RE: [PyMOL] Re:Wiki Brain Storming
I think a wiki to collect various PyMOL wisdom would be great. We have been using wikis internally for various project and they are very handy. A few thoughts/experiences: - a plan for the organization (especially upfront) is very important. Once it gets going, it will grow organically. Having a master plan will help with the growth. - require people to register if they want to edit pages. Makes people more responsible, could help with spam, gives users a contact for further info. - MoinMoin (our choice), is very simple, python based, and has nice markup for python code. - some examples: * wikipedia (the mother of all wikis... just an example - http://en.wikipedia.org/wiki/Main_Page), * wxPyWiki (wxPython... more along the lines of what we might want - http://wiki.wxpython.org/) Cheers, Ken -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net]on Behalf Of D. Joe Anderson Sent: Thursday, February 10, 2005 6:55 AM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Re:Wiki Brain Storming On Tue, Feb 08, 2005 at 09:36:29AM +, Kristian Rother wrote: On Tuesday 08 February 2005 01:44, Warren DeLano wrote: Say, what do people think about the idea of creating a PyMOL Wiki to hold nuggets of information like this? Or is there a better alternative to Wiki now available? As i have been maintaining sort of PyMOL FAQ for some time, i would definitely like a Wiki, too. Simply because it would take less time for me to update a Wiki rather than HTML pages. Thus, i strongly encourage setting up a Wiki, and i would like to transfer all the answers i have collected there. If anyone is wondering what i'm talking about, look at http://www.rubor.de/bioinf/pymol_tips.html I agree, a wiki could make that trove much easier to maintain, certainly to share out some of the maintenance. I know Wiki's that suffer or starve from inactivity, but i never heard of one that got unusable because malevolent users permanently put *graffitti* on the pages. Permanently? Probably not. But that may be because the better known wikis are the active ones. The active ones get attention from enough legitimately-interested folks to keep reverting back to topical content when graffiti gets added. More problematic has been the rise of wiki spambots, which have been ravaging some of the low-volume wikis I run for myself. I need to upgrade these to one of the newer versions of the wiki engine I use, which include several different features which protect against this type of spamming. However, a good Wiki needs to be structured beforehand, rather than having everything grow by itself. Users will add things where aproppriate, anyway. Thus, in a heavily used Wiki its definitely easy to get lost. Agreed. To have a better shot at success, a wiki needs to be seeded with some initial content, and some initial stylistic conventions (free links vs CamelCase wiki names, for instance) should be set down. -- D. Joe Anderson, Asst. Sci.2252 Molecular Biology Bldg Biochem, Biophys, Mol Bio Iowa State Univ, Ames, IA 50010 Configuring Mail Clients to Send Plain ASCII Text http://expita.com/nomime.html --- SF email is sponsored by - The IT Product Guide Read honest candid reviews on hundreds of IT Products from real users. Discover which products truly live up to the hype. Start reading now. http://ads.osdn.com/?ad_id=6595alloc_id=14396op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] picking atoms with latest version (0.95)
The lb and rb selections have changed in version 0.95. Looks like the new way to do this is with pk1 and pk2. Use ctrl-middle-click, or double-right-click to pick each atom. The first atom you pick will be pk1, the second will be pk2, etc. (up to pk4). You can then use ctrl-x to get the distance between pk1 and pk2, or ctrl-t to create a bond (or use the 'dist' or 'bond' commands). Ken -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net]on Behalf Of Carina Lobley Sent: Tuesday, April 13, 2004 12:51 AM To: Eksterowicz, John Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] picking atoms with latest version (0.95) Hi, I had that problem this weekend too. I've found that ctrl right click picks one atom and shift right double click picks a second atom. That seems to work for the 'dist' and 'bond' commands anyway! Regards, Carina On Mon, 12 Apr 2004, Eksterowicz, John wrote: I am using the latest version of Pymol and I cannot figure out how to pick more than one atom. In the past, ctrl-shft lb, picked the first atom, and ctrl-shft rb would pick a second atom. But now, ctrl-shft rb brings up a pop-up menu. Any help would be appreciated. Thanks, John John Eksterowicz Celera Genomics --- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id=1470alloc_id=3638op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Another question
Avram, You use the sphere_scale setting: i.e. set sphere_scale, 0.2 Best, Ken -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 12:40 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Another question Hi all, another question. Does anyone know how to make spheres smaller. I would like to make the ball and stick looking residues like those in Molscript thank you 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 --- This SF.net email is sponsored by: IBM Linux Tutorials. Become an expert in LINUX or just sharpen your skills. Sign up for IBM's Free Linux Tutorials. Learn everything from the bash shell to sys admin. Click now! http://ads.osdn.com/?ad_id=1278alloc_id=3371op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
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
