RE: [PyMOL] electron density settings
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 --- This SF.net email is sponsored by: SF.net Giveback Program. Does SourceForge.net help you be more productive? Does it help you create better code? SHARE THE LOVE, and help us help YOU! Click Here: http://sourceforge.net/donate/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[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
[PyMOL] pymol 0.93, fink source compile issues (os x)
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
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 --- This SF.net email is sponsored by: SF.net Giveback Program. Does SourceForge.net help you be more productive? Does it help you create better code? SHARE THE LOVE, and help us help YOU! Click Here: http://sourceforge.net/donate/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] DeLano Scientific Downtime (Dec. 22-Jan 7)
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