When we met in Cologne last August, Egon and I agreed that Jmol -- at least in our hands -- won't be in the business of doing quantum chem or molecular mechanics calculations. Of course, anyone who wants can implement whatever they can with Jmol, but we are more interested, as Angel describes, in Jmol being a full-service viewer.
The calculations that I introduced last summer and fall in relation to crystallographic symmetry and space groups and orbitals are all for the service of molecular visualization. As Angel points out, I did a bit of experimentation with "sprouting" hydrogens because I thought that molecular surfaces probably could benefit from that. I was mildly amused to find how MINIMAL the difference was -- it turns out that hydrogen atoms in general are little more than bumps on the overall atomic van der Waals surface. Anyway, this is implemented for carbon, at least, and it is even possible to get the coordinates for small sets, since the JVXL files are saved with (I think) up to 50 or 100 coordinates, but any such rendering is crude. There are obvious ambiguities: X--O (where is the OH?) , RCCC (Is this propyl or propenyl?), and R-C-O (Is that an alcohol or an aldehyde?). So right now we don't support the addition or deletion of atoms, hydrogen or otherwise. I apreciate these replies, Angel, as it appears this list is being blocked, and I never see the original messages. Please don't assume I'm ignoring messages. I'll see if it is St. Olaf that is blocking these. I know we've had mega spam problems -- as has everyone -- lately. Bob Angel Herraez wrote: >I am opening two new threads for Paul questions in his last post to " >loading jmol file from open babel" > >On 29 Jan 2007 at 10:44, H. Paul Benton wrote: > > >> To all the other uses I have one more question to ask >>"If a file was loaded with no Hydrogens how can I get >>Jmol to put them on?". >> >> > >Jmol cannot add hydrogens right now. Remebre it is a viewer, not a molecule >builder. >I can recommend two programs that allow you to do so. One is Discovery Studio >Visualizer, >from Accelrys (formerly known by several names such as WebLab Viewer, Accelrys >Viewer, >DS Viewer, etc.) >The other is ChemSketch, from ACDLabs. This is actually a 2D chemical drawing >package, >but imports and exports MOL files and has a 3D module. > >If you haven't used any of them, go for DS Visualizer. It will open your pdb, >mol, xyz etc files, >then go to menu Tools > Hydrgens > Add and save again. > > > > >------------------------------------------------------------------------- >Take Surveys. Earn Cash. Influence the Future of IT >Join SourceForge.net's Techsay panel and you'll get the chance to share your >opinions on IT & business topics through brief surveys - and earn cash >http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >_______________________________________________ >Jmol-users mailing list >Jmol-users@lists.sourceforge.net >https://lists.sourceforge.net/lists/listinfo/jmol-users > > ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
