From: Scott C. <cl...@uc...> - 2003-10-27 19:21:14
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Hi Warren, When will PyMol 0.92 be available via fink? Thanks, Scott On Oct 26, 2003, at 11:06 PM, Warren L. DeLano wrote: > 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:wa...@de... > Warren L. DeLano, Ph.D. > Principal Scientist > DeLano Scientific LLC > Voice (650)-346-1154 > Fax (650)-593-4020 > > > > ------------------------------------------------------- > 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 > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Scott Classen, Ph.D. ACS Postdoctoral Fellow Department of Molecular & Cell Biology University of California, Berkeley 237 Hildebrand Hall #3206 Berkeley, CA 94720-3206 LAB 510.643.9491 FAX 510.643.9290 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ |