CCL: Simple molecular graphics

[forli]=[unisi.it]

 Sent to CCL by: forli]|[unisi.it
 Dear Leif
 Try Pymol! It's powerful, well supported around the web, support
 raytrace of nice pics (internally), is easy enough to play with, and
 it's free.
 Linux, Mac and Win are supported.
 http://pymol.sourceforge.net/
 Hope this helps,
 Stefano
 >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>
 >
 >
 ---
 ***********************************
  Stefano Forli
  Dip. Farmaco Chimico Tecnologico
  Universita' degli Studi di Siena
  Via Aldo Moro
  I-53100 Siena, Italy
  Phone: ++39 0577 234307
  Fax: ++39 0577 234333
  e-mail: forli * unisi.it
 ***********************************