objects into multiple single-state objects automatically:

load 1f41_tetra.pdb
split_states 1f41_tetra
dele 1f41_tetra

With older versions, you'll need to create the new objects manually

load 1f41_tetra.pdb
create 1f41_tetra_1, 1f41_tetra, source_state=1, target_state=1
create 1f41_tetra_2, 1f41_tetra, source_state=2, target_state=1
dele 1f41_tetra 

Cheers,
Warren





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Fax   (650)-593-4020

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of René Wuttke
 Sent: Tuesday, December 02, 2003 1:08 PM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Viewing homotetramers with PyMol
 
 Hi everyone,
 
 I am quite new to PyMol and structural biology as well, since I am
 still a student. I installed PyMol via Fink on my iBook running
Panther
 10.3.1. I want to view the homotetramer of the TTR-protein. I got it
 from the PDB (PDB-id: 1f41). The asymmetric unit is a dimer. But the
 assumed biological molecule is the tetramer. One can download the
 coordinates of this molecule. But when I try to load it in Pymol, only
 the dimer shows up. I am quite sure that this file should contain the
 right coordinates, because the origin of rotation differs between
the
 tetramer file and the dimer file. How can display the other dimer?
This
 is necessary  in particular, because i am supposed to examine the
loops
 which mediates the dimer-dimer-interaction. Do you want me to send the
 coordinates file to the list?
 
 Thanks in advance and please apologize my bad english,
 René Wuttke
 
 
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RE: [PyMOL] residues deviate from protein secondary catoon representation

2003-12-02 Thread Warren L. DeLano
(becoming an FAQ)

For starters, 

set cartoon_smooth_loops, off
set cartoon_flat_sheets, off

If that doesn't meet your needs, then you'll need to split your object
into separate objects to get the desired effect of mixing smoothed and
non-smoothed cartoons.

Thankfully, the next version will provide an easier workaround for
this...

Cheers,
Warren

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Voice (650)-346-1154 
Fax   (650)-593-4020

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Yunfeng Hu
 Sent: Tuesday, December 02, 2003 1:57 PM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] residues deviate from protein secondary catoon
 representation
 
 Dear pymol users,
 
 I am trying to show some residues in sticks while the whole protein is
in
 cartton representation. However I find that some residues do not
attach
 to the cartoon at all. I understand that the secondary cartoon is an
 approximation along the backbone. Is there a way that I can show at
least
 those residues are anchored in the cartoon? Thanks.
 
 Yunfeng
 
 
 
 
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RE: [PyMOL] detecting the existence of a selection

2003-12-01 Thread Warren L. DeLano
Tina,

Use the Python in operator

selection-name in cmd.get_names(selections)

PyMOLprint foo in cmd.get_names(selections)
False
PyMOLselect foo, all
 Selector: selection foo defined with 1631 atoms.
PyMOLprint foo in cmd.get_names(selections)
True

Cheers,
Warren

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Voice (650)-346-1154 
Fax   (650)-593-4020

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Tina Li
 Sent: Monday, December 01, 2003 11:50 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] detecting the existence of a selection
 
 Hello,
 
 I wonder if there is a quick and simple way of detecting whether a
 selection
 exists without triggering any errors. e.g. to check if there are
currently
 any
 atoms picked (and collect the residue IDs if there is any), I do:
 
 cmd.iterate((lb),stored.list.append((resi)))
 
 if no atoms were picked, I would see the alarming error messages:
 
 Selector-Error: Unknown keyword or selection.
 Selector-Error: Malformed selection.
 ( ( lb--
 
 Is it possible to suppress them and still get the result?
 
 Thanks in advance!
 
 Tina
 
 
 
 
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[PyMOL] A Few Good Mac PyMOL OS X Beta Testers

2003-11-29 Thread Warren L. DeLano
Mac Users:

I have something new in the works for OS X/Aqua and need some beta
testers for the next couple of months.

Specifically, I am looking for users who:

1) have experience with full PyMOL (under Fink, X11, or Windows).
2) are current PyMOL sponsors/subscribers.
3) are running OS X 10.2.8 or 10.3.
4) have QuickTime 6.4 installed.
5) would value a Mac-enhanced PyMOL derivative.
6) don't mind closed-source software.

If you meet all of these qualifications, please email me.  If you don't,
then please sit tight for now -- more information will be forthcoming in
January.

Thanks,
Warren

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Voice (650)-346-1154 
Fax   (650)-593-4020






RE: [PyMOL] electron density settings

2003-11-25 Thread Warren L. DeLano
Igor is right.  However, there is a new command in recent versions
 
map_double map-name

that will cut the map spacing in half by interpolating a new map via
trilinear interpolation.  This will generate a map with 2^3 = 8-fold
more grid points (and require 8X more RAM!)

load map1.ccp4
map_double map1
isomesh mesh1, map1, 1.0

will generate a mesh with half the spacing of the original map.

Note that map_double can usually only be used once on a given map before
averaging artifacts appear.

Cheers,
Warren




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Voice (650)-346-1154 
Fax   (650)-593-4020

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Igor Pechersky
 Sent: Tuesday, November 25, 2003 7:23 AM
 To: mwilke
 Cc: pymol-users@lists.sourceforge.net
 Subject: Re: [PyMOL] electron density settings
 
  mwilke mwi...@interchange.ubc.ca:
  Does anyone know how to alter the isomesh settings?  I'm trying to
 prepare
  a figure with pretty electron density and would like to be able to
 decrease
  the gap size of the mesh.  I found the variables that seem to make
sense
  like mesh_quality and min_mesh_spacing, but changing these
variables
  doesn't seem to do anything.  mesh_width and mesh_radius only
 control
  the thickness of the mesh lines.
 
 Mark,
 you are correct, saying that mesh_quality and min_mesh_spacing
have
 nothing with
 isomesh. They are used only for surface maps (RepMesh). For map-based
 mesh, PyMOL uses
 dimension from the density map itself, without smoothing
interpolations.
 So, to
 increase visual toughness of your isomesh, you should just load more
 fine-grained
 density map...
 As a visualization trick, one might try to play with the set of
 isomeshes, based on
 the same density map and slightly differentiated by level, like this:
 
 isomesh mesh1, map1, 1.0
 isomesh mesh2, map1, 1.25
 isomesh mesh3, map1, 1.50
 isomesh mesh4, map1, 1.75
 isomesh mesh5, map1, 2.0
 
 and then color them differently.
 
 
 BTW, even with RepMesh you can't decrease gap size (via
min_mesh_spacing)
 less than
 some hard lower threshold - roughly, it is equivalent to 80 lines
per
 maximal
 dimension of the surrounding box for the underlying object.
 mesh_quality deals rather with the level of icosahedron approximations
for
 spheres...
 
 
 
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RE: [PyMOL] dss ribbon representation

2003-11-14 Thread Warren L. DeLano
There is one other convenient format:  .pkl, that works like PDB, but
is a Pickled copy of the PyMOL Model Class.  The main advantage this has
over .pdb is that it saves and restores extra properties such as
secondary structure code, atom types, van der waals radii, formal and
partial charges, etc.  

load myprot.pdb
dss
show cartoon
alter 100-110/, ss='H'
alter 65-67,ss='L'
save myprot.pkl

... quit program, complete your PhD, take a vacation, and come back...

load myprot.pkl
show cartoon

will work.

.pkl has the additional advantage of being a simple molecular object
useful in straight Python, outside of PyMOL.  All you need to do is have
a copy of PyMOL's chempy module available in your PYTHONPATH

from chempy import io

model = io.pkl.fromFile(myprot.pkl)
for atom in model.atom:
   print atom.name
   
Cheers,
Warren


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

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net 
 [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of 
 Igor Pechersky
 Sent: Friday, November 14, 2003 3:07 AM
 To: andr...@biochem.utah.edu; Andreas Foerster
 Cc: pymol
 Subject: Re: [PyMOL] dss  ribbon representation
 
 
  Andreas Foerster andr...@biochem.utah.edu:
 
  - The dss algorithm is great, a very quick way to assign secondary 
  structure. Is there a way of conserving the information when saving 
  the pdb?
 There are at least 3 ways to store SS assignments from PyMOL. 
 Depends on your needs:
 
 1. Save PyMOL session (*.pse). Atom properties, including 
 ss, will be restorable by 
 PyMOL.
 
 2. Print SS in PHD-like format. So, assuming that unfamous 
 1tii.pdb is loaded
 PyMOLimport pymol
 PyMOLstored.ss = []
 PyMOLiterate 1tii//a//ca, stored.ss.append(string.ljust(ss,1))
 PyMOLprint string.join(stored.ss,)
 
 will print single string like 
 LSSLLLHHHLHHLLLSLL
 LLL
 LSSSHLLHHHLLHHHLSSSLLL
 LLLHHHLLLLL
 HLLHHHLL
 
 3. Wait for Warren to vivify cSetting_save_pdb_ss :)
 
 
  Sometimes it's nice to edit the assignment.
 I haven't understood your question. You might edit dss 
 assignment just by
 PyMOLalter pk1, ss='S'
 
 Is it sufficient? 
 
 -igor
 
 
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[PyMOL] RE: Stereo parameters, again

2003-11-13 Thread Warren L. DeLano
 I still do not understand your stereo parameters: the 
 stereo_angle should 
 define the rotation (around the y-axis) between the pictures 
 for the left and 
 right eye, whereas the stereo_shift should define whether the 
 origin or 
 midpoint of the picture is within the plane of the screen or 
 in front of or 
 behind it. However, changing the settings of these parameters lead to 
 completely unexpected results: setting the stereo_shift to 
 0 and the 
 stereo_angle to 3.0 results in a mono picture with no 
 separation at all, 
 whereas setting the stereo_shift to 3.0 and the 
 stereo_angle to 0 leads 
 also to a mono picture shifted to the back. So, could you 
 please check this 
 and maybe explain it again to me?

After looking back at the code, I realize that these parameters
are perhaps misnamed.  These are not the rotations of the objective, but
rather parameters input into the stereo equations.

stereo_shift is the separation between the two cameras observing the
image, expressed as a % of the distance from the objective.  

stereo_angle is a scaling factor applied to the natural angular
difference which would occur between two eyes at that distance, both
looking at the objective.  

Generally speaking stereo_shift is the main depth control parameter, and
stereo_angle should remain close to 2 in order to generate correct
stereo geometry.  However, adjusting stereo_angle can reduce ghosting
and change the apparent Z location of the objective.

Detting stereo_shift to zero makes you a Cyclops (you're basically
telling PyMOL that your eyes are superimposed).

The defaults are:

PyMOLget stereo_shift,
 get: stereo_shift = 2.0
PyMOLget stereo_angle,
 get: stereo_angle = 2.1

which are tuned to minimize CrystalEyes ghosting in the foreground.

The actual translation(+/-) and rotation(+/-) of the camera at
distance are:

translation = distance * (stereo_shift/100)

rotation = (stereo_angle/2) * (arctan(stereo_shift/100))
(default = +/- 1.2 deg)

If you want a stronger stereo effect, set stereo_shift to 3, 4, or 5
(resulting in rotations of 1.8, 2.4, and 3.0 degrees, respectively).

Cheers,
Warren




RE: [PyMOL] Reference

2003-11-13 Thread Warren L. DeLano
http://pymol.sourceforge.net/faq.html#CITE


--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax   (650)-593-4020 
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Chris
Sent: Tuesday, November 11, 2003 1:29 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Reference


Hi Warren 

Could you tell me how I should reference Pymol in papers etc? I've tried
finding it one the web and i've not seen it

Ta

Chris




RE: [PyMOL] Re:labeling atoms in GUI

2003-11-12 Thread Warren L. DeLano
Eric,

PyMOL will source startup files in your home directory -- just
put your commands in there:

On Mac/Unix:

$HOME/.pymolrc  (for PyMOL commands)
$HOME/.pymolrc.py   (for Python code)

On Windows:

%HOMEPATH%\pymolrc(for PyMOL commands)
%HOMEPATH%\pymorc.py  (for Python code)

To show distances, use the distance wizard:

wizard distance

then ctrl-middle-clock on two atoms in succession.

Cheers,
Warren


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

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net 
 [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Eric Hu
 Sent: Wednesday, November 12, 2003 11:22 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Re:labeling atoms in GUI
 
 
 Warren, I want to be able to use those useful
 definations every time I load pymol. I wonder how to
 edit the general startup script pymol in order to do
 that? By the way, I also want pymol to show distance
 when I click two atoms. Thank you.
 
 Eric
 
 
  Quoting Warren L. DeLano
  war...@delanoscientific.com:
  
   Richard,
   
   It's not GUI, but you could simply bind a function
  key such as F1 to
   that command:
   
   cmd.set_key('F1',lambda :cmd.label((lb),'%s %s
   %s%(name,resn,resi)'))
   
   You might then want to bind 'F2' to something
  which hides all labels.
   
   cmd.set_key('F2',cmd.label)
   
   Cheers,
   Warren
   
   --
   mailto:war...@delanoscientific.com
   Warren L. DeLano, Ph.D.
   Principal Scientist
   DeLano Scientific LLC
   Voice (650)-346-1154 
   Fax   (650)-593-4020
   
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net]
  On Behalf Of
rbax...@uchicago.edu
Sent: Wednesday, October 29, 2003 5:14 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] labeling atoms in GUI


Dear All,

I want to look at my structure in PyMOL and,
  having centered
on something defined by my selection script,
  pick atoms
nearby and see what residues they belong to.
  That is, I want
to pick select an atom with the mouse and have
  its name,
residue name and residue number appear on
  screen, like it does in O.

I figured out that [Ctrl] + Left-Mouse-Button
  selects the
atom as lb, and that the command 'label
  (lb),%s %s %s %
(name,resn,resi)' gives me the label I want. Now
  how could I
get something like that to appear as a menu
  function in the
GUI so I don't have type it in all the time? Can
  it be a
command executed as part of my startup script?

Maybe some function like this already exists,
  otherwise I
think it is a very useful thing.

regards,

Richard Baxter
  
  
 
 
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 http://antispam.yahoo.com/whatsnewfree
 
 
 
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RE: [PyMOL] surface area calculation

2003-11-12 Thread Warren L. DeLano
Joel,
 
Yes, PyMOL does have this capability, but it is immature and not
routinely validated.
 
The basic concepts are:
 
1) get_area selection command will return the effective surface area
of the dots that you would see from show dots, selection.  This is a
discrete approximation -- not an exact calculation.
 
2) you can use the dot_solvent setting to control whether you get
solvent surface area or a molecular surface area.  1=solvent,
0=molecular
 
3) the accuracy of the measurement depends on the density of dots, which
is controlled by the dot_density setting (1-4).
 
4) the solvent radius is controlled by the solvent_radius setting
(default 1.4).
 
For example:
 
PyMOL load $TUT/1hpv.pdb
PyMOL show dots, resn arg
PyMOL get_area resn arg
cmd.get_area: 1147.956 Angstroms^2.
PyMOLset dot_solvent, on
PyMOLget_area resn arg
 cmd.get_area: 673.084 Angstroms^2.
PyMOLset dot_density, 3
PyMOLget_area resn arg
 cmd.get_area: 674.157 Angstroms^2.
PyMOLset dot_density, 4
PyMOLget_area resn arg
 cmd.get_area: 672.056 Angstroms^2.
PyMOLget_area all
 cmd.get_area: 13837.804 Angstroms^2.
 
