RE: [PyMOL] stop an accidental or problematic ray trace
Anthony, I agree that we need one, but it doesn't currently exist. The same can be said for surface calculations, especially when you've loaded a 500 frame MD trajectory and accidentally "show surface" (doh!). My advice: save sessions often and make liberal use of PyMOL's logging capability. When you goof up, kill the process and then reopen the session or resume the log file after editing out the offending command(s). Cheers, Warren (Hmm...A save session button might be nice...) -- mailto:war...@sunesis.com Warren L. DeLano, Ph.D. Informatics Manager Sunesis Pharmaceuticals, Inc. 341 Oyster Point Blvd. S. San Francisco, CA 94080 (650)-266-3606 FAX:(650)-266-3501 > -Original Message- > From: Anthony Duff [mailto:a.d...@staff.usyd.edu.au] > Sent: Tuesday, January 28, 2003 4:29 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] stop an accidental or problematic ray trace > > > > > > It would be nice if there were a button to stop a ray trace, > for when it is > started accidentally, or if something is wrong and it is > taking too long. > > > Is there one? > > > > > -- > Anthony Duff > Postdoctoral Fellow > School of Molecular and Microbial Biosciences > Biochemistry Building, G08 > University of Sydney, NSW 2006 Australia > Phone. 61-2-9351-7817 Fax. 61-2-9351-4726 > -- > > > > --- > This SF.NET email is sponsored by: > SourceForge Enterprise Edition + IBM + LinuxWorld = Something 2 See! > http://www.vasoftware.com > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
[PyMOL] stop an accidental or problematic ray trace
It would be nice if there were a button to stop a ray trace, for when it is started accidentally, or if something is wrong and it is taking too long. Is there one? -- Anthony Duff Postdoctoral Fellow School of Molecular and Microbial Biosciences Biochemistry Building, G08 University of Sydney, NSW 2006 Australia Phone. 61-2-9351-7817 Fax. 61-2-9351-4726 --
Re: [PyMOL] non-related question & related: electrostatics
Thanks for the reply ... Do you have a list of which programs pymol might accept input from? Thanks again- Doug DeLano, Warren wrote: Doug, (1) I've got a hard deadline to have this capability in the program less than 1 month from now...not the pot. calc., just the import, rendition, and coloring. (2) no clue Warren -- mailto:war...@sunesis.com Warren L. DeLano, Ph.D. Informatics Manager Sunesis Pharmaceuticals, Inc. 341 Oyster Point Blvd. S. San Francisco, CA 94080 (650)-266-3606 FAX:(650)-266-3501 -Original Message- From: Douglas Kojetin [mailto:djkoj...@unity.ncsu.edu] Sent: Tuesday, January 28, 2003 3:14 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] non-related question & related: electrostatics Hi All- I'll ask my related question first: does anyone know if/when electrostatic calculations might be incorporated into pymol? Or if you can import calcs from another (hopefully free) program? Unrelated question: does anyone know of a secondary structure prediction program that outputs "pretty" graphics to related 'helix' and 'sheet' structures? similar to how ESPript outputs ... but i do not have an input PDB file (yet) to use that program Thanks, Doug --- This SF.NET email is sponsored by: SourceForge Enterprise Edition + IBM + LinuxWorld = Something 2 See! http://www.vasoftware.com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] q: discrete colors and adjacent cartoon segments
Bartholomeus, You have run into limitations in PyMOL's handling of single objects. The answer to both these questions is to split your molecule into multiple object and color/show independently. Use the "create" command to make copies, and then use alter to reassign secondary structure codes where needed. Warren -- mailto:war...@sunesis.com Warren L. DeLano, Ph.D. Informatics Manager Sunesis Pharmaceuticals, Inc. 341 Oyster Point Blvd. S. San Francisco, CA 94080 (650)-266-3606 FAX:(650)-266-3501 > -Original Message- > From: Bartholomeus Kuettner [mailto:bkuett...@epost.de] > Sent: Tuesday, January 28, 2003 3:06 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] q: discrete colors and adjacent cartoon segments > > > Dear PyMol users, > > 1. > I'm puzzled with a coloring problem while coloring a protein molecule > accordingly to its secondary structure by using 'discrete > color' option: > If there are a helix and/or strand adjacent together (e.g. > helix from 1-10 > and sheet from 11-20) the small pseudo-loop region between > (arising from > atoms between last Calpha of the helix and first Calpha of > the strand) gets > colored like the latter partner (maybe because of its color > was defined at > last). What I'd like to do is to color this small pseudo loop > in a different > color. I've tried to color the atoms between last Calpha and > next Calpha > (C,N) individually but there was no effect. It seems to me, > that cartoon > coloring only corresponds to Calpha positions. So, is there a > way around to > color cartoon regions between secondary structure elements as > described > before? > > 2. > Is there a way to force PyMol to draw a cartoon which shows > two