[PyMOL] molecular editing in pymol
Hi, I should probably google about some more for an answer to this, but maybe someone who's reading this already knows -- is a detailed description of pymol's molecular editing functionality available anywhere online (e.g., ctrl-right-click to select a bond and ctrl-d to delete it, and so on...)? Thanks, Cameron
[PyMOL] Getting Closer to Wiki Time!
PyMOL Users, Jason Vertrees (UTMB) has volunteered to lead the creation of a PyMOL Wiki, and has found a suitable location for hosting. We now need your input on how the Wiki should be organized. Please summarize your ideas to the mailing list in the next 24-48 hours so that Jason has your input as he lays down an initial framework for content on the Wiki. At the very least, we need to nail down the major categories/branches that can be used to build an outline of sorts. Later on, once the Wiki is up, we'll likely be asking for some volunteers to help populate pages based on existing information, either on the mailing list or other sites. Here is a snapshot of topics from the manual to get you started: - Mouse Controls - Command Language - Atom Selections - Ray-tracing - Movies and Animations - Cartoon Representations - Settings Reference (all settings and what they do) - Stereo 3D Display - Hardware Options - Linux XFree86 Configuration - Crystallography Aplications - Symmetry - Electron Density - Arbitrary Graphics Objects - Python Integration - Scenes Please revise, extend, and embellish. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com
Re: [PyMOL] Getting Closer to Wiki Time!
Another potentially useful category: Plugin/Modules -- ex. Michael George Lerner's APBS plugin -- other existing and future plugins This would make it easy for others to contribute tips/explanations/experiences/etc. to these extremely useful add-ons. On Feb 15, 2005, at 1:11 PM, Warren DeLano wrote: PyMOL Users, Jason Vertrees (UTMB) has volunteered to lead the creation of a PyMOL Wiki, and has found a suitable location for hosting. We now need your input on how the Wiki should be organized. Please summarize your ideas to the mailing list in the next 24-48 hours so that Jason has your input as he lays down an initial framework for content on the Wiki. ... Please revise, extend, and embellish.
Re: [PyMOL] Getting Closer to Wiki Time!
Please revise, extend, and embellish. - structure alignment (pretty simple, but a lot of people don't know how to use the various commands) - as part of movies, a large section on available 3rd-party apps and codecs would be very useful (as well as workarounds for PowerPoint madness) -Nat
Re: [PyMOL] Getting Closer to Wiki Time!
While we're throwing out all these ideas and possibilities: Is it ... possible? ... relatively painless? ... difficult? ... to use BioPython modules in PyMOL scripts? Doug
Re: [PyMOL] Getting Closer to Wiki Time!
On Tue, 15 Feb 2005, Douglas Kojetin wrote: While we're throwing out all these ideas and possibilities: Is it ... possible? ... relatively painless? ... difficult? ... to use BioPython modules in PyMOL scripts? if you compile python from source (it's pretty easy on most linux systems (i had a lot of trouble with gentoo recently, though)), you can just point it at a version of python that already has biopython installed. pymol works just fine with python 2.4, by the way. -michael Doug --- 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] Getting Closer to Wiki Time!
On Tue, 15 Feb 2005, Douglas Kojetin wrote: While we're throwing out all these ideas and possibilities: Is it ... possible? ... relatively painless? ... difficult? ... to use BioPython modules in PyMOL scripts? if you compile python from source (it's pretty easy on most linux systems (i had a lot of trouble with gentoo recently, though)), you can just point it at a version of python that already has biopython installed. pymol works just fine with python 2.4, by the way. -michael Doug --- 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