This code has not been recently validated (though I did check it a
couple years back), so I would suggest that people perform some kind of
independent check on their system before trusting the results.  
 
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax   (650)-593-4020 

-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Harp, Joel
M
Sent: Wednesday, November 12, 2003 2:10 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] surface area calculation




Is it possible to get pymol to calculate surface area for a defined
object?  For instance, can it calculate surface area occupied by
arginines.

Thanks,
Joel

Joel M. Harp
Vanderbilt University 



RE: [PyMOL] surface area calculation

2003-11-12 Thread Warren L. DeLano
Close, but it depends on whether you want the surface area of the
residues alone, or in the context of the molecule.  

load protein.pdb
get_area resn arg 

  will be less than

create arg_object, resn arg
get_area arg_object

This is because the first example will give you only the exposed area of
the arginines in the presence of the other atoms, whereas the second
gives the area of the arginines in isolation.

Cheers,
Warren


--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax   (650)-593-4020 
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Kaushik
Raha
Sent: Wednesday, November 12, 2003 2:50 PM
To: Harp, Joel M
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] surface area calculation


To calculate surface area for a defined object from the PyMOL command
line type:

print cmd.get_area(obj)

where obj is the name of your object.

for arginines:

create ARG, resn ARG
print cmd.get_area(ARG)

Kaushik.

On Wednesday, November 12, 2003, at 05:10 PM, Harp, Joel M wrote:




Is it possible to get pymol to calculate surface area for a defined
object?  For instance, can it calculate surface area occupied by
arginines.

Thanks,
Joel

Joel M. Harp
Vanderbilt University




RE: [PyMOL] DSSP

2003-11-03 Thread Warren L. DeLano
Ben,

Great response! Indeed, the PDB's limited capacity for secondary
structure does indeed represent this as one single helix, not two.

 +/- 15 degrees is pretty difficult to see - so I think that DSSPs 
 +assignment
 in this case, while liberal, is certainly acceptable.

I hardly think it acceptable that one residue with 3-10 PHI/PSI
constitutes a helix when you have so many other telltale characteristics
of a Type II' beta turn, including a Glycine in position i+1 and all
deviations within 22 deg. of ideal turn, as well as four planer CA atoms
(actually five, C-alphas 98-102 are all nearly planer).  Some turns do
look like helices, but not this one -- not even close.

 Great example of where DSSP fails, but perhaps a bit contrived.

I don't think this example is contrived.  One of the many tests
I put PYMOL through regularly is to render the entire PDB over several
hours, so I literally see thousands of structures on a routine basis.
Such objective but bogus assignments are far more common than one
would like to think.  It is a real problem.

 The reason that consistency is of paramount importance in assigning
secondary structure 
 is so that different scientists can talk about the same protein in
context.  
 If everyone uses the same definition of secondary structure - helix
1 is always helix 1. 

Good point, but I disagree.  In acknowledging the subjective and
relative nature of assignments, I think it is more reasonable to ask
scientists to define their terms rather than to perpetuate broken
conventions.  Given how evolution, crystallization, and protein
processing work, even with DSSP, Helix 3 can easily be Helix 2 or 4 in
another structure of the identical or a related protein, so the savings
in confusion is slight.   Also, keep in mind that all numbering is
relative and increasingly problematic as more and more homologous
structures are solved, and explicit conceptual labels are far more
general than numeric ones.  

But finally, do understand that I would provide DSSP as an
option if it were possible to do so, but frankly, it's not.  The paper
does not enable an exact reimplementation, and the owners of DSSP,
instead of making DSSP source code usable and redistributable as an open
standard, have decided to use the software for revenue generation
(presumed modest at best).  It is exatly this kind of short-sighted
restrictiveness that PyMOL was created to combat.  We must end this
dismal pattern of scientists developing research software that is so
drastically and artificially limited by licensing terms that it has
little or no ability to enable future scientific advances.

Computer-dependent scientific fields like structural biology and
computational chemistry will be handicapped until we can all effectively
access and improve upon existing software systems.  That will not happen
until research scientists and academic institutions stop viewing such
software programs as potentially lucrative intellectual properties and
start viewing them as the critical building blocks that will enable
future breakthroughs if and when they become widely shared.   

Imagine... What would happen if all scientists stopped
publishing their discoveries and kept all information within one lab or
institution?  Scientific progress would come to a halt.  That's
basically what has occurred with so much scientific software over the
last 20 years.  Don't get me wrong -- some great code has been written
-- and some of that code has been shared without cost to some or for a
low fee to others.  However, most of that code has almost never been
shared in such a way as to enable extension, modification, and
redistribution.  As a result, we are not making much cumulative
progress.  Software programs resemble ideas: they must be shared,
questioned, altered, and refined in order for lasting progress to occur.
Otherwise they stagnate just like old ways of thinking.  

DSSP (circa 1983) is a great example of how many
computer-dependent sciences remain trapped in the 1980s.  Whether it
works better than PyMOL or not is almost beside the point.  It is simply
not an appropriate standard for us to be using today in this age of open
standards, open source, and composite systems.  We can and should do
better than this.

My hope is that if PyMOL and enough similar projects are
successful, that governments, companies, and funding agencies will begin
to back these kinds of efforts wholeheartedly with money and policies,
and thus drive rapid progress and widespread benefits throughout the
sciences. 

Cheers,
Warren

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

 -Original Message-
 From: Ben Hitz [mailto:bh...@exelixis.com] 
 Sent: Monday, November 03, 2003 11:01 AM
 To: Warren L. DeLano; pymol-users@lists.sourceforge.net
 Subject: Re: [PyMOL] DSSP
 
 
 Warren

RE: [PyMOL] secondary structure assignment and surface potential calc/mapping

2003-10-31 Thread Warren L. DeLano
 1) Is the secondary structure assignment function in 0.92 
 more reliable?  Or does the WARNING: it will make mistakes, 
 so don't publish anything based on this algorithm! statement 
 still apply?

Good question!  I added that warning message to util.ss back when I
believed that there was such as thing as correct secondary structure
assignment and because util.ss had a very primitive H-bonding definition
-- distance only.  dss is something completely new.

In creating the new dss, I took some time to go through the 1983 DSSP
paper (Kabsch  Sander) and discovered much to my surprise that the
H-bond criterion used by DSSP has very little to do with what
crystallographers today think about hydrogen bonds.  Did you know that
DSSP H-bonds can be as long as 5.2 Angstroms between heavy atoms (Fig
1)?  Plus, there is no simple analytic form of their criterion provided
which could be implemented by something like PyMOL.   

Furthermor, and more disturbing, I discovered that DSSP doesn't take
backbone torsion geometry into account at all, which finally explained
to me why so many DSSP-assigned PDB structures have obviously
non-helical regions assigned as HELIX.  It's just a naive algorithm, and
as far as I'm concerned, H-bonds just aren't the whole story when it
comes to secondary structure.

Thus, I had to admit that DSSP itself wasn't correct with repect to my
personal interpretation of secondary structure.  In looking at RasMOL's
code it suffers from some of the same problems, and I don't think it
actually implements DSSP -- just an approximation to it.

So I decided to create my own best-attempt at a secondary structure
assignment algorithm based on the spirit of DSSP, but which also takes
into account backbone geometry as well as hydrogen-bonding .  Like DSSP,
PyMOL's hydrogen-bonding criteria is angle-dependent, but the default
range is more contemporary (within 3.2 A at 63 deg, 3.6 A at 0 deg).  

After validating the algorithm manually on ten structures, I sat down
and visually compared PDB (DSSP) assignments to PyMOL's dss over
several hundreds proteins.  In general, both programs find the same set
of helices and large sheets.  However, they differ on the exact start
and stop points of these elements.  On small sheets or helices, one
program may miss something that the other finds.  However, divergent
regions seemed to involve borderline cases for the most part.  dss and
DSSP seem to do equally well on cut-and-dry idealized systems.  So dss
is reasonably validated, in my view, but I am looking for feedback and
specific problem cases when they're found.

But speaking as an artist rather than as a scientist, I think dss has
better aesthetics than DSSP when it comes to cartoon diagrams -- there
are simply fewer goofy-looking assignments.  Whether it is more
scientifically correct or not is an open question.  Cartoons themselves
are pretty misleading...one might add.

By the way, there are a some new settings in PyMOL 0.92 which cover
h-bond detection and secondary structure assignment.  Here are the most
important ones:

h_bond_max_angle, 63.0
h_bond_cutoff_center, 3.6
h_bond_cutoff_edge, 3.2

ss_helix_psi_target, -48.0
ss_helix_phi_target, -57.0

ss_strand_psi_target, 124.0
ss_strand_phi_target, -129.0

Basically, if helix or sheet hydrogen bonds are present, and backbone
geometries are close to the target values, PyMOL will assign residues as
helix or sheet.  Otherwise, they're considered loops.   The allowable
Phi/Psi inclusion/exclusion boxes are adjustable with settings too.

For the curious, my algorithm is about 1,000 lines of code and consists
of the SelectorAssignSS function found in layer3/Selector.c around line
500.

 2) Is there a 0.92 function to calculate and map surface 
 potential?  This would be useful beyond compare.

I wish.  Your choices for this are Grasp, MEAD, Delphi, or Zap.  Only
MEAD is freely available.

Cheers,
Warren

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

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net 
 [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of 
 Neiditch, Matthew
 Sent: Friday, October 31, 2003 12:46 PM
 To: 'pymol-users@lists.sourceforge.net'
 Subject: [PyMOL] secondary structure assignment and surface 
 potential calc/mapping
 
 
 Dear List,
 
   
 
 Regards,
 
 Matthew Neiditch
 
 Postdoc
 Hughson Lab
 Princeton University
 neidi...@molbio.princeton.edu 
 
 
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RE: [PyMOL] labeling atoms in GUI

2003-10-31 Thread Warren L. DeLano
Richard,

It's not GUI, but you could simply bind a function key such as F1 to
that command:

cmd.set_key('F1',lambda :cmd.label((lb),'%s %s
%s%(name,resn,resi)'))

You might then want to bind 'F2' to something which hides all labels.

cmd.set_key('F2',cmd.label)

Cheers,
Warren

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

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net 
 [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of 
 rbax...@uchicago.edu
 Sent: Wednesday, October 29, 2003 5:14 PM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] labeling atoms in GUI
 
 
 Dear All,
 
 I want to look at my structure in PyMOL and, having centered 
 on something defined by my selection script, pick atoms 
 nearby and see what residues they belong to. That is, I want 
 to pick select an atom with the mouse and have its name, 
 residue name and residue number appear on screen, like it does in O.
 
 I figured out that [Ctrl] + Left-Mouse-Button selects the 
 atom as lb, and that the command 'label (lb),%s %s %s % 
 (name,resn,resi)' gives me the label I want. Now how could I 
 get something like that to appear as a menu function in the 
 GUI so I don't have type it in all the time? Can it be a 
 command executed as part of my startup script?
 
 Maybe some function like this already exists, otherwise I 
 think it is a very useful thing.
 
 regards,
 
 Richard Baxter
 
 
 ---
 This SF.net email is sponsored by: SF.net Giveback Program. 
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RE: [PyMOL] How to load O/BRIX map

2003-10-30 Thread Warren L. DeLano
Huiying,

PyMOL will recognize the following extensions for O maps:

.o
.omap
.brix

The following will render the entire brick at 1 sigma:

load map.o
isomesh m1, map, 1

Or if you have a pdb

load model.pdb
isomesh m1, map, 1, 100/, 8

will give you an 8 A brick around residue 100, etc.

Cheers,
Warren

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

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net 
 [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of 
 Huiying Li
 Sent: Wednesday, October 29, 2003 3:52 PM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] How to load O/BRIX map
 
 
 
 I am wondering how to load the O/BRIX maps into Pymol using 
 version 0.92. Is there a default file extension, say *.dsn6, 
 for O map, or need to define the map format with a keyword?
 
 Thanks for any help.
 
 --
 Huiying Li, Ph. D
 Department of Molecular Biology and Biochemistry
 Natural Sciences I, Rm 2443
 University of California at Irvine
 Irvine, CA 92697, USA
 Tel: 949-824-4322(or -1953);  Fax: 949-824-3280
 email: h...@bragg.bio.uci.edu
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[PyMOL] RE: Writing info to files

2003-10-27 Thread Warren L. DeLano
 Currently, i 
 work on a complexe proteinic which includes two proteins.
 I calculate distances (in a cut-off of 10 Angström in order 
 to obtain atoms 
 which are within the interface of both molecules) between 
 these proteins. Now, i would like to know what atoms belong 
 to my selection and write them 
 in a file. Could you help me please ?

iterate selection, python-code

For example:

load $PYMOL_DATA/demo/pept.pdb
output= open(output.txt,'w')
iterate (name ca), output.write(%s %s %s %s\n%(resn,chain,resi,name))
output.close()

Would create output.txt containing:

ASP E 1 CA
CYS E 2 CA
ALA E 3 CA
TRP E 4 CA
HIS E 5 CA
LEU E 6 CA
GLY E 7 CA
GLU E 8 CA
LEU E 9 CA
VAL E 10 CA
TRP E 11 CA
CYS E 12 CA
THR E 13 CA

Notice how you can freely intersperse Python and PyMOL commands in PyMOL
command scripts in order to accomplish tasks such as this.

Cheers,
Warren


--
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Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020





RE: [PyMOL] Save session on Mac OSX latest version?

2003-10-26 Thread Warren L. DeLano
Douglas,

Simply:

save filename.pse

ie

save today.pse

Cheers,
Warren



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

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net 
 [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of 
 Douglas Freymann
 Sent: Sunday, October 26, 2003 2:26 PM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Save session on Mac OSX latest version?
 
 
 I'm having a hard time finding how to save my session running on a G4 
 Powerbook, using PyMOL v0.91.  The command, File::Save, is grayed 
 out, and there's no command File::Save Session as described in the 
 Users Manual.  Is there a trick, or a command line statement? 
 By the way, is there a way to set a default working directory when 
 PyMOL starts?
 Sorry if these are FAQ's but I didn't find the answers 
 anywhere. Thanks, Doug
 
 -- 
 
 Douglas M. Freymann  freym...@northwestern.edu
 
 Molecular Pharmacology  Biological Chemistry
 Ward 7-247,  Northwestern University
 303 E. Chicago Ave., Chicago, IL  60611
 
 (312) 503-1877fax: (312) 503-5349
 
 
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RE: [PyMOL] solvent accesible surface

2003-10-26 Thread Warren L. DeLano
Marcelo,

PyMOL doesn't currently do a very good job with a solid solvent
accessible surfaced because they aren't smooth like the Connolly
surface. But here's what you can do:

show spheres
set sphere_solvent,1

   or

hide spheres
show mesh
set solvent_mesh,1

   now add in

show surface

   for a nice combination of the solvent and molecular surfaces.

Cheers,
Warren


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

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net 
 [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of 
 Marcelo Castilho
 Sent: Sunday, October 26, 2003 4:04 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] solvent accesible surface
 
 
 Dear all,
 
 I am new to pymol and appologyze if his is an easy 
 question, anyway here it goes;
 
 Is it possible to change the surface radius in pymol so that 
 I can represent the solvente accesible surface ?
 
