[PyMOL] PyMOL 0.92 Released
PyMOL version 0.92 can be obtained from http://pymol.sf.net at your convenience. Though this is mostly an "under the hood" improvements release, there are some developments worth noting: Significant changes - New "dss" command assigns secondary structure quickly. - PyMOL can now read O/BRIX maps and some Biosym GRiDs maps. - Improved ray tracing quality and speed. - Long lists of residues in selections are now allowed. Other changes - New "import pymol" support for RPM & Win32 builds that use system Python. [Don't forget to call pymol.finish_launching() afterwards though!] - Improved alpha-channel support for transparent surfaces and backgrounds. - API's "cmd.do" can now take multi-line strings and lists. - New "split_states" command for separating NMR ensembles. - New "cartoon_transparency" setting. - Can display bond valences while in stick mode. - New "stick_ball", "stick_ball_ratio" settings for ball & stick models. - Gaussian map generation from model coordinates. - Can preserve original PDB atom IDs (pdb_retain_ids) & order (retain_order). - Much much faster loading of multi-model PDB files and trajectories. - Deuterium and Calcium handling improved. - New "set_symmetry" & "get_symmetry" commands. - Mutagenesis wizard preserves cartoons. - New "get_pdbstr" API function. - New "movie_loop" setting can disable looping. - Sculpting engine now aware of simple sp3-sp3 torsions. - Finer Z-scaling/movement control. - Upgrade facility for secure enterprises running Windows. PyMOL 0.92 also includes various bugs fixes with cartoons, rendering, CGOs, sessions, endianness, multithreading, raytracing, OS X, and isosurfaces. As always, upgrade with caution. Don't update right before an important presentation, and be sure to test your existing session files. Please report any trouble. Probably the most problematic aspect of the new version will be the increased WYSIWYG behavior of the ray-tracer with respect to line widths. If the bonds in your figure just got thinner, that's the culprit. You can manually adjust the various *_width or *_radius settings to achieve the desired results. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020
RE: [PyMOL] solvent accesible surface
Marcelo, PyMOL doesn't currently do a very good job with a solid solvent accessible surfaced because they aren't smooth like the Connolly surface. But here's what you can do: show spheres set sphere_solvent,1 or hide spheres show mesh set solvent_mesh,1 now add in show surface for a nice combination of the solvent and molecular surfaces. 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 > Marcelo Castilho > Sent: Sunday, October 26, 2003 4:04 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] solvent accesible surface > > > Dear all, > > I am new to pymol and appologyze if his is an "easy > question", anyway here it goes; > > Is it possible to change the surface radius in pymol so that > I can represent the solvente accesible surface ? > > By the way, I am running pymol 0.90 under windows XP > > Thanks, > > Marcelo Castilho > > = > Marcelo Santos Castilho > tel 016 273 98 68 > R; Américo J. Canhoto 223 Apto 23 Bl 2 > São Carlos CEP 13564-350 > e-mail alternativo: casti...@if.sc.usp.br > > __ > Do you Yahoo!? > Exclusive Video Premiere - Britney Spears > http://launch.yahoo.com/promos/britneyspears/ > > > > --- > This SF.net email is sponsored by: The SF.net Donation > Program. Do you like what SourceForge.net is doing for the > Open Source Community? Make a contribution, and help us add > new features and functionality. Click here: > http://sourceforge.net/donate/ > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/p> ymol-users >
RE: [PyMOL] Save session on Mac OSX latest version?
Douglas, Simply: save filename.pse ie save today.pse 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 > Douglas Freymann > Sent: Sunday, October 26, 2003 2:26 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Save session on Mac OSX latest version? > > > I'm having a hard time finding how to save my session running on a G4 > Powerbook, using PyMOL v0.91. The command, File::Save, is grayed > out, and there's no command File::Save Session as described in the > Users Manual. Is there a trick, or a command line statement? > By the way, is there a way to set a default working directory when > PyMOL starts? > Sorry if these are FAQ's but I didn't find the answers > anywhere. Thanks, Doug > > -- > > Douglas M. Freymann freym...@northwestern.edu > > Molecular Pharmacology & Biological Chemistry > Ward 7-247, Northwestern University > 303 E. Chicago Ave., Chicago, IL 60611 > > (312) 503-1877fax: (312) 503-5349 > > > --- > This SF.net email is sponsored by: The SF.net Donation > Program. Do you like what SourceForge.net is doing for the > Open Source Community? Make a contribution, and help us add > new features and functionality. Click here: > http://sourceforge.net/donate/ > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/p> ymol-users >
[PyMOL] Save session on Mac OSX latest version?
I'm having a hard time finding how to save my session running on a G4 Powerbook, using PyMOL v0.91. The command, File::Save, is grayed out, and there's no command File::Save Session as described in the Users Manual. Is there a trick, or a command line statement? By the way, is there a way to set a default working directory when PyMOL starts? Sorry if these are FAQ's but I didn't find the answers anywhere. Thanks, Doug -- Douglas M. Freymann freym...@northwestern.edu Molecular Pharmacology & Biological Chemistry Ward 7-247, Northwestern University 303 E. Chicago Ave., Chicago, IL 60611 (312) 503-1877fax: (312) 503-5349
[PyMOL] solvent accesible surface
Dear all, I am new to pymol and appologyze if his is an "easy question", anyway here it goes; Is it possible to change the surface radius in pymol so that I can represent the solvente accesible surface ? By the way, I am running pymol 0.90 under windows XP Thanks, Marcelo Castilho = Marcelo Santos Castilho tel 016 273 98 68 R; Américo J. Canhoto 223 Apto 23 Bl 2 São Carlos CEP 13564-350 e-mail alternativo: casti...@if.sc.usp.br __ Do you Yahoo!? Exclusive Video Premiere - Britney Spears http://launch.yahoo.com/promos/britneyspears/
[PyMOL] Release in progress...
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 | Message: 4 | From: "Warren L. DeLano" | To: | Date: Sat, 25 Oct 2003 13:12:51 -0700 | Subject: [PyMOL] Release in progress... | | (in a whisper) | | I'm still in the process of building binaries, but pioneers are welcome | to start downloading 0.92, if your platform is represented. It has been | a long time since our last release, so proceed with caution! | | http://sourceforge.net/project/showfiles.php?group_id=4546 | | Please bring any problems to my attention ASAP, before the Monday | deluge. Looks nice, I found one little glitch (or is it a feature) which might have been there before: A raw traceback if you type a command which does not exist: For example: PyMOL>k Traceback (most recent call last): ~ File "//tuxprog/pymol/pymol_0.92/modules/pymol/parser.py", line 255, in parse ~exec(com2[nest]+"\n",pymol_names,pymol_names) ~ File "", line 1, in ? NameError: name 'k' is not defined which makes perfect sense, but might look a bit strange to the end-user (something like "command "k" not found" might be more usefull). Also probably not good without another security-measure: Typing "q" (will immediately quit Pymol). - -- Bye, Marc Saric http://www.marcsaric.de -BEGIN PGP SIGNATURE- Version: GnuPG v1.0.7 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQE/m7VYvKxJUF29wRIRArhbAJ928s/6nrRnCqg4mfEEAPO4WarTMQCgx08I wyMNr7nlUUmDsIJh4tvv1pk= =rsZP -END PGP SIGNATURE-
