PyMOL Users.
Yes, 0.88 has been released. However, many of the new features
are not yet documented, so I wouldn't necessarily rush out to download
it and expect to immediately utilize all new functionality.
Honestly, this release is a bit premature, but I had a firm
external deadline to meet -- so here is. Fortunately, a good part of
the new stuff is exposed in updated Menus (Mac users will need to use an
updated Fink version in order to access the new menus).
Some of the new features include:
- Standalone installer for Windows (no external Python required)
***heavily requested by corporate IT groups***
- CMYK color support ("space cmyk" better for pubs)
- Roving detail mode (hard to explain -- best seen)
- Improved transparency for surfaces
- Cartoon highlight color (ala Molscript)
- Opaque/solid objects in ray_tracer
- Spectrum command for fast color ramps
- Electrostatic map reading and color ramp support (.phi format)
- Wizards now saved in session file
- Wizards stack
- Scenes (more powerful than views; more convenient than
sessions)
- Updated demonstrations
- Single click-and-drag rotation of bonds in editing mode
- Tear off menus
- Stereo support on Mac (native version only)
- Improved performance on certain tasks (rainbow, color by chains)
- Better support for stereo figure generation with "ray
angle=-3",
"ray angle=3" etc.
My advice is not to try to figure out all this stuff by yourself, but
rather to try the new demos and then ask questions via the mailing list.
Or, simply wait until I get some time later this month or next to update
the documentation. THERE IS SOME GREAT NEW STUFF IN THERE! Scenes and
Roving are my personal favorites.
Scenes allow you to store multiple vantage points with all object and
atom display information within a single session file. This will
greatly aid in communication of structures and models to
non-computational scientists, and will better enable use of PyMOL in
live presentations.
Roving allows you to "rove" through a structure at will, inspecting
detailed molecular interactions, hydrogen bonds, and electron density.
PyMOL automatically shows and hides the representations and adjusts
clipping planes for you.
Also, I must warn you that some default behaviors have changed.
In particular, mouse tracking is different. Origin of rotation now
follows translation of the mouse. THIS IS AN EXPERIMENT. Please let me
know if you love/hate the new behavior. It can be easily turned on/off
by setting "roving_origin" to zero or by clicked off the option in the
Mouse menu. My experience watching novice users is that the old
approach was harder to learn than the new one, but they both have
downsides. If you get lost, simply fall back on CTRL-Shift-Middle-Click
to re-center on any atom.
As always, DON'T update to the new version unless you are confident that
you can revert to the old version should something about the new version
fail to work. Exercise due caution with PyMOL updates.
By the way, we just passed our 2 month anniversary, and I am happy to
say that we're off to a great start here at DeLano Scientific. I wish I
could give each one of you a tour of our rugged new development facility
in the previously unused bay of my garage. It is quite a sight, with
over 10 computers, 6 displays, several fans, and over a dozen
cold-swappable hard disks, with every flavor of Linux and Windows from
the past 5 years. It may not look like a software company, surrounded
by rakes, shovels, woodworking tools, and boxes, but we have most of the
equipment we need to develop and publish software for most relevant
platforms (still missing Sun...).
Somewhat less impressive was my monster electric bill for April/May.
Unfortunately, the electric company does not offer any discount on
electricity used for Open-Source software development!
So in closing, we have geared up for some heavy duty PyMOL development
in coming years, and I hope that the 0.88 release can give you a taste
of what is in store if we can continue to gain steady sponsorship from
academia and industry. DeLano Scientific is serious about developing,
documenting, and supporting great new scientific software with an
Open-Source approach. We hope you are equally serious about enabling it
through your sponsorship. Let's continue to work together in a global
partnership to help PyMOL reach its full potential! Please buy a
license and maintenance subscription if you can afford to do so.
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