 By the way, I am running pymol 0.90 under windows XP
 
 Thanks,
 
 Marcelo Castilho
 
 =
 Marcelo Santos Castilho
 tel 016 273 98 68
 R; Américo J. Canhoto 223 Apto 23 Bl 2
 São Carlos CEP 13564-350
 e-mail alternativo: casti...@if.sc.usp.br
 
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RE: [PyMOL] pymol 0.90 on redhat 9.0 - no Tk window

2003-10-25 Thread Warren L. DeLano
Florian,

The main trick is to use an X11/Fink build of PyMOL.  Under 10.3, I'm
hoping OpenGL performance under X11 will be more that of the native
version -- any early returns on this yet?

For proficient developers with X11 installed, there another trick you
can try:  Link source-built PyMOL against native GLUT/OpenGL frameworks
while simultaneously linking against X11-based Python/Tkinter/Tcl/Tk.
This is what I call the hybrid build, which gives native-like OpenGL
performance and X11-like user interface compatibility.  Stability was a
problem with this config though, which is why I've never tried to
distribute such a build.

Finally, there is a native Tcl/Tk Aqua port which doesn't require X11,
and which in theory at least would enable a native-like GUI without
having to write Aqua code directly.  However I've heard that there are
stability problems with this Tcl/Tk, and I'm not sure Python's Tkinter
can even work with it.  Does anyone out there have experience using
Tkinter on OSX without X11?

Cheers,
Warren

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

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Florian Nachon
 Sent: Thursday, October 23, 2003 5:53 AM
 To: pymol-users@lists.sourceforge.net
 Subject: Re: [PyMOL] pymol 0.90 on redhat 9.0 - no Tk window
 
 
 On Oct 22, 2003, at 8:42 PM, pymol-users-requ...@lists.sourceforge.net
 wrote:
 
  Tkinter is a separate Python module that's an interface to the Tcl
Tk
  library.  It's probably just not installed on your system, but it is
  included in the RH 9 distribution (tkinter-2.2.2-26.i386.rpm) so it
  should
  be easy to find and install.
 
 By the way, isn't there a trick to get the Tk menu in the native MacOS
 X version of Pymol?
 
 
 
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[PyMOL] Release in progress...

2003-10-25 Thread Warren L. DeLano
(in a whisper) 

I'm still in the process of building binaries, but pioneers are welcome
to start downloading 0.92, if your platform is represented.  It has been
a long time since our last release, so proceed with caution!

http://sourceforge.net/project/showfiles.php?group_id=4546

Please bring any problems to my attention ASAP, before the Monday
deluge.

Warren





RE: [PyMOL] Using PyMol as a library - no GUI

2003-10-24 Thread Warren L. DeLano
Truls,

That looks to me like a crash where the PyMOL API was somehow
called before PyMOL was initialized...how and why this could happen is a
mystery to me though -- that's what pymol.finish_launching() is supposed
to prevent -- but there may be some flaw in the logic.

Cheers,
Warren


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

 -Original Message-
 From: Debian Chooser [mailto:ker...@herocamp.org] On Behalf Of Truls
A.
 Tangstad
 Sent: Friday, October 17, 2003 3:18 PM
 To: Warren L. DeLano
 Cc: pymol-users@lists.sourceforge.net
 Subject: Re: [PyMOL] Using PyMol as a library - no GUI
 
 On Fri, Oct 17, 2003 at 09:41:24AM -0700, Warren L. DeLano wrote:
   Truls A. Tangstad wrote:
   I'm very interested in using alot of the functionality that PyMol
   offers programmatically from Python, i.e. without using a GUI at
   all. The chempy package seems to cover alot of my needs, loading
   different file formats etc. even though it doesn't seem to be
   documented.
  
   Is it also possible to use the rest of the functionality in PyMol
from
   other Python scripts? Right now, just importing the pymol package
   seems to force the GUI to open.
 
  If you've got PyMOL configured to open on
 
  import pymol
  pymol.finish_launching()
 
  You can suppress the GUI feature and suppress startup output by
  providing command line arguments as follows.  Before importing
PyMOL,
  set a pymol_argv list in the __main__ namespace.  PyMOL will
interpret
  this as a sys.argv styled list of command line arguments.
 
  import __main__
  __main__.pymol_argv['pymol','-qc']
 
  import pymol
  pymol.finish_launching()
 
 Thanks, seems to work like a charm in scripts after adding the
 assignment operator:
 __main__.pymol_argv = ['pymol', '-qc'] # adding miss
 
 Somehow it segfaults when trying the same thing in an interactive
 python interpreter though, right after importing pymol. This might be
 due to a shoddy install on my part, but I'm including a gdb backtrace:
 
 #0  0x41d7b21a in SettingGetGlobal_f () from /usr/lib/python2.3/site-
 packages/pymol/_cmd.so
 #1  0x41d7c683 in SettingGet () from /usr/lib/python2.3/site-
 packages/pymol/_cmd.so
 #2  0x41d6296d in OrthoAddOutput () from /usr/lib/python2.3/site-
 packages/pymol/_cmd.so
 #3  0x41d679a5 in PCatchInit () from /usr/lib/python2.3/site-
 packages/pymol/_cmd.so
 #4  0x4006d74d in PyCFunction_Call () from
/usr/lib/libpython2.3.so.1.0
 #5  0x40045e37 in PyObject_Call () from /usr/lib/libpython2.3.so.1.0
 #6  0x400a2a4a in PyEval_CallObjectWithKeywords () from
 /usr/lib/libpython2.3.so.1.0
 #7  0x4000 in PyFile_WriteObject () from
/usr/lib/libpython2.3.so.1.0
 #8  0x400556e6 in PyFile_WriteString () from
/usr/lib/libpython2.3.so.1.0
 #9  0x400d56b6 in PySys_WriteStderr () from
/usr/lib/libpython2.3.so.1.0
 #10 0x400d4b2c in PySys_WriteStderr () from
/usr/lib/libpython2.3.so.1.0
 #11 0x400d2c74 in Py_AtExit () from /usr/lib/libpython2.3.so.1.0
 #12 0x40101043 in _PyUnicode_TypeRecords () from
 /usr/lib/libpython2.3.so.1.0
 
 Any idea why it shouldn't work interactively?
 
 I'm using PyMol 0.90 and Python 2.3.2 on Debian unstable.
 
 --
 Truls - kerfue+pymol-us...@herocamp.org




RE: [PyMOL] Off screen drawing bug on a nForce 2 computer

2003-10-22 Thread Warren L. DeLano
Paulo,

As far as I know, what you're reporting is a platform-dependent
OpenGL bug (or feature).  Many graphics cards don't support rendering to
display context that is not visible.  Ray-tracing doesn't have this
limitation of course, but in theory we could teach PyMOL how to use
auxillary buffers to enable off-screen OpenGL rendering as well.

Unfortunately there isn't any way to color bonds independent of
atoms in PyMOL.  The closest thing you can do is create a new object
consisting of just those to bonds and to color that object separately.

Cheers,
Warren

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

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Paulo Lai
 Sent: Tuesday, October 21, 2003 7:55 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Off screen drawing bug on a nForce 2 computer
 
 Hi,
 
 I have added a very limited SOAP interface to PyMol and I've found
that
 when the viewer window is covered there are errors in the png files it
 generates. For example if I load a structure and rotate it, it will
save
 the image of the structure in its new orientation overlaid on top of
its
 original position. It works fine on my laptop which uses the ATI
 Mobility Radeon 7500, and I can get it to work on my nForce 2 desktop,
 if I use the minimal level of hardware acceleration (when using the
 latest version of the NVIDIA drivers). The other issue I've had is
PyMol
 freezes if I have it open normally, and then I use remote desktop to
 connect to that computer, neither of these are critical.
 
 If anyone is interested, the SOAP libraries for Python (SOAPpy and
ZSI)
 are still quite rough with many relatively simple things not
functioning
 correctly, I've resorted to passing lists around.
 
 Final thing, is there a way to colour a single bonds in sticks view
 without affecting the colour of the other bonds the atom is connected
to?
 
 Cheers,
 Paulo
 
 
 
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RE: [PyMOL] atom sphere radius

2003-10-22 Thread Warren L. DeLano
Robert,

alter selection, vdw=number


for example:

alter elem fe, vdw=1.0
rebuild

Cheers,
Warren



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

 -Original Message-
 From: Robert Schwarzenbacher [mailto:robe...@sdsc.edu]
 Sent: Wednesday, October 22, 2003 1:43 PM
 To: Warren L. DeLano
 Cc: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] atom sphere radius
 
 Hi there,
 
 I would like to show an active site metal but the sphere radius is too
 big. Is there a way to change the sphere radius for an atom or display
 it otherwise with a radius of say 1A.
 
 
 thanks,
 robert
 
 ---
 Robert Schwarzenbacher, PhD
 The Joint Center for Structural Genomics
 phone: 858 822 3637





RE: [PyMOL] pymol 0.90 on redhat 9.0 - no Tk window

2003-10-22 Thread Warren L. DeLano
Fred,

The tkinter dependency is missing.  RPM is supposed to check that, but I
forget to add it to the list. 

Look for the tkinter RPM on your RH9.0 CDROM (or on the net).

Cheers,
Warren

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

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of fr...@mit.edu
 Sent: Wednesday, October 22, 2003 3:33 PM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] pymol 0.90 on redhat 9.0 - no Tk window
 
 Hi PyMOLers,
 
 Can someone tell me why I don't get the Tk window with all of the
menus
 when I
 start PyMOL under redhat 9.0?  I installed the RPM file
 pymol-0.90-1.rh90.py22.i386.rpm and got no errors during installation.
 
 Here's the content of the shell window after starting PyMOL:
 
 
 Xlib:  extension XFree86-DRI missing on display :0.0.
 
  PyMOL(TM) Molecular Graphics System, Version 0.90.
  Copyright (C) 1998-2003 by DeLano Scientific LLC.
  All Rights Reserved.
 
 Created by Warren L. DeLano, Ph.D.
 
 Other Major Authors and Contributors:
 
Ralf W. Grosse-Kunstleve, Ph.D.
 
 PyMOL is user-supported open-source software.  Although most
versions
 are freely available, PyMOL is not in the public domain.
 
 If PyMOL is helpful in your work or study, then please volunteer
 support for our ongoing campaign to create open and affordable
 software
 for molecular research.
 
 Updates and other information can be found at
http://www.pymol.org;.
 
 Please cite PyMOL in publications and presentations:
 
Warren L. DeLano The PyMOL Molecular Graphics System.
DeLano Scientific LLC, San Carlos, CA, USA.
http://www.pymol.org
 
 Enter help for a list of commands.
 Enter help command-name for information on a specific command.
 
  Hit ESC anytime to toggle between text and graphics.
 
  OpenGL based graphics front end:
   GL_VENDOR: Mesa project: www.mesa3d.org
   GL_RENDERER: Mesa GLX Indirect
   GL_VERSION: 1.3 Mesa 4.0.4
 Traceback (most recent call last):
   File modules/pymol/__init__.py, line 177, in exec_str
 exec s in globals(),globals()
   File string, line 1, in ?
   File modules/pymol/__init__.py, line 292, in launch_gui
 __import__(invocation.options.gui)
   File modules/pmg_tk/__init__.py, line 22, in ?
 # as /usr/lib/python2.1/site-packages
   File modules/pmg_tk/PMGApp.py, line 15, in ?
 ImportError: No module named Tkinter
 
 
 Thanks everyone.
 
 
 
 
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RE: [PyMOL] new error

2003-10-20 Thread Warren L. DeLano
Tom,
 
Yes you're right: MGL's stuff messes with PYTHONPATH and possibly
PYTHONHOME.  These need to be undefined for PyMOL to work correctly.
 
Cheers,
Warren
 
 
 
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax   (650)-593-4020 
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Tom
Thompson
Sent: Friday, October 17, 2003 11:42 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] new error
 
I just started to get this error mac-osx 10.2.6.  Could it be correlated
with a recent installation of the python-based molecular  visualization
programs from the MGL at Scripps.  I have reinstalled the program and I
get the same error.
 
Traceback (most recent call last):
  File /Applications/PyMOL/Darwin/modules/pymol/__init__.py, line 58,
in ?
import threading
  File /Applications/PyMOL/Darwin/ext/lib/python2.2/threading.py, line
4, in ?
import time
ImportError: No module named time
 
Thanks,
 
-Tom
 
-- 
__
Tom Thompson, Ph.D.PH 847-467-4049
Northwestern University
2205 Tech Drive
Evanston IL 60208-0001


[PyMOL] 2004 PyMOL Budget Reminder

2003-10-20 Thread Warren L. DeLano
PyMOL Users,

For all of you fortunate enough to have recurring annual software
budgets, this is a gentle reminder and request for you to consider
leaving room in your 2004 budget plans for a PyMOL support subscription
( license for new sponsors).  

We have been functioning as an independent open-source software company
for a little over six months, and I am thrilled to be able to now state
with confidence that as long as present trends continue, DeLano
Scientific LLC will endure to support PyMOL and pursue its development
indefinitely.  We have reached a minimal break even point where our
current (albeit low) costs are met by current revenue.  PyMOL is now
officially a sustainable long-term project with a bright future!

However, we are not yet running as efficiently as possible because
current sponsorship can just barely support one full-time equivalent,
meaning that my time is split between support, development, system
administration, management of contractors, and (unavoidable) paperwork.
This achievement of minimal sustainability is an important milestone,
but we are not yet able to tap into the significant gains in
productivity that can be had through effective divisions of labor.

Of course, I will multi-task for as long as is needed to insure the
project's vitality -- that goes almost without saying.  However, the
greatest benefits to you, our users, will accrue when we can afford
separate dedicated people, each focusing on one area: support (training,
documentation, site-visits, etc.), development (new features, bug-fixes,
customization), or general administration (including preparation of SBIR
grant applications to cover aggressive new development projects).  

My hope is that with gradually increasing sponsorship, we will reach
that level within the next year or so.  However, control over our growth
rate and the rate of PyMOL improvement ultimately lies in your hands.
What would you like to see happen with the project?  Do you share our
vision for accessible and ubiquitous molecular graphics software?  Are
you willing and able to help bring it about sooner or later?  

If you have a budget, then please make room for a PyMOL subscription in
it.  Alternatively, if you are preparing a new grant, then please
consider adding a line item for PyMOL along with any new hardware or
software purchases.  We can provide quotes to help with this kind of
advanced planning upon request ( http://www.pymol.org/funding.html ).

Thanks to all of you who have already sponsored the effort -- you are
making this all possible.  Thank you especially for your trust, your
patience, and your continued belief in the value of our mission 
( http://www.delanoscientific.com/about.html ).  

