[ccp4bb]: PyMOL v0.63: CCP4 Maps & Pub. Quality Figures

["DeLano, Warren" <warren@sunesis.com>]

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PyMOL v0.56 was announced a short time ago, so this is just an update of
important new features in v0.63 which bring considerable benefit to CCP4
users.  
 
1) PyMOL can now read binary CCP4 maps across multiple architectures.
2) PyMOL now has near-Molscript quality ribbons BUILT-IN (wow!).
3) A density map "wizard" has been added which enables single-click
traversal of structures with electron density that automatically
follows.
4) A simple hierarchical selection language has been added "(A/145/ca)",
etc.
5) Many more minor features have been implemented...
 
PyMOL is the world's most powerful free and unrestricted open-source
molecular graphics program.  It is an early arrival from the next
generation of software packages(*) which will revamp crystallographic
computing and make everyone's work much easier.  
 
If you haven't visited the PyMOL web site in the past month, then you
owe yourself a tour ( http://pymol.sf.net ).  The program still has
plenty of rough edges, but the images it creates do no longer.  The
animations which can be rendered with PyMOL are nearly unbeatable.

PyMOL is also probably the FASTEST tool for perusing maps calculated out
of Refmac or CNS/X-PLOR.  You can even have your refinement program
launch PyMOL scripts to automatically display maps after they have been
calculated.  Or, you can conveniently examine maps on your desktop PC or
OS-X Mac without expensive hardware or license fees.
 
Although not yet an efficient "builder", PyMOL can be used to adjust
main-chain and side-chain conformations, as well as to move waters and
ligands.  All conformational editing in PyMOL follows an intuitive
click-and-drag scheme using the mouse and keyboard.  Basic building
capabilities are likely to be in place by early 2002, but PyMOL won't be
a general replacement for "O" for some time without external help.

My belief is that anywhere from one-half to three-quarters of all
crystallographers will find PyMOL to be a valuable component in their
toolbox within the next 6-12 months!  PyMOL has a good shot at becoming
the minimum common denominator for molecular visualization within two
years unless displaced by something equally open, but more powerful.

Those who do not learn to use it (or a superior package) will be wasting
considerable time engaged in outdated figure preparation techniques, and
but for a few exceptions, will be unable to beat PyMOL's quality.
Furthermore, PyMOL's capabilities extend far beyond mere figure
preparation.  It is also an ultra-high-performance, general-purpose 3D
viewer, and it is the easiest tool for rapidly splitting, altering, and
recombining PDB files.  But wait, there's more...
 
PyMOL is DISTINCT from nearly all similar programs because of its
completely unrestrictive open-source license.  Anyone can use PyMOL for
ANY purpose, now and forever.  No one can take PyMOL away from you, and
you can freely customize and embellish its capabilities using scripts,
Python, or even C/C++/Fortran.  Every time a scientist adds and shares a
new feature or script, we all stand to benefit, but no one is required
to do so by any burdensome license (like GPL).  You can derive new
programs from PyMOL source code and keep them private, if that is what
you desire.  Typically, that won't be in your self-interest though,
since then you'll miss out on all the ongoing improvements!

For all intensive purposes, you can treat and apply PyMOL just as if YOU
created it (only the Copyright notices can't be removed).  Since it is
"YOUR" package, you should nurture its growth and educate yourself on
how to apply it!  Learning PyMOL is a worthwhile investment which will
bring both immediate gratification and enduring rewards.  Furthermore,
learning Python as a means of getting the most out of PyMOL is an
excellent way to prepare yourself for the future of crystallographic
computing.
 
PyMOL is my personal gift to you, and with it nearing its second
birthday, it is now ready for widespread usage.  So go make the most of
it!  The manual and web site will serve as your companions in this
endeavor.  I will keep them updated with tips, scripts, and FAQ's to
save you time and help foster a self-supporting community of PyMOL
users. Just send feedback and suggested postings my way, or even better,
set up your own PyMOL-oriented web sites and send me the URLs for
linking!  Even though PyMOL lacks some documentation right now, we can
quickly build a huge on-line database of practical knowledge via the
internet.

Cheers,

Warren L. DeLano, Ph.D.
warren@delanoscientific.com
Creator of PyMOL and Founder
DeLano Scientific
"Enabling New Science with Advanced Open-Source Software"

(*)Next generation packages are object-oriented software tools which use
Python as a common scripting language and data-interchange medium:  For
example:  cctbx, Phenix, Birdwash, Clipper, CCP43d, Michel Sanner's
Viewer, MMTK, VMD, and so on.  With all this momentum, it is highly
likely that Python will be the common language of crystallographic
computing for the next 5-10 years.  The benefits from such
standardization will be awe-inspiring.