CCL: Simple molecular graphics

 Sent to CCL by: "Warren DeLano" [warren(a)delsci.com]
 Leif,
 PyMOL can now do black & white nicely, as well as photorealistic color
 on black, white, or transparent backgrounds.  It can be used for
 everything from electron density, ball & stick, and cartoon, all the way
 way up to megadalton EM tomography surface representations.
 Some examples at:
 http://www.pymolwiki.org/index.php/Ray
 Latest builds d/l at
 http://delsci.com/beta
 Cheers,
 Warren
 --
 Warren L. DeLano, Ph.D.
 Principal Scientist
 . DeLano Scientific LLC
 . 400 Oyster Point Blvd., Suite 213
 . South San Francisco, CA 94080 USA
 . Biz:(650)-872-0942  Tech:(650)-872-0834
 . Fax:(650)-872-0273  Cell:(650)-346-1154
 . mailto:warren|a|delsci.com
 > -----Original Message-----
 > From: owner-chemistry|a|ccl.net [mailto:owner-chemistry|a|ccl.net]
 > Sent: Wednesday, January 11, 2006 10:46 AM
 > To: Warren DeLano
 > Subject: CCL: Simple molecular graphics
 >
 > Sent to CCL by: "Leif  Olson" [leif.olson,,kodak.com] Hi CCL
 people,
 >
 > I know this is similar to previous questions that have been
 > sent to the list in the past.  But I am going to ask it
 > anyway...I keep searching for a program that will make simple
 > publication quality molecular graphics pictures (usually
 > black-and-white), but with a couple of added features, and
 > runs on Windows or Linux.
 >
 > Vast numbers of molecular graphics programs are advertised
 > for their capability to make "publication quality" images.
 > But what this always seems to refer to is the ability to
 > create stunning color pictures complete with shadows, fog
 > effects, dramatic backgrounds, etc., perhaps rendered with
 > the help of POV-Ray.  Nice, but not what I usually need for
 > figures to put into journal articles or technical reports.  I
 > usually just want ball-and-stick, black-and-white (or a
 > simple color scheme to highlight heteroatoms), maybe some
 > cross-hatching to suggest depth, and some labeling
 > capability, with the end result a high-resolution image or
 > vector output.
 >
 > An example of a program that comes pretty close to what I
 > would like is XChemEdit, where I can read in a structure, and
 > quickly rotate/translate it to a desired orientation.  Then,
 > with a few mouse clicks I can remove undesired bonds, make
 > dashed bonds (e.g. for hydrogen bonds or transition states),
 > label bond distances/angles/dihedrals, resize and move
 > labels, etc.  This only takes a minute or two, unfortunately
 > the resulting images are not, in my opinion, good enough for
 > external publication.  They are nicely labeled and clear, but
 > low-resolution.
 >
 > As an alternative, I have tried Schakal99, which can make
 > excellent publication-quality b/w molecular graphics, and it
 > seems that one has extensive control over the final image.
 > But I find it difficult to use even after studying the manual
 > and going through quite a few examples, and I am not sure
 > that certain things like labeling bond angles can even be done.
 >
 > I have also looked at XBS, Molden, ORTEP, and WebLab Viewer,
 > but they aren't quite what I am looking for either.  We don't
 > own Cache, Chem3D, or Gaussview, so I haven't tried
 > them...what about those or other software?  Is it best to
 > just put in the time to really learn Schakal usage?  Would
 > you agree that fancy photorealistic "publication quality"
 > graphics are often discouraged by journal editors anyway?
 >
 > Thanks!
 >
 > Leif Olson
 > Eastman Kodak Research Laboratories
 >
 >
 >
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