Cheers,
Warren
--
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Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020




RE: [PyMOL] Using PyMol as a library - no GUI

2003-10-17 Thread Warren L. DeLano
If you've got PyMOL configured to open on

import pymol
pymol.finish_launching()

You can suppress the GUI feature and suppress startup output by
providing command line arguments as follows.  Before importing PyMOL,
set a pymol_argv list in the __main__ namespace.  PyMOL will interpret
this as a sys.argv styled list of command line arguments.

import __main__
__main__.pymol_argv['pymol','-qc']

import pymol
pymol.finish_launching()

Cheers,
Warren

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

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Truls A. Tangstad
 Sent: Friday, October 17, 2003 4:48 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Using PyMol as a library - no GUI
 
 I'm very interested in using alot of the functionality that PyMol
 offers programmatically from Python, i.e. without using a GUI at
 all. The chempy package seems to cover alot of my needs, loading
 different file formats etc. even though it doesn't seem to be
 documented.
 
 Is it also possible to use the rest of the functionality in PyMol from
 other Python scripts? Right now, just importing the pymol package
 seems to force the GUI to open.
 
 --
 Truls - kerfue+pymol-us...@herocamp.org
 
 
 ---
 This SF.net email is sponsored by: SF.net Giveback Program.
 SourceForge.net hosts over 70,000 Open Source Projects.
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RE: [PyMOL] Command line equivalent available?

2003-10-15 Thread Warren L. DeLano
Nick,

 There are a few commands that I've been using for which I can't seem
to
 find a command line equivalent:

This actions can be performed using selections with standard atom
identifiers:

 show/hide mainchain atoms

show lines, object-nameca+c+n+o+h
hide lines, object-nameca+c+n+o+h

where object-name is the name of your object

 show/hide sidechain atoms

show lines, object-name and ((not name c+n+o+h) or pro/n)
hide lines, object-name and ((not name c+n+o+h) or pro/n)

Of course, you can substitute sticks, sphere, etc. for lines in the
above.

 select atoms for 'dist' command (H-bond creation)

dist dist-name, selection1, selection2

i.e.

dist d1, prot//N/23/CA, lig//X/1/O
dist d2, prot//O/24/CA, lig//X/2/N

Cheers,
Warren





RE: [PyMOL] Underside of surface color

2003-10-11 Thread Warren L. DeLano
Jason,

Not really -- it's either blackish or lit, just like the front.

To see the backside of surfaces:

set two_sided_lighting,1
set backface_cull,1

Also, sometimes it is helpful to get rid of shadows when doing this:

set ray_shadows, 0

Cheers,
Warren

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

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Jason Thomas Maynes
 Sent: Friday, October 10, 2003 3:11 PM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Underside of surface color
 
 Hello:
 
 Is there any way to change the color of the underside of a surface.
Right
 now it is a very dark version of the top color.  I would like to be
able
 to look at the surface contour from underneath.
 
 Thanks in advance.
 
 Cheers,
 JTM
 
 We can be sure that if a detailed understanding of the molecular
basis of
 chemo-therapeutic activity were to be obtained, the advance of
medicine
 would be greatly accelerated.
 
 Linus Pauling, Nobel Laureate 1954
 
 ...everything that living things do can be understood in terms of the
 jigglings and wigglings of atoms.
 
 Richard Feynman
 
 *
 Jason Thomas Maynes
 PhD/MD Program
 Department of Biochemistry
 Faculty of Medicine
 University of Alberta
 ja...@biochem.ualberta.ca
 *
 
 
 
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RE: [PyMOL] Accessing PyMol's commands from outside (or without viewer)

2003-10-08 Thread Warren L. DeLano
Shu-hsien

Sure, instead of cmd.select, use

cmd.do(select ligand, resn XYZ)
cmd.do(select protein, ! ligand )

etc.

./pymol -qc select_box.py

Is the command line mode of PyMOL.  pymol -qc can be used like
python in most cases.

Cheers,
Warren

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Voice (650)-346-1154 
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 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Shu-Hsien Sheu
 Sent: Saturday, November 08, 2003 10:58 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Accessing PyMol's commands from outside (or without
 viewer)
 
 Hi,
 
 This should be a trial question though I cannot find a way of doing
it.
 I have a simple script that looks like this:
 (the original commands, rather than cmd.select..)
 select ligand, resn XYZ
 select protein, ! ligand
 select box, protein within 8 of ligand
 select box, box or byres box
 save box as box.pdb
 
 I don't need the viewer at all and would be even more efficient if I
can
 call the PyMol API from the shell. Or, in a python script.
 For example, I would like to have something like:
 ./pymol select_box.py
 
 thanks!
 
 
 
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RE: [PyMOL] Pymol script screenplay

2003-10-05 Thread Warren L. DeLano
Nat,

PyMOL's ray-tracer is pretty simple -- it just divides 3D space up into
equally sized boxes, so that ray-intersection and identification
calculation can be performed rapidly.  The smaller the boxes, the fewer
the number of partial geometries will be present in the box.

Hash_max is a hint to the ray tracer about the maximum number of
subdivisions it should allow on each axis.  In principle, the amount of
RAM used is a 3rd-order function of this value.  However, the ray-tracer
will often use less RAM than that for a variety of reasons.

PyMOL usually ships with hash_max set to 100, since that is reasonable
for a machine with 256 MB of RAM.  300 is about the highest I've tried,
and you could easily require over a Gig of RAM for a situation like
that.  

However, there is definitely a point of diminishing returns, which
depends on scene complexity, total number of pixels, etc.  Typically
each ray-tracing scene will have a different optimum, but usually
140-180 gives the shortest overall rendering times.  

Cheers,
Warren




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

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Nat Echols
 Sent: Sunday, October 05, 2003 2:28 PM
 To: pymol-users@lists.sourceforge.net
 Subject: RE: [PyMOL] Pymol script screenplay
 
  By the way, you can also use extra RAM to speed up ray-tracing
  by 2-3 fold if you set hash_max to 150-200.
 
 Wait, I'm curious - what does this command do, and what are the
limits?
 For a machine with 2GB of memory, what can I get away with?  Will I
have
 problems if I run multiple invocations of PyMOL at once?
 
 -Nat
 
 
 
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RE: [PyMOL] why is PyMOL renaming my residues?

2003-10-03 Thread Warren L. DeLano
 Also note that by some conventions, 2OA2 in a PDB file really means
 atom OA22.
 
 I didn't know that.  What conventions are those?

Well, PDB atom names are supposed to have the atomic symbol right
justified in the first two columns followed by a remoteness indicator
and then a branching number.  However, that isn't a sufficient number of
fields for all situations, such as when significant symmetry is present
in a system, and so a third field is required.  This numeric field
occupies the first column when the atom symbol itself is only one
character.

With hydrogens, this first numeric field has the additional defined
purpose of enumerating (NMR?) equivalent hydrogens, so you will see
atoms like 2HD and 3HD in ARG for instance.

However, in the Amber world, the atomic symbol always comes first.  Thus
a PDB hydrogen 2HH2 becomes HH22 in Amber.  Going from PDB to Amber is
easy, but the reverse is not trivial, since Amber CD1 remains PDB
CD1, but Amber HE2 becomes 2HE and HH22 becomes 2HH2.  

Ambiguity occurs when there is a four-letter atom name which is not a
hydrogen.  OA22 in Amber would thus need to become 2OA2 in order to
comply with the PDB convention of having the Atomic symbol right
justified in the first two columns of the file.  However, that
convention is only explicitly enforced for amino acids, so in theory
OA22 would be legal for a non-amino acid, whereas 2OA2 is required
if the residue is an amino acid.  

What a mess!

Cheers,
Warren






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

 Also note that by some conventions, 2OA2 in a PDB file really means
 atom OA22.
 
 I didn't know that.  What conventions are those?
 
 Furthermore, in your example, they [ATOM IDs] are not unique (a
 mistake?).
 
 yup, a mistake.
 
 However, I am trying to bend PyMOL around to meet your needs a bit
 better.
 
 Towards this end, I've created a new setting pdb_retain_ids which
 preserves the original PDB serial numbers in the output file.
 
 In future PyMOL versions, so long as
 
 set retain_order, 1
 set pdb_retain_ids, 1
 set pdb_no_end_record, 1
 
 That's absolutely fantastic.  Right now, I have to use PyMOL, MOE and
 AMBER (sander and carnal are the real problems) on the same systems,
and
 anything that makes this less painful is great!  I'll probably set
 retain_order and pdb_retain_ids in my .pymolrc.py and upgrade to the
CVS
 version within the next couple of days.
 
 Thanks!
 
 -michael
 --
 michael lerner
 
 
 
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RE: [PyMOL] Pymol script screenplay

2003-10-02 Thread Warren L. DeLano
Alan,

VMD is more memory efficient that PyMOL.  Probably the main
reason for this is that PyMOL pre-calculates and stores all of the
geometries it is going to show down to the last vertex.  

You can reduce the amount of memory PyMOL needs for cartoons by
setting:

set cartoon_sampling, 3

But the real way to solve your problem is to get more RAM.  If
you're using PyMOL to visualize MD trajectories, I recommend buying as
much RAM as you can afford (and your system can take).  1 GB is a
reasonable minimum.  1.5-2 GB is definitely better.  I don't know what
prices are like in Brazil, but a GB of RAM can be purchased here in the
states for $150-400.

By the way, you can also use extra RAM to speed up ray-tracing
by 2-3 fold if you set hash_max to 150-200.

To answer to your second question:

import os
os.system(mencoder \*.png -mf on:fps=30 -o mvc1ec2.avi
-ovc lavc -lavcopts  vcodec=mpeg4:vbitrate=6000:vhq:keyint=30)

Cheers,
Warren

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

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Alan Wilter Sousa da Silva
 Sent: Thursday, October 02, 2003 5:32 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Pymol script screenplay
 
 
 Hi List!
 
 I finally got a Pymol script which does what I want, but I still have
 problems.  I follows my actual script:
 
 -
 del all
 mclear
 set cache_frames=0
 set cartoon_fancy_helices, 1
 load c1/forcedin.pdb,c1
 frame 1
 hide all
 run Pymol/stride_ss.py
 stride2pymol c1
 stride2pymol c2
 show sticks, (resi 199)
 show cartoon, all
 color red, c1
 color blue, c2
 set orthoscopic=1
 viewport 640,480
 run Pymol/eixos.py
 translate [18,18,20],object=axes
 run Pymol/cgotext.py
 translate [18,55.5,40],object=txt
 reset
 zoom all,-55
 clip near,2
 mset 1 x10 1 x72 -28 28 x72 28 x10
 util.mroll(11,82,1)
 util.mroll(111,182,1)
 set antialias=1.0
 set ray_trace_frames=1
 mpng png2/mvc1e2
 ---
 
 It works for a 28 frames of MD. But a test.  Extending it for a real
MD
 (~500 frames) I found out that Pymol crashes when command 'show
cartoon,
 all' is running (after done the half of frames, I believe).  Problably
 memory problems, right?  However a similar operation works fine in VMD
 (sorry for comparison). I use a P4 1.6 GHz with 256 Mb Ram.
 
 BTW, how could I insert in Pymol script (python language) such command
 bellow:
 
 mencoder \*.png -mf on:fps=30 -o mvc1ec2.avi -ovc lavc -lavcopts
 vcodec=mpeg4:vbitrate=6000:vhq:keyint=30
 
 
 Thanks in advance for any help.
 
 Cheers,
 
 --
 --
 Alan Wilter Sousa da Silva
 --
 B.Sc. - Dep. Física - UFPA
 M.Sc. - Dep. Física - PUC/RJ
 D.Sc. - IBCCF/UFRJ
 Bolsista Pesquisador LAC-INPE
 São José dos Campos (SP), Brasil
 www.lac.inpe.br/~alan
 
 
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RE: [PyMOL] why is PyMOL renaming my residues?

2003-09-26 Thread Warren L. DeLano
Michael,

PyMOL's PDB handling is an attempt to navigate a minefield of
incompatible standards which exist in the conventions of various
software packages.  Amber in particular poses significant challenges, as
its PDB files are unusual.

Since version 0.90, PyMOL's behavior has changed.  Nowadays,
your input data:

HETATM 1313 OA22 NAP   164  28.315  61.969  12.250   31.54
O 
HETATM 1314 OA23 NAP   164  26.554  62.174  14.275   21.05
O 
HETATM 1314 ABCD NAP   164  28.554  64.174  16.275   11.05
O 
HETATM 1314 XYZ  NAP   164  30.554  66.174  18.2751.05
O 
HETATM 1314  LMN NAP   164  32.554  68.174  20.275   41.05
O

Would be returned as:

HETATM1 OA22 NAP   164  28.315  61.969  12.250  0.00 31.54
O
HETATM2 OA23 NAP   164  26.554  62.174  14.275  0.00 21.05
O
HETATM3 ABCD NAP   164  28.554  64.174  16.275  0.00 11.05
O
HETATM4  LMN NAP   164  32.554  68.174  20.275  0.00 41.05
O
HETATM5  XYZ NAP   164  30.554  66.174  18.275  0.00  1.05
O
END

...which does preserve atom names, but not the order.  Note that
white-space in the atom names is not preserved (an inherent limitation
in PyMOL -- significant white-space within identifier is hell on users
and parsers).  

Conventionally, atom names of length 3 or less are placed in the second
column, not the first -- so your LMN  atom may cause trouble.

Also note that by some conventions, 2OA2 in a PDB file really means
atom OA22.  PyMOL used to work this way (up to 0.90).  Nowadays
(v0.91+), 2OA2 is treated as 20A2 unless pdb_literal_names is on, in
which case the old behavior returns.  

Note that in PyMOL, the PDB ATOM IDs are treated more as a property of
the PDB file than of the atoms themselves since TER records also have
unique IDs in that sequence and repeated MODELs sometimes do as well.
Furthermore, in your example, they are not unique (a mistake?).

However, I am trying to bend PyMOL around to meet your needs a bit
better.

Towards this end, I've created a new setting pdb_retain_ids which
preserves the original PDB serial numbers in the output file.

In future PyMOL versions, so long as

set retain_order, 1
set pdb_retain_ids, 1
set pdb_no_end_record, 1

The following behavior will be obtainable:

Assuming input of:

HETATM 1313 OA22 NAP   164  28.315  61.969  12.250   31.54
O 
HETATM 1314 OA23 NAP   164  26.554  62.174  14.275   21.05
O 
HETATM 1315 ABCD NAP   164  28.554  64.174  16.275   11.05
O 
HETATM 1316 XYZ  NAP   164  30.554  66.174  18.2751.05
O 
HETATM 1317  LMN NAP   164  32.554  68.174  20.275   41.05
O

You'll get an output of:

HETATM 1313 OA22 NAP   164  28.315  61.969  12.250  0.00 31.54
O
HETATM 1314 OA23 NAP   164  26.554  62.174  14.275  0.00 21.05
O
HETATM 1315 ABCD NAP   164  28.554  64.174  16.275  0.00 11.05
O
HETATM 1316  XYZ NAP   164  30.554  66.174  18.275  0.00  1.05
O
HETATM 1317  LMN NAP   164  32.554  68.174  20.275  0.00 41.05
O

Which is as close as I think PyMOL is going to get...

Cheers,
Warren



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

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of michael lerner
 Sent: Friday, September 26, 2003 8:44 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] why is PyMOL renaming my residues?
 
 Hi,
 
 If I load up a PDB file that looks like this:
 
 HETATM 1313 OA22 NAP   164  28.315  61.969  12.250
 31.54   O
 HETATM 1314 OA23 NAP   164  26.554  62.174  14.275
 21.05   O
 HETATM 1314 ABCD NAP   164  28.554  64.174  16.275
 11.05   O
 HETATM 1314 XYZ  NAP   164  30.554  66.174  18.275
 1.05   O
 HETATM 1314  LMN NAP   164  32.554  68.174  20.275
 41.05   O
 
 and then save it from PyMOL, the resulting PDB file looks like this:
 
 HETATM1 2OA2 NAP   164  28.315  61.969  12.250  0.00
 31.54   O
 HETATM2 3OA2 NAP   164  26.554  62.174  14.275  0.00
 21.05   O
 HETATM3 DABC NAP   164  28.554  64.174  16.275  0.00
 11.05   O
 HETATM4  LMN NAP   164  32.554  68.174  20.275  0.00
 41.05   O
 HETATM5  XYZ NAP   164  30.554  66.174  18.275  0.00
 1.05   O
 END
 
 You'll note that OA22 has been renamed to 2OA2, OA23 has been renamed
to
 3OA2 and ABCD has been renamed to DABC.  It looks to me like residue
 with a four-letter name is getting renamed.
 
 No .. wait .. it's a little stranger than that .. if I open up the
 second file (the one with DABC) and save *it*, I get this:
 
 HETATM1 2OA2 NAP   164  28.315  61.969  12.250  0.00
 31.54   O
 HETATM2 3OA2 NAP   164  26.554  62.174  14.275  0.00
 21.05   O
 HETATM3 CDAB NAP   164  28.554  64.174  16.275

RE: [PyMOL] two_sided_lighting

2003-09-22 Thread Warren L. DeLano
Meitian,

Sorry, this is not possible.

Cheers,
Warren


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Warren L. DeLano, Ph.D.
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DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of M Wang
 Sent: Monday, September 22, 2003 9:49 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] two_sided_lighting
 
 Hello everybody,
 
 For two_sided_lighting, is there a way to change the relative
brightness
 of the two lights?
 
 Thanks,
 
 Meitian Wang
 
 
 
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[PyMOL] RE:

2003-09-22 Thread Warren L. DeLano
 One quick question... how do I tell PyMOL to draw a cylinder (or bond)
 of a given radius between two positions X,Y,Z and X', Y',Z'?

(From Python...)

from pymol.cgo import *
from pymol import cmd

obj = []

obj.extend( [ CUSTOM_CYLINDER,
   1.0, 2.0, 3.0,  # XYZ 1
   4.0, 5.0, 6.0,  # XYZ 2
   2.0,# Radius
   1.0, 1.0, 1.0,  # RGB Color 1
   1.0, 1.0, 1.0,  # RGB Color 2
   1, 1,   # End caps (0=none, 1=flat, 2=round)
   ] )

cmd.load_cgo(obj,'my_cgo')

Cheers,
Warren

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RE: [PyMOL] getting color of a residue + selecting non-natural residues

2003-09-19 Thread Warren L. DeLano
Tina,

 I have two operations that I want to perform, and am not aware of a
simple
 way
 (if possible) of doing them. So here it goes:
 
 1. how (if possible) to retrieve the color for a residue as identified
in
 an
 expression, e.g. resi 9? Note that it's not a range so no multiple
 answers
 is possible. I guess the question could extend to other attributes
like
 representation, etc. The reason I need that is to be able to switch
back
 to a
 residue's original color after highlighting it in another.

The iterate command can do this...

iterate all, print color

import pymol
pymol.color_list = []
iterate all, color_list.append(color)
print pymol.color_list

 2. how to select all non-natural residues (anything that's not in the
list
 of
 20 standard AAs)?
 
 I'm going the brute-force way, i.e.
 
 naturals1='asp+glu+lys+arg+phe+tyr+cys+met+ser+thr'
 naturals2='asn+gln+leu+val+ile+gly+ala+his+trp+pro'
 select naturals1, resn naturals1
 select naturals2, resn naturals2
 select nonnaturals, !naturals1  !naturals2

Does the above work?  I wouldn't expect variables to function in PyMOL
statements, but perhaps you're actually using cmd.select(...), which can
access variables.  

However, you don't need to brake it up quite so much:

select naturals, resn asp+glu+lys+arg+phe+tyr+cys+met+ser+thr \
or resn asn+gln+leu+val+ile+gly+ala+his+trp+pro 

select nonnaturals, !naturals

Cheers,
Warren






RE: [PyMOL] bug in rpm?

2003-09-19 Thread Warren L. DeLano
Nat,

Are you running stock RedHat 9.0?  The threading library in RH90 is
broke.  You may need to apply the glibc patches released by RedHat in
order to get a stable system.

Warren


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

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Nat Echols
 Sent: Friday, September 19, 2003 12:47 AM
 To: PyMOL-users@lists.sourceforge.net
 Subject: [PyMOL] bug in rpm?
 
 
 I just got a shiny new Gateway laptop - essentially a ripoff of the
15
 Apple (but cheaper), with NVidia chipset.  I installed RedHat 9.0,
NVidia
 drivers, and the PyMOL rpm for rh9, but I get segfaults when I try to
run
 'pymol'.  The tar.gz file works perfectly, so it's not a problem for
me,
 but I figured I should check and see if this was a known issue or if
I'm
 doing something dumb.
 
 -Nat
 
 
 
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RE: [PyMOL] modifying atom coordinates

2003-09-19 Thread Warren L. DeLano
Edmund,

No, this kind of technical information isn't documented...

If I recall correctly, when PyMOL hooks fragments together, it
replaces hydrogen with a bond along the existing vectors.  In other
words, one fragment is translated so as to fit onto another.

Peptides are a special case because the phi-psi vectors are
fairly well defined.  Nevertheless, I wouldn't trust peptide geometries
generated by PyMOL until they've passed through some external
force-field, such as MMFF or Amber/OPLS.  

PyMOL is a reasonable builder for defining the covalent scaffold
of peptides and arbitrary small molecules, but it knows nothing about
forces and energies.  

Cheers,
Warren

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Voice (650)-346-1154 
Fax   (650)-593-4020

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Edmund Kump
 Sent: Thursday, September 18, 2003 8:59 PM
 To: pymol-users@lists.sourceforge.net
 Subject: RE: [PyMOL] modifying atom coordinates
 
 Yes, but what happens when, for example, I take a lysine residue, and
 connect a glutamine residue? Shouldn't all the atoms have different
 coordinates from when they are stand alone, based on the forces from
 nearby atoms? Does pymol account for this as residues are added, or is
 there a command or wizard which accounts for nearby atomic forces that
I
 would execute after I build my chain?
 
 To give some background to what I'm trying to do, the end goal of my
 project is to modify the forces involved in protien folding. I'm sorry
if
 I'm asking questions that are documented, but I haven't seen anything
that
 answers my question yet.
 
 Much Thanks,
 Edmund
 
 
  On Wed, 17 Sep 2003, Warren L. DeLano wrote:
 
  Hi Edmund,
 
  Actually, PyMOL uses a set of stored coordinates for fragments
  and residues.  They can be found in
$PYMOL_PATH/data/chempy/fragments.
  The files have .pkl extensions, which stands for pickled chempy
model.
  These files can be viewed directly in PyMOL, or can be introspected
by
  unpickling them in a Python interpreter.
 
  Cheers,
  Warren
 
  --
  mailto:war...@delanoscientific.com
  Warren L. DeLano, Ph.D.
  Principal Scientist
  DeLano Scientific LLC
  Voice (650)-346-1154
  Fax   (650)-593-4020
 
   -Original Message-
   From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
   ad...@lists.sourceforge.net] On Behalf Of Edmund Kump
   Sent: Wednesday, September 17, 2003 3:49 AM
   To: pymol-users@lists.sourceforge.net
   Subject: [PyMOL] modifying atom coordinates
  
   Greetings,
  
   I am interested in modifying how pymol generates the coordinates
of
   atoms in a peptide chain as you add residues to it. I am an
   undergraduate math student, so my knowledge in this area is in the
   range of nothing.  I would assume that this would be in the
bonding
   or editor modules, but so far I haven't found what I'm looking
for. In
   what Chempy or Pymol module(s) can I find the code that determines
   these coordinates?
  
   Thanks,
   Edmund Kump
   ek...@mathlab.sunysb.edu
   Applied Mathematics and Statistics
   SUNY Stony Brook
  
  
  
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RE: [PyMOL] negative images

2003-09-18 Thread Warren L. DeLano
Jules,

I think there's a problem with the alpha channel with certain
PyMOL images, which means that portions end up being transparent when
they shouldn't be.  A quick workaround is to put a black rectangle
behind the PyMOL image, but I'd like to get a little more information
about when the problem occurs so that we can generate a permanent
bug-fix.

1) Does it happen with ray-traced images, OpenGL images, or both?
2) Does is only happen with transparent surfaces?
3) Does it only happen on selected platforms?  

And if possible, can you send me directly (not to the mailing list), a
copy of the problematic PNG file.

Thanks,
Warren

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

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Jules Jacobsen
 Sent: Thursday, September 18, 2003 12:37 AM
 To: Pymol users list
 Subject: [PyMOL] negative images
 
 Hello Pymol types,
 
 I have a quick question- has anyone had any trouble printing out
images
 in word using version 0.9 in word XP?
 
 The images look fine when viewed on the screen yet when it comes to
 printing them out they appear as negatives, including the white
 background which becomes black. I though this might be a ray_trace_fog
 problem as my newer images were using this set to 1 but either on or
 off, the same problem arises. I have other images rendered using 0.86
 and there is no problem with them.
 
 Has anyone else had this problem and found a fix for it?
 
 thanks in advance
 
 Jules
 
 
 
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RE: [PyMOL] A couple of movie questions

2003-09-18 Thread Warren L. DeLano
 First up: Is there any way to tell PyMol *not* to change its view when
 loading a
 PDB file

set auto_zoom,0

 Secondly: Below is an example of a small hack I have written when
making
 one
 particular movie.  This one overlays two molecules related by a 2-fold
 axis by
 doing a simple rotation.
 
  def overlay_chains(write_frames=0, ray=0):
# Now interpolate each point in the matrix
i = 1
n = 45
while i = n:
  # This is the only code I would imagine I should need:
  # cmd.mdo( %d % (i), rotate y,2,chain_a; rotate y,-2,chain_b
)
  # In the end I used the following cludge:
  cmd.do( rotate y,2,chain_a )
  cmd.do( rotate y,-2,chain_b )
  if ( ray ):
cmd.do( ray )
  if ( write_frames ):
cmd.do( png overlay_frames/overlay_%03d.png % (i) )
  i = i+1
  cmd.extend( overlay_chains, overlay_chains )
 
 What is wrong with the cmd.mdo line above?  The functionality I would
 expect
 would be that in each frame of the movie both chains are rotated 2 deg
(in
 the
 relevant directions).  What I get is that the change only occurs once
per
 loop
 of the movie.  That is to say that if I set up a movie using 'mset 1
-45'
 the positions only get updated once per 45 frames, not once per frame
 (which is
 what I would have expected).

Do you have 45 states, or just one?  If you have just one, did you use
the mset 1 x45 statement to create 45 frames consisting of that one
state?  And finally, are you using mpng to write the movie?

 Thridly:  Is there any command to tell PyMol to play a movie ONLY
ONCE.
 This
 would be *really* useful if it has not yet been implemented.

I just added a movie_loop setting for you.  Look for it in the next
version.

 Fourth (and last): Is there a difference b/w the ray-tracing used by
the
 standard 'ray' command and the 'mpng' command?  I have noticed that if
I
 take a
 still of a molecule, and then render the molecule rotating (for
example)
 all
 within the one script I observe real differences b/w what should be
 identical
 frames.  The clipping planes and the z camera distance move
considerable.
 I can
 post code if that would help.

Ray simply passes the current scene to the ray tracer.  Mpng runs
through the movie from the beginning and applies any mmatrix, mdo, or
mappend operations you may have defined for the movie before handing
each scene off to ray.  (Note that movie.rock and movie.roll use mdo)

What you describe sounds more like the difference between having a
perspective view in OpenGL and orthoscopic in the rendered scene, but
that difference should occur with both ray and mpng.

Cheers,
Warren
 






RE: [PyMOL] alternative method for loading coordinates

2003-09-17 Thread Warren L. DeLano
Rob,

There isn't a public API function which does this at present but
the private _cmd.get_pdb call does exactly that.  To see an example of
how it is used, look at the save function in
modules/pymol/exporting.py.  I'll add a cmd.get_pdbstr() function to the
next version of PyMOL, since _cmd isn't meant to be called by anyone
except PyMOL.

Cheers,
Warren

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

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Robert Campbell
 Sent: Thursday, September 11, 2003 7:07 AM
 To: pymol-users@lists.sourceforge.net
 Subject: Re: [PyMOL] alternative method for loading coordinates
 
 Warren,
 
 * Warren L. DeLano war...@delanoscientific.com [2003-09-09 17:42]
wrote:
 
  If you're willing to switch into Python, there is an
  undocumented read_pdbstr function which can take a PDB file as a
  string variable.  See modules/pymol/importing.py for the code.
  Temporary files are unnecessary.
 
 This could be very handy, but is there a way to write a pdb string
from
 within PyMOL? I've found export_coords, but that creates a PyCObject
 and I'm not sure how that can be used. I suppose it needn't be PDB
 format, but something that could be used (or converted for use) by
other
 programs or user-written routines.
 
 Cheers,
 Rob
 --
 Robert L. Campbell, Ph.D.
r...@post.queensu.ca
 Senior Research Associatephone:
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




RE: [PyMOL] modifying atom coordinates

2003-09-17 Thread Warren L. DeLano
Hi Edmund,

Actually, PyMOL uses a set of stored coordinates for fragments
and residues.  They can be found in $PYMOL_PATH/data/chempy/fragments.
The files have .pkl extensions, which stands for pickled chempy model.
These files can be viewed directly in PyMOL, or can be introspected by
unpickling them in a Python interpreter.

Cheers,
Warren

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

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Edmund Kump
 Sent: Wednesday, September 17, 2003 3:49 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] modifying atom coordinates
 
 Greetings,
 
 I am interested in modifying how pymol generates the coordinates of
 atoms in a peptide chain as you add residues to it. I am an
 undergraduate math student, so my knowledge in this area is in the
 range of nothing.  I would assume that this would be in the bonding
 or editor modules, but so far I haven't found what I'm looking for. In
 what Chempy or Pymol module(s) can I find the code that determines
 these coordinates?
 
 Thanks,
 Edmund Kump
 ek...@mathlab.sunysb.edu
 Applied Mathematics and Statistics
 SUNY Stony Brook
 
 
 
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RE: [PyMOL] Transparent cartoons?

2003-09-15 Thread Warren L. DeLano
Christian,

Transparent cartoons have been implemented, but not yet released
excepted in the latest G4/G5 Mac demo version.  If you have a Mac, you
can 

set cartoon_transparency, 0.5

using that version.  Note that cartoon transparency is really only
useful when ray-tracing, because visual artifacts will occur with
standard OpenGL rendering.

If you're on a PC, then you'll need to wait for the next big
release, which will probably happen next week.

Cheers,
Warren


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

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Christian Siebold
 Sent: Monday, September 15, 2003 10:11 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Transparent cartoons?
 
