From owner-chemistry #at# ccl.net Thu Jan 12 10:32:00 2006 From: "Tamas E. Gunda tgunda2005 : puma.unideb.hu" To: CCL Subject: CCL: Simple molecular graphics Message-Id: <-30472-060112073603-15632-+TjqmewJBQNzeb9ynCiOgQ=-=server.ccl.net> X-Original-From: "Tamas E. Gunda" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-15" Date: Thu, 12 Jan 2006 11:37:29 +0100 MIME-Version: 1.0 Sent to CCL by: "Tamas E. Gunda" [tgunda2005 * puma.unideb.hu] The 9th and the forthcoming 10 versions of Chem3D are capable to produce images with arbitrary resolutions (I tried up to 1200 dpi) in monochromatic (actually grayshade) mode, too. You can control rotations, edit bonds etc, but some things are more or less out of control, for example many features of atom labels are predefined. I think it is difficult to find a modelling program to fit exactly to our individual tastes. Often it might be necessary to edit the image or add special labels with an image editor like Photoshop. Dr. Tamas E. Gunda University of Debrecen Medical and Health Science Center Dept. of Pharmaceutical Chemistry POBox 36 H-4010 Debrecen Hungary e-mail: tgunda2005 *AT* puma.unideb.hu ----- Original Message ----- > From: "Leif Olson leif.olson~~kodak.com" To: "Gunda, Tamas E " Sent: Wednesday, January 11, 2006 19:05 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 >