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

--
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
 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] Pymol batch question

2003-12-10 Thread Torin Huzil

I have a quick question regarding pymol and batch files.
First, I am using pymol to render images of a membrane simulation that uses 
point particles, as opposed to molecules.


My problem arises when making movies of the simulation.  My computer 
(either mac or PC) will not allow pymol to handle the large number of 
points in the simulation to render more than 1 or 2 frames (the simulation 
currently has 25,000 particles in it).  So I have been ray tracing each 
frame individually and saving the png files.


I currently have a script that does everything as far as set up, ray 
tracing and saving.  but I still need to load each pdb file (represents an 
iteration of the simulation) into pymol and execute the script.


I have a folder with, say, 3000 pdb files in it.  I would like to have 
pymol open the first file, run the script and save the image as the 
original file name, then open the second file and do the same thing  
3000 times.  It would be preferable to run this without the GUI.


Any help would be greatly appreciated.

---
Dr. Torin Huzil

Department of Physics
444 Avadh Bhatia Physics Laboratory
University of Alberta
Edmonton, Alberta
Canada
T6G 2J1

Office: (780) 492-1064
Cell:   (780)721-7222
email:  j...@scibuzz.com



[PyMOL] pymol 0.93, fink source compile issues (os x)

2003-12-10 Thread Douglas Kojetin

Hi All-

It's be over a month since pymol 0.93 has been released ... anyone know 
when a Fink distribution will be available?  Or how to do it manually 
(using Fink, without the main/online Fink database knowing about it)?


I tried compiling the source manually, but I got an error similar to 
the following error previously reported here:


http://sourceforge.net/mailarchive/message.php?msg_id=6454630

Many thanks,
Doug




RE: [PyMOL] Pymol batch question

2003-12-10 Thread Lind, Kenneth
It is probably easiest to do this with a python script.  Example render.py 
script:

from pymol import cmd
import glob

files = glob.glob(*.pdb)
for f in files:
cmd.load(f, tmp)
cmd.show(sticks, tmp) ## or whatever you display, color, etc.
cmd.ray(320,240)  ## or a different size
cmd.png(f+.png) ## or a different filename/location
cmd.delete(tmp)


Then run pymol as 'pymol -c render.py'  (-c option is for command mode... no 
gui)

Hope this helps.
Ken
---
Kenneth E. Lind, Ph.D.
Scientist, Computational Chemistry
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
South San Francisco, CA 94080
(650) 266-3662 



-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net]on Behalf Of Torin Huzil
Sent: Wednesday, December 10, 2003 4:09 PM
To: pymol
Subject: [PyMOL] Pymol batch question


I have a quick question regarding pymol and batch files.
First, I am using pymol to render images of a membrane simulation that uses 
point particles, as opposed to molecules.

My problem arises when making movies of the simulation.  My computer 
(either mac or PC) will not allow pymol to handle the large number of 
points in the simulation to render more than 1 or 2 frames (the simulation 
currently has 25,000 particles in it).  So I have been ray tracing each 
frame individually and saving the png files.

I currently have a script that does everything as far as set up, ray 
tracing and saving.  but I still need to load each pdb file (represents an 
iteration of the simulation) into pymol and execute the script.

I have a folder with, say, 3000 pdb files in it.  I would like to have 
pymol open the first file, run the script and save the image as the 
original file name, then open the second file and do the same thing  
3000 times.  It would be preferable to run this without the GUI.

Any help would be greatly appreciated.

---
Dr. Torin Huzil

Department of Physics
444 Avadh Bhatia Physics Laboratory
University of Alberta
Edmonton, Alberta
Canada
T6G 2J1

Office: (780) 492-1064
Cell:   (780)721-7222
email:  j...@scibuzz.com


---
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Does SourceForge.net help you be more productive?  Does it
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YOU!  Click Here: http://sourceforge.net/donate/
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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

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