 Dear Pymol users
 
 How can I create transparent cartoon?
 I tried to use the transparency option from the setting panel, but
 this only worked for surfaces and not for cartoons.
 
 Thanks a lot,
 Christian
 
 
 --
 Dr. Christian Siebold
 Division of Structural Biology
 Wellcome Trust Centre for Human Genetics
 University of Oxford
 Roosevelt Drive, Oxford OX3 7BN, UK
 
 Tel: (+44)-1865-287550
 Fax: (+44)-1865-287547
 Email: christ...@strubi.ox.ac.uk
 Website: http://www.strubi.ox.ac.uk
 
 
 
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RE: [PyMOL] pymol raytracing crash

2003-09-15 Thread Warren L. DeLano
Thomas,

I tried running your script on the current development version
and on a version 0.90 binary, and wasn't able to get PyMOL to crash.

How is PyMOL installed on your system?

Cheers,
Warren

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

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Thomas Siegmund
 Sent: Wednesday, September 10, 2003 6:16 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] pymol raytracing crash
 


 Hi everybody,
 
 I am new to pymol. So maybe I'm doing something wrong, but pymol
almost
 everytime crashes when I try to raytrace a picture. I had some success
 with
 small protein structures in cartoon representation. The same molecule
in
 lines or sticks representation crashes the pymol raytracer.
 
 Here some console output:
 
 siegm...@siegmund:~ /usr/local/bin/python
 /usr/local/lib/python2.3/site-packages/pymol/__init__.py -x
 /tmp/pymol/7LYZ.pdb
 
  PyMOL(TM) Molecular Graphics System, Version 0.90.
  Copyright (C) 1998-2003 by DeLano Scientific LLC.
 // I cut some lines here
  OpenGL based graphics front end:
   GL_VENDOR: NVIDIA Corporation
   GL_RENDERER: RIVA TNT2/AGP/SSE2
   GL_VERSION: 1.4.0 NVIDIA 44.96
  PDBStrToCoordSet: Attempting to read symmetry information
  Crystal: Unit Cell   27.400   31.900   34.400
  Crystal: Alpha Beta Gamma88.000  108.000  112.000
  Crystal: RealToFrac Matrix
  Crystal:0.03650.01470.0133
  Crystal:0.0.03380.0031
  Crystal:0.0.0.0307
  Crystal: FracToReal Matrix
  Crystal:   27.4000  -11.9500  -10.6302
  Crystal:0.   29.5772   -3.
  Crystal:0.0.   32.5785
  Crystal: Unit Cell Volume26402.
  Symmetry:  1.0  0.0  0.0  0.0
  Symmetry:  0.0  1.0  0.0  0.0
  Symmetry:  0.0  0.0  1.0  0.0
  Symmetry:  0.0  0.0  0.0  1.0
  Executive: object 7LYZ created.
 PyMOLutil.ss
  util.ss: WARNING: This is not a correct secondary structure
 // I cut some lines here
  util.ss: assignment complete.
 PyMOLhide lines
 PyMOLshow cartoon
 PyMOLray
  Ray: total time: 1.14 sec. = 3145.7 frames/hour. (1.15 sec. accum.)
 PyMOLhide cartoon
 PyMOLshow sticks
 PyMOLray
 Speicherzugriffsfehler (segmentation fault)
 
 Pymol is version 0.9, installed from source package on SuSE linux 8.2.
To
 make
 sure that it is not a problem of the python installation (standard
SuSE
 8.2
 rpm, python-2.2.2) I installed python 2.3 from source. Same result. In
the
 mailing list archive I found comments about memory usage for
raytracing.
 This
 machine has 500 MB RAM. Top shows about 150-200 MB free RAM and 1GB
 untouched
 swap just before the raytracing. I tried the command set hash_max,
60 as
 recommended, but this also did not help.
 
 Any hints?
 
 Tanks for your help
 
 Thomas
 
 --
 Thomas Siegmund, Ph.D.
 DeveloGen AG
 Bioinformatics and Data Management
 Phone: +49(551) 505 58 651
 
 
 
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RE: [PyMOL] individual surfaces?

2003-09-09 Thread Warren L. DeLano
Dirk,

The trick for displaying contact surfaces in PyMOL is to
create separate objects for each surface:

create res431, resi 431
create res440, resi 440

show surface, res431 or res440


For CPK, you don't need to do this

show spheres, resi 431+440

Cheers,
Warren

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

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Dirk Kostrewa
 Sent: Monday, September 08, 2003 11:15 PM
 To: PyMOLBB
 Subject: [PyMOL] individual surfaces?
 
 Dear PyMol users,
 
 I'm currently trying to display individual surfaces around different
 selections of a molecule to show how they contact each other. However,
 either
 I get only the last surface displayed or a joined surface using the
 command
 examples below:
 
 this one gives only the surface of residue 440
 
 show surface, (  resid 431 )
 flag ignore, (  not resid 431  )
 show surface, (  resid 440 )
 flag ignore, (  not resid 440  )
 rebuild
 
 whereas this one gives the joint surface of residues 431 and 440
 
 show surface, ( resid 431 or resid 440 )
 flag ignore, (  not ( resid 431 or resid 440 )  )
 rebuild
 
 How can I display the individual surfaces separately?
 
 Alternatively, is there a command to display atoms in a CPK
 representation?
 
 Best regards,
 
 Dirk.
 
 --
 
 
 Dirk Kostrewa
 Paul Scherrer Institut
 Life Sciences, OSRA/007
 CH-5232 Villigen PSI, Switzerland
 E-mail: dirk.kostr...@psi.ch
 Phone: +41-56-310-4722
 Fax: +41-56-310-4556
 WWW: http://www.sb.psi.ch
 
 
 
 
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RE: [PyMOL] incorporation of unusual amino acids

2003-09-09 Thread Warren L. DeLano
Uwe,

 We plan a research project where we want to stepwise incorporate
D-amino
 acids into a peptide. To determine the exchanges it would be very
useful
 if
 PyMol could assist.
 If I might dream I would like to have D-amino acids (and maybe other
un-
 usual amino acids) available in the mutation-tool; 

You can flip residue 5 from L to D with the following two commands

edit 5/ca
invert 5/n, 5/c

 some simple energy
 minimization / bond relaxation; storing the resulting molecule in PDB-
 format.

Sculpting can relax VDW/bond/angle strain, but it is not energy
minimization by any means.

 Can I hope ? Is this something others find useful as well ?

We'd all like to see a real forcefield in PyMOL, but no one has written
the code yet.  

Cheers,
Warren






[PyMOL] PyMOL for Mac G5, with Demos

2003-09-07 Thread Warren L. DeLano
 sponsor of the PyMOL
project, but they have taken steps to promote PyMOL on Macintosh by
providing early access to hardware, exposure, and limited developer
assistance.

DISCLIAMER to the DISCLAIMER:  So what?  We're not afraid to
criticize Apple.  Apart from the iPod, the dual 2 Ghz G5 PowerMac is the
ONLY system we recommend you purchase from the company at this time.
Their laptops, cluster nodes, single-processor G5s, and mid-range G4
systems are arguably still behind the competition, even after taking OS
X's advantages into account.   I'm no Mac-addict, but I do like to
recognize and celebrate a good product when I see one.  The dual 2 Ghz
G5 running Mac OS X is a killer desktop computer for research --
Apple's first in a long time, and hopefully more will come if we
appropriately reward this one with our business.

Cheers,
Warren

--
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Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC






RE: [PyMOL] adding a new external GUI

2003-09-07 Thread Warren L. DeLano
Tina,

You don't want to create a new thread -- Tcl/tk can only support
a single thread.  Instead, you either need to wholly replace the
external GUI with your GUI, or you simply need to make your gui work
with the standard external GUI.  The latter is generally done by adding
your own menu, which then creates it's own window in response to user
requests.

Cheers,
Warren


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

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Tina Li
 Sent: Friday, September 05, 2003 11:49 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] adding a new external GUI
 
 Hello,
 
 I'm trying to add another external GUI to be positioned at the bottom
of
 the
 structure window for displaying sequence alignments, with not much
luck.
 Here
 is what I want and what I've done:
 
 Goal: when opening a sequence alignment file in the existing GUI,
launch a
 new
 GUI at the bottom displaying the alignments. So:
 
 - in \modules\pmg_tk, add a new class alignApp that inherits from
 AbstractApp
 (very similar to PMGApp for the exsting GUI), which adds widgets to
the
 new
 GUI and will parse files, etc..
 
 - in \modules\pmg_tk\startup, add startNewGUI.py, whose __init__()
adds an
 additional file open option (all files in this directory are
__init__'d
 upon
 startup of the existing GUI) to the existing GUI's File menu:
 
 ---
 from pmg_tk.alignApp import *
 
 def run_alignApp():
 if not hasattr(sys,argv):
   sys.argv=[pymol]
 alignApp(balloon_state='both').run()
 
 def alignment_open(self):
   ofile = askopenfilename(initialdir = self.initialdir,
   filetypes=[(XML File,*.xml),
  (All Files,*.*),
  (All Files,*),])
   if len(ofile):
  self.initialdir = re.sub(r[^\/\\]*$,,ofile)
  t_alignApp = threading.Thread(target=run_alignApp,args=())
  t_alignApp.setDaemon(1)
  t_alignApp.start()
 
 def __init__(self):
   self.menuBar.addmenuitem('File', 'command', 'Open alignment
file.',
 label=self.pad+'Open alignments',
 command=lambda s=self:alignment_open(s))
 ---
 
 The result: the new GUI appears as a one-piece small square frame
(1/6
 the
 width of the existing). No menu, output area or other widgets is
shown.
 After
 clicking in either GUI, the cursor turns busy, and both GUIs turn
 non-responding.
 
 I'm not sure if it's a Python thread problem on my part. Has anyone
done
 something similar before? Let me know if it's more appropriate to ask
in a
 Python newsgroup.
 
 Thanks much!
 
 Tina
 
 
 
 
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RE: [PyMOL] Filled view for deoxyribose rings, bases in DNA ???

2003-09-07 Thread Warren L. DeLano
Raji,

Sorry, PyMOL can't do that yet.  However, since you are probably
the 10th person to ask for this, so it has become high priority for a
future version...

Cheers,
Warren

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

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of raji
 Sent: Saturday, September 06, 2003 7:34 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Filled view for deoxyribose rings, bases in DNA ???
 
 Hi Everyone,
 How can I show the deoxyribose sugar and the bases in the DNA in the
stick
 mode but as filled representations ?
 Thanks,
 Raji
 
 Raji Edayathumangalam
 Dept. of Biochemistry  Molecular Biology
 Colorado State University
 Fort Collins, CO 80523 USA
 Tel:(970)491-4614
 Fax:(970)491-0494
 
 
 
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RE: [PyMOL] Re: cannot find _cmd module

2003-08-27 Thread Warren L. DeLano
Tina,

Did you do a full installation?  After running:

python setup.py build install
python setup2.py 

(in that order)

pymol.bat should just work.  There shouldn't be any need to copy
anything over, nor should you set PYMOL_PATH -- that is all taken care
of automatically with this approach.  

Cheers,
Warren


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

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Tina Li
 Sent: Wednesday, August 27, 2003 8:34 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Re: cannot find _cmd module
 
 Hello,
 
 So I figured that in my $PYMOL_PATH\build\lib.win32-2.2\pymol, there
is a
 _cmd.pyd that's missing in $PYMOL_PATH\modules\pymol. I copied it
over,
 and
 PyMOL started up, but said that it failed to import the xray module,
which
 however exists in $PYMOL_PATH\modules\pymol, so I don't understand why
it
 doesn't import that. Anyways, it seems to be up. I guess every time I
 build
 PyMOL, I'll have to copy the _cmd.pyd file over.
 
 Tina
 
 - Original Message -
 | From: Tina Li t...@bioinformaticssolutions.com
 | To: pymol-users@lists.sourceforge.net
 | Date: Mon, 25 Aug 2003 11:57:27 -0400
 | Subject: [PyMOL] cannot find _cmd module
 |
 | Hello,
 |
 | Eh, I think this is a rather basic question. So I built PyMOL on
Win32,
 tried
 | to run pymol.bat, which calls python
 $PYMOL_PATH/modules/pymol/__init__.py,
 | which complained:
 |
 | Traceback (most recent call last):
 |   File D:\thli\root\misc\pymol-0.90\modules\pymol\__init__.py,
line
 92, in
 ?
 | import pymol
 |   File D:\thli\root\misc\pymol-0.90\modules\pymol\__init__.py,
line
 300,
 in
 | ?
 | import _cmd
 | ImportError: No module named _cmd
 |
 | I have PYTHONPATH set to $PYMOL_PATH/modules. Is it something
obvious
 I'm
 | missing?
 |
 | Thanks much!
 |
 | Tina
 
 
 
 
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RE: [PyMOL] Python commands and variables

2003-08-27 Thread Warren L. DeLano
Yes, but you need to write in Python directly.  For example:

from pymol import cmd
cmd.select(mysel,none)
for i in range(10,20): cmd.select(mysel,mysel or resi %d%i)

Would work in a .py file.

Cheers,
Warren

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DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Shu-Hsien Sheu
 Sent: Wednesday, August 27, 2003 1:10 PM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Python commands and variables
 
 Hi,
 
 I am new to Pymol with some experiences with Python.
 I have a basic question which maybe a little stupid.
 Does Pymal take Python commands in selecting atoms?
 For instance:
 
 i = range(1, 299)
 select resi i
 
 or, further:
 for i in range(1, 299)
 select  resi i
 
 I understand the above can be easily done with:
 select resi 1-288
 
 However, I am wondering if variables can work in Pymol in general.
 
 Thanks!
 
 
 
 
 
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RE: [PyMOL] linker errors on win32?

2003-08-22 Thread Warren L. DeLano
Tina,

layer0/MemoryCache.c is missing from the list of sources in
the setup.py file.  If you add that in right after the
layer0/MemoryDebug.c, it should build.

Sorry about that!

Cheers,
Warren


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

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Tina Li
 Sent: Friday, August 22, 2003 10:31 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] linker errors on win32?
 
 Hello,
 
 I was following instructions in setup/INSTALL.win32 (as in pymol-0_90-
 src.tgz)
 to build PyMOL. I have all the external components (glut, zlib,
libpng) in
 place. When I tried
 
 python setup.py build
 
 It generated linker errors:
 
 C:\Program Files\Microsoft Visual Studio\VC98\BIN\link.exe /DLL
/nologo
 /INCREME
 NTAL:NO /LIBPATH:win32/lib /LIBPATH:C:\Python22\libs opengl32.lib
 glu32.lib
 glut
 32.lib libpng.lib zlib.lib /EXPORT:init_cmd
 build\temp.win32-2.2\Release\Block.o [...more .obj here...]
 ...
Creating library build\temp.win32-2.2\Release\_cmd.lib and object
 build\temp.win32-2.2\Release\_cmd.exp
 Map.obj : error LNK2001: unresolved external symbol _MemoryCacheFree
 MemoryDebug.obj : error LNK2001: unresolved external symbol
 _MemoryCacheFree
 Basis.obj : error LNK2001: unresolved external symbol _MemoryCacheFree
 Ray.obj : error LNK2001: unresolved external symbol _MemoryCacheFree
 Map.obj : error LNK2001: unresolved external symbol _MemoryCacheMalloc
 MemoryDebug.obj : error LNK2001: unresolved external symbol
 _MemoryCacheMalloc
 Basis.obj : error LNK2001: unresolved external symbol
_MemoryCacheMalloc
 Ray.obj : error LNK2001: unresolved external symbol _MemoryCacheMalloc
 Map.obj : error LNK2001: unresolved external symbol _MemoryCacheCalloc
 MemoryDebug.obj : error LNK2001: unresolved external symbol
 _MemoryCacheRealloc
 main.obj : error LNK2001: unresolved external symbol _MemoryCacheDone
 main.obj : error LNK2001: unresolved external symbol _MemoryCacheInit
 build\lib.win32-2.2\pymol\_cmd.pyd : fatal error LNK1120: 6 unresolved
 externals
 
 error: command 'C:\Program Files\Microsoft Visual
 Studio\VC98\BIN\link.exe'
 failed with exit status 1120
 
 I wonder if I'm missing a particular library.
 
