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