different > secondary strcuture elements (helix, strand) ending and > beginning at the > same residue? Maybe one can image a scenario where the N atom makes a > strand-like conformation while the CO group of the same > residue starts with > a helix. In another program it is/was possible to assign > helix and strand > ending and beginning in the same residue but when I try to > perfom with PyMol > only the last partner is shown correctly while the first partner gets > overrided in its last residue, e.g. cartoon "strand 1-10" and > "helix 10-20" > looks the same like "strand 1-9" and "helix 10-20". How one > could circumvent > this dilemma? > > Many thanks in advance! > > Greetings, > Bartholomeus > > > > --- > This SF.NET email is sponsored by: > SourceForge Enterprise Edition + IBM + LinuxWorld = Something 2 See! > http://www.vasoftware.com > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
RE: [PyMOL] non-related question & related: electrostatics
Doug, (1) I've got a hard deadline to have this capability in the program less than 1 month from now...not the pot. calc., just the import, rendition, and coloring. (2) no clue Warren -- mailto:war...@sunesis.com Warren L. DeLano, Ph.D. Informatics Manager Sunesis Pharmaceuticals, Inc. 341 Oyster Point Blvd. S. San Francisco, CA 94080 (650)-266-3606 FAX:(650)-266-3501 > -Original Message- > From: Douglas Kojetin [mailto:djkoj...@unity.ncsu.edu] > Sent: Tuesday, January 28, 2003 3:14 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] non-related question & related: electrostatics > > > Hi All- > > I'll ask my related question first: does anyone know if/when > electrostatic calculations might be incorporated into pymol? > Or if you > can import calcs from another (hopefully free) program? > > Unrelated question: does anyone know of a secondary structure > prediction > program that outputs "pretty" graphics to related 'helix' and 'sheet' > structures? similar to how ESPript outputs ... but i do not have an > input PDB file (yet) to use that program > > Thanks, > Doug > > > > > --- > This SF.NET email is sponsored by: > SourceForge Enterprise Edition + IBM + LinuxWorld = Something 2 See! > http://www.vasoftware.com > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
[PyMOL] non-related question & related: electrostatics
Hi All- I'll ask my related question first: does anyone know if/when electrostatic calculations might be incorporated into pymol? Or if you can import calcs from another (hopefully free) program? Unrelated question: does anyone know of a secondary structure prediction program that outputs "pretty" graphics to related 'helix' and 'sheet' structures? similar to how ESPript outputs ... but i do not have an input PDB file (yet) to use that program Thanks, Doug
[PyMOL] q: discrete colors and adjacent cartoon segments
Dear PyMol users, 1. I'm puzzled with a coloring problem while coloring a protein molecule accordingly to its secondary structure by using 'discrete color' option: If there are a helix and/or strand adjacent together (e.g. helix from 1-10 and sheet from 11-20) the small pseudo-loop region between (arising from atoms between last Calpha of the helix and first Calpha of the strand) gets colored like the latter partner (maybe because of its color was defined at last). What I'd like to do is to color this small pseudo loop in a different color. I've tried to color the atoms between last Calpha and next Calpha (C,N) individually but there was no effect. It seems to me, that cartoon coloring only corresponds to Calpha positions. So, is there a way around to color cartoon regions between secondary structure elements as described before? 2. Is there a way to force PyMol to draw a cartoon which shows two different secondary strcuture elements (helix, strand) ending and beginning at the same residue? Maybe one can image a scenario where the N atom makes a strand-like conformation while the CO group of the same residue starts with a helix. In another program it is/was possible to assign helix and strand ending and beginning in the same residue but when I try to perfom with PyMol only the last partner is shown correctly while the first partner gets overrided in its last residue, e.g. cartoon "strand 1-10" and "helix 10-20" looks the same like "strand 1-9" and "helix 10-20". How one could circumvent this dilemma? Many thanks in advance! Greetings, Bartholomeus
[PyMOL] Installation of PyMol on Macs
I found the receipes on your homepage to install PyMol on Macs kind of convoluted, so here is what I figured after some working hours: Installation on Mac-OsX 10.2 1) Download fink from www.apple.com and install 2) add "source /sw/bin/init.csh" to /etc/csh.login to let the system know about fink 3) sudo fink configure (give as proxy something like http://www-cache.fh- giessen.de:3128) 4) get cvs-proxy..info and cvs-proxypatch from http:// fink.sourceforge.net/faq/usage-fink.php and put them into /sw/fink/dists/local/ main/finkinfo 5) sudo fink install cvs-proxy 6) cd to folder pymol-0.86; sudo fink update-all 7) open X11-Terminal 8) start pymol: /sw/bin/pymol & Best Uwe Hobohm