 
 Thanks much,
 
 Tina
 
 
 
 
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[PyMOL] RE: E-mail worm is going around

2003-08-21 Thread Warren L. DeLano
Jan,

Thanks for that -- copy hereby sent to the PyMOL list.  This is
a relief.  I was wondering why strange bounced email was coming back and
had become concerned that infection had occurred here despite every
precaution. 
SMTP-based email is indeed a hopeless cause.  I vote for a
return to smoke signals and semaphores.

- Warren

Summary:

The current viruses add a bogus From field, so don't get upset
at the person who seemed to have sent that infected email to you since
it wasn't really them.  They are not infected -- someone else is.  

 -Original Message-
 From: Computational Chemistry List [mailto:chemistry-requ...@ccl.net]
On
 Behalf Of Dr. Jan K Labanowski
 Sent: Thursday, August 21, 2003 9:50 AM
 To: chemis...@ccl.net
 Cc: Dr. Jan K Labanowski
 Subject: CCL:E-mail worm is going around
 
 Dear CCL,
 
 Since I got few a questions, I will post an answer to the whole list
to
 cool you down...
 
 There is a malicious Internet worm going on, which infects the (guess
 what...)
 Windows machines. It is an e-mail message which carries a virus with
it
 (so it is about 100kB large to be able to pack the virus executable).
 It grabs addresses from the victim address book, and resends itself
 to these addresses, and to make things worse, it also changes its
From:
 (i.e., the address from which the message is supposedly coming from)
 to some address from the victim's address book. Of course, according
to
 the old saying: The worse, the better Microsoft will sell us
 upgraders, and improved products, and scoop millions of dollars in
 consulting hours from people who use their maintainance program.
 Hopefully events like this will revive economy and create new job
 opportunities.
 
 Obviously, the chemis...@ccl.net is in many people address books, as
well
 as,
 my personal address. Many of you got the mail which is supposedly
coming
 from, say, chemis...@ccl.net, but it really did not come from this
 address.
 
 If you want to know more about this malice, read on... The e-mail
message
 consist of header and body. The header should contain the information
 about
 intended recipients, message origin, path which message traveled
 (gateways)
 before it got to you and the information about the type and methods of
 encoding used for the body of the message. The message body is the
actual
 pay-load of the e-mail message). But make no mistake... Header is not
the
 envelope of your mail. It is not used by mail software (mail transfer
 agent - MTA) to deliver your mail. Header has only an informational
 (or lately often dis-informational) value.
 
 The problem is that you can put anything you want in the header
(beside
 maybe the top Received: header line, which is usually added by your
own
 computer or mail gateway). The top Received: line (depending on the
way
 your
 mail is configured) contains the information about the IP address of
the
 machine which had sent you the the message, and the destination of the
 message
 (i.e., in most cases it lists your own machine and sometimes your user
id,
 or
 mail alias). However, beside the first Received: line (or maybe more,
if
 the mail was traveling to you via some trusted gateways as each
legitimate
 MTA should add its Received: line to the header -- SHOULD, but DOES
NOT
 HAVE TO!!!), all other header lines can be set by the mail originators
to
 anything they want. Most importantly: the To:, From:, Cc: do not have
to
 be
 real, and THESE FIELDS ARE NOT USED IN DELIVERING THE MESSAGE !!!.
 
 To be more precise, if you use a legitimate mail composing program,
 the destination of your mail message will be taken from the To: and/or
 Cc: lines, and the From: line will point to you, when your
 message is passed to your own mail transfer agent. BUT THE BAD GUYS
 DO NOT USE STANDARD AND LEGITIMATE MAIL COMPOSERS AND TRANSFER
AGENTS!!!
 Note that the mail is delivered to your mail server by a special
protocol
 (SMTP), where the recipient's and originator's address is given to
your
 local
 mail server as a part of delivery process, and THEY DO NOT HAVE TO BE
EVEN
 CLOSE to what is being given on the To: and From: lines of your
message.
 
 At the same time, what is displayed in your e-mail browsing tool as
 message
 origin, is the From: line from header. CURRENTLY, THERE IS NO WAY TO
 ESTABLISH
 THE IDENTITY OF THE PERSON WHO HAD SENT MAIL TO YOU!!! The only thing
 which
 can be (in most cases!!!, not always!!!) established is the IP address
 of the machine which forwarded you the message (this can be guessed
from
 inspecting the top Received: line of the header). In most cases the IP
 address
 of the originating machine is a TOTALLY USELESS information, since it
 gives
 you the pointer to the machine which was:
 
1)  either hacked by spammers,
2)  or infected by the virus (i.e., a victim like you),
3)  or represents an open relay machine (made an open relay either
intentionally or not)
 
 We badly need a new electronic 

RE: [PyMOL] Pymol 3D printing

2003-08-21 Thread Warren L. DeLano
Thanks for your code!

 P.S. I wish this mailing list had archives ...

But it does!

http://sourceforge.net/mailarchive/forum.php?forum_id=60

You can search by keyword.  Look for the text box upper-left.

Cheers,
Warren





RE: [PyMOL] Different symmetry positions

2003-08-19 Thread Warren L. DeLano
Alex,

Symexp creates object with names of the form:

prefixSSXXYYZZ

After the prefix, the first two digits SS are the symmetry
operation.  The next six digits correspond to the relative integral unit
cell translation XXYYZZ *after* an initial unit cell translation
intended to bring the translated atoms back into closest adjacency. 

In other words, the exact XXYYZZ will depend on the atoms in the
object, since that will determine the initial origin 00
translation.  Nevertheless, the actual symmetry mates displayed should
be equivalent, even if their names differ slightly.

Are you finding otherwise?

Cheers,
Warren


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

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Alexander Zuev
 Sent: Tuesday, August 19, 2003 2:43 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Different symmetry positions
 
 Dear  All,
 
 I have two pdb files: 1) protein trp and
 2) the same protein with crystallographic water - tr.
 After creating symmetry related objects with
   symexp sp=trp,(trp),3.2
 and
   symexp s=tr,(tr),3.2
 the corresponding objects have different symmetry operations, for
 example,
 sp0201 corresponds s0200.
 Could you explain please, what this does mean?
 
 Thanks in advance,
 
 Alexander Zuev
 
 
 
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RE: [PyMOL] Delete Bonds

2003-08-18 Thread Warren L. DeLano
Jose,

Select the bond using Ctrl-right-click, then either unbond
pk1,pk2 or hit Ctrl-D.

Cheers,
Warren


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Voice (650)-346-1154 
Fax   (650)-593-4020

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Jose Avalos
 Sent: Monday, August 18, 2003 6:45 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Delete Bonds
 
 Hi
 
 I would like to know how can I break bonds that are wrongly drawn in
 pymol. I am only using a coordinate file with no connectivities. I
know
 how to select the bond, but then I don't know how to delete the bond
 without deleting other correct bonds that involve one of the atoms in
the
 incorrect bond.
 
 Thank you in advance
 
 Jose
 
 
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RE: [PyMOL] strand representation + free label

2003-08-14 Thread Warren L. DeLano
Tina,

That would be very difficult to do at present...I'll take this
as a suggestion for a future version.

Cheers,
Warren


--
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Warren L. DeLano, Ph.D.
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DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Tina Li
 Sent: Thursday, August 14, 2003 8:19 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] strand representation + free label
 
 Hello,
 
 I'm wondering if it's possible to simulate RasMol-styled strand
 representation (a number of smooth curves that run parallel to one
another
 along the peptide plane of each residue). I would like something like
that
 to
 repersent gaps in a structural alignment (i.e. a segment that doesn't
 exist
 in an approximated structure). Currently I'm using the dash lines as
for
 bonds. However, is there a way to change the distance label into
something
 I
 can specify, like 7 AA to indicate the gap length?
 
 
 Thanks,
 
 Tina
 
 
 
 
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RE: [PyMOL] cartoons through nonstandard residues

2003-08-06 Thread Warren L. DeLano
David,

You found a bug -- it turns out PyMOL was getting confused by
the presence of a P atom in P-tyr.  It thought the residue contained
both protein and DNA, and so the cartoon had an extra gap.

The following workaround should get you a complete cartoon with 1fmk.
Future versions of PyMOL should not suffer from this problem.

alter all.type='ATOM'
alter name P,name='P1'
sort

Thanks for your help in quashing that bug!

Cheers,
Warren

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

 -Original Message-
 From: David A. Horita [mailto:dhor...@wfubmc.edu]
 Sent: Wednesday, August 06, 2003 5:27 AM
 To: Warren L. DeLano
 Subject: RE: [PyMOL] cartoons through nonstandard residues
 
 Warren,
 Thanks for the reply, but I still don't get the cartoon running
through
 the phosphotyrosine.  I've tried it on Src (1fmk.pdb), and still get a
 break between residues Gln526, Ptr 527 and Gln 528.
 Regards,
 David Horita
 
  -Original Message-
  From: Warren L. DeLano [mailto:war...@delanoscientific.com]
  Sent: Tuesday, August 05, 2003 7:17 PM
  To: David A. Horita; pymol-users@lists.sourceforge.net
  Subject: RE: [PyMOL] cartoons through nonstandard residues
 
 
  David,
 
  The problem: PyMOL sorts PDB hetatms apart from molecules.  The
  solution:
 
  alter all, type='ATOM'
  sort
  rebuild
 
  I'm thinking about disabling this behavior before the next
release...
 
  Cheers,
  Warren
 
  --
  mailto:war...@delanoscientific.com
  Warren L. DeLano, Ph.D.
  Principal Scientist
  DeLano Scientific LLC
  Voice (650)-346-1154
  Fax   (650)-593-4020
  -Original Message-
  From: pymol-users-ad...@lists.sourceforge.net
  [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
  David A. Horita
  Sent: Tuesday, August 05, 2003 1:53 PM
  To: pymol-users@lists.sourceforge.net
  Subject: [PyMOL] cartoons through nonstandard residues
 
  Hi,
  When I try to draw a cartoon through the backbone of a
  nonstandard residue (in this case, phosphotyrosine), the
  cartoon strand stops prior to the PTR and starts after.  How
  do I get a continuous strand through the phosphotyrosine
  backbone (or other residues, in the general case)?
  Ribbons seem to go through the PTR without problem, and
  selenomets don't seem to cause trouble, either. Thanks, David Horita
  -
  David A. Horita, Ph.D.
  Department of Biochemistry
  Wake Forest University School of Medicine
  Winston-Salem, NC 27157-1016
  Tel: 336 713-4194
  Fax: 336 716-7671
  email:  dhor...@wfubmc.edu
  web:  http://www.wfubmc.edu/biochem/faculty/Horita/
 
 
 




RE: [PyMOL] electrostatic potential ramp

2003-08-06 Thread Warren L. DeLano
If I understand the question correctly, the answer is

disable ramp-name

Cheers,
Warren

 Hello:
 
 Is there anyway to remove the colour ramp from an electrostatic
potential
 figure via a script (help hide doesn't list anything reasonable for
this
 and there is nothing that I can see in the settings).
 
 Cheers,
 JTM
 





RE: [PyMOL] cartoons through nonstandard residues

2003-08-05 Thread Warren L. DeLano
David,
 
The problem: PyMOL sorts PDB hetatms apart from molecules.  The
solution:
 
alter all, type='ATOM'
sort
rebuild
 
I'm thinking about disabling this behavior before the next release.
 
Cheers,
Warren
 
--
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Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax   (650)-593-4020 
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of David A.
Horita
Sent: Tuesday, August 05, 2003 1:53 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] cartoons through nonstandard residues
 
Hi,
When I try to draw a cartoon through the backbone of a nonstandard
residue (in this case, phosphotyrosine), the cartoon strand stops prior
to the PTR and starts after.  How do I get a continuous strand through
the phosphotyrosine backbone (or other residues, in the general case)?
Ribbons seem to go through the PTR without problem, and selenomets don't
seem to cause trouble, either.
Thanks,
David Horita
- 
David A. Horita, Ph.D.
Department of Biochemistry
Wake Forest University School of Medicine
Winston-Salem, NC 27157-1016 
Tel: 336 713-4194
Fax: 336 716-7671 
email:  dhor...@wfubmc.edu
web:  http://www.wfubmc.edu/biochem/faculty/Horita/
 


RE: [PyMOL] cartoons through nonstandard residues

2003-08-05 Thread Warren L. DeLano
David,

The problem: PyMOL sorts PDB hetatms apart from molecules.  The
solution:

alter all, type=’ATOM’
sort
rebuild

I’m thinking about disabling this behavior before the next release…
 
Cheers,
Warren

--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax   (650)-593-4020 
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of David A.
Horita
Sent: Tuesday, August 05, 2003 1:53 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] cartoons through nonstandard residues

Hi,
When I try to draw a cartoon through the backbone of a nonstandard
residue (in this case, phosphotyrosine), the cartoon strand stops prior
to the PTR and starts after.  How do I get a continuous strand through
the phosphotyrosine backbone (or other residues, in the general case)? 
Ribbons seem to go through the PTR without problem, and selenomets don't
seem to cause trouble, either.
Thanks,
David Horita
- 
David A. Horita, Ph.D.
Department of Biochemistry
Wake Forest University School of Medicine
Winston-Salem, NC 27157-1016 
Tel: 336 713-4194
Fax: 336 716-7671 
email:  dhor...@wfubmc.edu
web:  http://www.wfubmc.edu/biochem/faculty/Horita/
 




[PyMOL] Upcoming Rendering Changes. Comments?

2003-08-04 Thread Warren L. DeLano
PyMOLer's

I've made some changes in the development version which I am
considering for the next release.  However, they will affect existing
scripts, so I am warning people now, and asking for objections (if there
are any).

*** Subject 1:  Ray tracing of lines, dots, mesh, dash, isomesh, ribbon,
and nonbonded representations.

Currently, when you ray, you have to manually adjust the radius of
these objects for optimum quality.  I propose that in version 0.92, that
PyMOL will do this automatically to match the OpenGL image, unless you
explicitly specify otherwise

THIS WILL CHANGE THE OUTPUT OF EXISTING SCRIPTS, but it will be much
easier for users going forward.  PyMOL raytracing will be more WYSIWYG
-- what you see in OpenGL will be closer to what you get when you ray
trace.  

Prior behavior can be restored by setting the radii explicitly to their
original values.

*** Subject 2:  Antialiased rendering

The next version of PyMOL will default to a different antialiasing
algorithm.  

In the past, we're used blanket 2X over-sampling of the complete image.
The next version will focus that extra rendering energy where it counts:
on the edges of objects.  This turn out to be so much faster that I plan
to make it the default (antialias=1).  In most cases, image quality will
improve and rendering times will improve by about 1 to 4-fold for
antialiased images!.  

Blanket 2X, 3X, and 4X oversampling will still be possible using
antialias=2, 3, or 4.   

Prior behavior can be restored by changing two settings
(ray_oversample_cutoff-0 and antialias-0 or 2).

If you have strong objections to these changes, please speak up.

Cheers,
Warren


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Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020





RE: [PyMOL] comprehensive rules for selection-expressions

2003-08-04 Thread Warren L. DeLano
Hi Tina,

Welcome to PyMOL!

 We plan to use PyMOL as the alignment/structure viewer in a protein
 threading package we developed. Mostly there will be some new
 features/enhancements on the existing viewer. e.g.

Great.  That is one of the ways I hope people will make use of
PyMOL.  Do realize however that we're still in early days, and so
don't expect it to be easy.  PyMOL may be inexpensive from a cost
standpoint, but you still need to invest substantial resources in order
to get the most out of it.

 - highlight/color by mappings of amino acid porperties (cysteines,
charge
 and hydrophobicity, size, secondary structure)
 - a sequence alignment pane in sync with the structure window;
selecting
 residues in one selects them in the other
 - show multiple alignments simultaneously
 - permit structural superposition of templates (i.e. structures)

There are all things PYMOL should be capable of doing in tandem with an
external application.

 I'm personally new to PyMOL, and am poking around to explore the
features
 (BTW, excellent graphics!). Right now I'm having difficulty with the
 syntax
 of selection-expressions. I don't see a comprehensive documentation
of
 what counts as selections. Can cysteines already be highlighted? Is
any of
 the mappings already available? On another note, I'm aware of the
 following
 way to color by secondary structures:

The most comprehensive selection docs can be found at:

http://pymol.sourceforge.net/newman/user/S0220commands.html#7

Getting started with commands in another must read

http://pymol.sourceforge.net/newman/user/S0210start_cmds.html#6


 color red, ss h
 color yellow, ss s
 color green, ss l+
 
 which however seems a bit cumbersome. I'd prefer having a Color
by...
 with
 options like secondary structure, charge, size, etc. under the
menu
 item Display. But then, I figure many prefer command lines.

The idea with PyMOL (from a developer/integrators standpoint) is that
you can create the menus which suit the needs of your specific
application.

 These are just some initial random thoughts. BTW, could someone
explain
 what
 the different elems CHNOS* represent? I'd really appreciate more
 comprehensive documentation.

That's just the coloring for Carbon, Hydrogen, Nitrogen, Oxygen, Sulfur,
in the color pop-up menu.

Cheers,
Warren
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RE: [PyMOL] H-bond display

2003-07-18 Thread Warren L. DeLano
Gareth,

CGO is currently the way to go...

Cheers,
Warren


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Voice (650)-346-1154 
Fax   (650)-593-4020

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Gareth Stockwell
 Sent: Friday, July 18, 2003 2:46 AM
 To: pymol-users
 Subject: [PyMOL] H-bond display
 
 
 I am using distance objects at the moment, to display h-bonding
 contacts.  My question is ... is there any easy way to display the
 direction of an h-bond using distances (i.e. putting a little arrow on
 the dashed line)?
 
 I am prepared to bash out some functions which do this using CGOs, but
 of course I won't if it's already implemented!
 
 Gareth
 
 
 --
 Gareth Stockwell gar...@ebi.ac.uk
 European Bioinformatics Institute
 
 
 
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[PyMOL] 0.90 Two Minor Bug Advisories

2003-07-12 Thread Warren L. DeLano
Two bugs to watch out for in version 0.90:

(1) When ray tracing on a light background with antialiasing enabled, a
one pixel wide border may appear.  To workaround this, either crop your
image after saving using something like Photoshop, or simply don't
antialias (just ray with dimensions 2X as large).  Thanks to David
Chimento for finding this one!

(2) Sessions containing isosurface-generated surfaces may not be
saveable due to a Python exception.  There is no workaround for this in
the current version.

Both bugs have been fixed in the development version under CVS.

Cheers,
Warren

PS. Today I also added support for InsightII's ascii/formatted grid file
(just in case anyone has some old Biosym GRD files lying around...).

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Voice (650)-346-1154 
Fax   (650)-593-4020





RE: [PyMOL] Interaction surfaces

2003-07-11 Thread Warren L. DeLano
Joe,

Currently with PyMOL, you are selecting are atoms, not points on
the surface.  Thus, you may need to increase the distance by 1-2 A or so
to get what you want.  It's also possible that something else is going
on.  

I would not expect to see whole at the points of contact, but
between them, where the contacts aren't so close.  If the above advice
doesn't help, then perhaps you could send me an example PNG file which
illustrates the problem as an attachment?

Cheers,
Warren

(PS.  Selection of individual surface points will likely come in a
future version...)

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Fax   (650)-593-4020

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Becker, Joseph W
 Sent: Friday, July 11, 2003 10:45 AM
 To: PyMOL (E-mail)
 Subject: [PyMOL] Interaction surfaces
 
 I have a problem representing the contact surface between, e.g., a
protein
 and its ligand.  The surface is displayed, but it is full of holes,
 apparently at the points of contact.  The script:
 
 load protein.pdb, protein
 load ligand.pdb, ligand
 hide everything
 show surface, (protein and (ligand around 4))
 
 gives something like one wants, but full of holes.
 
 With that object displayed, if one says show surface, protein one
gets
 the
 full surface, without the holes.  Any ideas on how to get the
*partial*
 surface *without* the holes?
 
 Joe Becker
 Merck Research Labs
 
 P.S.
 
 load protein.pdb, protein
 load ligand.pdb, ligand
 hide everything
 create junk, (protein and (ligand around 4))
 show surface, junk
 
 gives a similar (holey) result
 
 
 
 
 


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 privileged, and is intended solely for the use of the individual or
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[PyMOL] New Map Formats Coming...

2003-07-10 Thread Warren L. DeLano
PyMOLers,

In response to user requests, I have added support for BRIX (O maps)
and FLD (AVS Field) map formats in the current development version.  

Are there any other map formats which people would use heavily if PyMOL
were able to support them?  

Thanks,
Warren

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Voice (650)-346-1154 
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RE: [PyMOL] pymol on OSX

2003-07-09 Thread Warren L. DeLano
John,

The native OSX port is incomplete with respect to the user
interface.  You can get the complete package if you use the Fink version
under X11.

PyMOL doesn't export 3D data well at present.  

Cheers,
Warren


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Warren L. DeLano, Ph.D.
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Voice (650)-346-1154 
Fax   (650)-593-4020

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of John Holt
 Sent: Tuesday, July 08, 2003 7:02 PM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] pymol on OSX
 
 I've just started experimenting with Pymol on OS X.  The close, save,
 save as items are greyed out in the file menu.  Could someone explain
 this to me?  Also, is  Pymol capable of saving as vrml files or some
 other 3D format?
 John Holt
 John Holt Studio
 25 Drydock Ave.
 Boston,  MA 02210
 617.426.4658
 617.426.1425 fax
 visiond...@johnholtstudio.com
 www.johnholtstudio.com
 
 
 
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RE: [PyMOL] Electrostatic potential maps in PyMOL

2003-07-09 Thread Warren L. DeLano
Yes, you have identified the problem:  PyMOL 0.90 currently only reads
PHI files in one of the two endian formats (not sure if it is big or
little).  

The problem is, how it PyMOL to determine which format the incoming map
is in?  The file format is so darn implicit, I haven't yet come up with
any effective way of doing it without risking a floating exception on
finicky hardware.  
 
Any ideas?  If we can just determine the enddian-ness of the incoming
file, then the rest is a snap.

Warren

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RE: [PyMOL] ca trace

2003-07-09 Thread Warren L. DeLano
Jason,

In version 0.90, there is a ribbon_trace setting which allows
you to do this for the ribbon representation.  In versions 0.91+, I've
added the same thing for cartoons cartoon_trace.

Cheers,
Warren


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Voice (650)-346-1154 
Fax   (650)-593-4020

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Jason Thomas Maynes
 Sent: Wednesday, July 09, 2003 10:30 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] ca trace
 
 Hello:
 
 I think this was asked before but the list archives are down:
 
 If I have a pdb of Ca's only, is there a way to trace through them
without
 iteratively bonding them all (change allowed bond distance??)
 
 Can the tube cartoon recognize this?  If I bond all the Ca together
 iteratively, the cartoon tube doesn't recognize that and go through
the
 bonds, is there another way?
 
 Cheers,
 JTM
 
 We can be sure that if a detailed understanding of the molecular
basis of
 chemo-therapeutic activity were to be obtained, the advance of
medicine
 would be greatly accelerated.
 
 Linus Pauling, Nobel Laureate 1954
 
 ...everything that living things do can be understood in terms of the
 jigglings and wigglings of atoms.
 
 Richard Feynman
 
 *
 Jason Thomas Maynes
 PhD/MD Program
 Department of Biochemistry
 Faculty of Medicine
 University of Alberta
 ja...@biochem.ualberta.ca
 *
 
 
 
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[PyMOL] RE: (no subject)

2003-07-08 Thread Warren L. DeLano
 I just download PYMOL into my Linux and it's working very nicely but I
 want to check
 whether it is possible to move a pdb file within a 3D density map
 independently to get a
 best fitting.

Yes, you can move the molecule, but not the map.

First, get into editing mode:

edit_mode  

(or select 3 Button Editing Mode from the Mouse menu, if you have one)

Then, to move the whole molecule:

shift-middle-click-and-drag on the molecule to translate
shift-left-click-and-drag on the molecule to rotate 
ctrl-shift-middle-click on an atom to reset origin of rotation

To rotate bonds,

Ctrl-right-click-and-drag.  Always click on the mobile side of the
bond, otherwise, you'll end up moving the wrong portion of the molecule.

To write out the new coordinates...

save file.pdb, object-name 

NOTE: some of the above is specific to version 0.90, so make sure that's
the version you have.

Cheers,
Warren






RE: [PyMOL] Further functionality

2003-07-08 Thread Warren L. DeLano
 1- calculation of surface potentials- will this be coming soon?

Creation of a Possion-Boltzman solver is a bit of work, so this will not
happen very soon -- probably not until we accumulate enough sponsorship
to contract with someone to perform the task.  But perhaps someone might
volunteer to write an open-source Python PB module in the meantime?
[sounds like a good summer project for a graduate student in
computational chemistry : )]

In the meantime, I recommend using Grasp to calculate the potential,
saving the potential as a .phi file, and then loading the potential
into PyMOL for visualization.  Delphi should work too in theory, but
we're currently working to resolve a few problems with the approach...

 2- Are you thinking of including any kind of sequence viewer and 
 sequence alignment tools to tie in with the fitting - as seen with 
 swissPDB? This would be verh high on my wishlist.

It is high on my list as well.

 3- Will you be including any more NMR biased features like a quick 
 fitting and RMSD calculation for ensembles of structures?

This is currently possible using intra_fit if the ensemble is loaded
as a single object.  Between objects, you can do pair-wise fits using
fit or align, but that gets tedious with a lot of structures.  The
sequence viewer will hopefully make multi-object fitting easier.

 4- Is there any chance you will be able to include non-continuous 
 selections ie select (resi 10-20,30-40) rather than just 10-20 and 
 ignore residues 30-40?

This is already possible using the selection macros:

   10-20,30-40/

which is equivalent to

   resi 10-20 or resi 30-40

Please see the new Command Syntax and Atom Selections chapter in the
User's Manual for more information on selections.

http://pymol.sourceforge.net/newman/user/S0220commands.html#7

Cheers,
Warren





RE: [PyMOL] can't initialize module sglite

2003-07-07 Thread Warren L. DeLano
Yu Chen,

There are two likely causes of this problem:

(1) An old pymol.com file

This may be caused by use of an outdated pymol.com startup
script.  The launch requirements for PyMOL changed slightly in this new
version, so it may be necessary to create a fresh pymol.com from one
of the templates in the setup directory.

(2) Linking against Python 1.52

Make sure that Python is linking against version 2.x if
possible.  If you must use 1.52, you will need to compile the older
versions of ExtensionClass.c and ExtensionClass.h located in the
contrib/modules directory.

I hope this helps.

Cheers,
Warren

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Warren L. DeLano, Ph.D.
Principal Scientist
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Voice (650)-346-1154 
Fax   (650)-593-4020

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Yu Chen
 Sent: Monday, July 07, 2003 12:34 PM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] can't initialize module sglite
 
 Hello, pymolers
 
 I installed pymol-0.90 from tar file on Redhat Linux 7.2 the same way
as I
 installed pymol-0.88, the compiling all went well. But when running
pymol,
 it gives out:
 Fatal error: can't initialize module sglite
 
 Not sure what happened, any help would be appreciated!
 
 Thanks in advance!
 Yu
 
 
 ===
 Yu Chen
 Howard Hughes Medical Institute
 Chemistry Building, Rm 122
 University of Maryland at Baltimore County
 1000 Hilltop Circle
 Baltimore, MD 21250
 
 phone:(410)455-6347
   (410)455-2718
 fax:  (410)455-1174
 email:c...@hhmi.umbc.edu
 ===
 
 
 
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RE: [PyMOL] stereo parameters?

2003-07-03 Thread Warren L. DeLano
Dirk,

stereo_angle is the amount of toe-in 

stereo_shift is the horizontal displacement of the camera 

Initially, stereo_angle=2.1 and stereo_shift=2.0

Generally, you don't need to adjust stereo_angle very much.
Stereo_shift is what you want to focus on.  Try increasing it by 1 or 2.

   For hardware or cross-eye,

  set stereo_shift, 4

   For walleye,

  set stereo_angle, 1.95
  set stereo_shift, 4

Cheers,
Warren



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 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
 ad...@lists.sourceforge.net] On Behalf Of Dirk Kostrewa
 Sent: Thursday, July 03, 2003 4:06 AM
 To: PyMOLBB
 Subject: [PyMOL] stereo parameters?
 
 Dear PyMol users,
 
 my subjective stereo impression with pymol in window stereo mode is
too
 flat, both on SGI and on Linux, at least when I compare it with my
~10
 years or so experience using other applications. I started to fiddle
 around
 with the stereo parameters stereo_angle and stereo_shift, but the
 results
 were not as expected from the presumed meaning for these parameters.
Could
 anyone (maybe Warren?) please explain to me what the exact meaning of
 these
 two parameters IN PYMOL is? If I will find a subjectively better set
of
 parameters I will post them as a suggestion on this board, then.
 
 Best regards,
 
 Dirk.
 
 --
 
 
 Dirk Kostrewa
 Paul Scherrer Institut
 Life Sciences, OSRA/007
 CH-5232 Villigen PSI, Switzerland
 E-mail: dirk.kostr...@psi.ch
 Phone: +41-56-310-4722
 Fax: +41-56-310-4556
 WWW: http://www.sb.psi.ch
 
 
 
 
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