I have been thinking about why this would not be useful. Looking at protein structures, I now understand that given the large number of atoms in a protein molecule it makes sense to download the file directly into Jmol rather than have a facility where you enter atom positions by hand.
I would like to briefly describe what I had in mind when I tried to use Jmol, though I now feel it does not have the functionality I need. Crystal structres of materials are relatively speaking small "molecules" when compared to protein molecules. One of the largest structures I have studied has about 102 atoms in the unit cell, with just about 38 atom positions to be entered by hand. Jmol would be useful for the visualisation of such structures as well as of planes, directions and defects in the lattice, if I could enter into it any crystal structure. I could visualise these as 2D / 3D models. I need to enter these by hand since I do not have access to electronic versions of crystal structure databases. Further, suppose I am trying to understand some interface structures in crystals. I would need to build a crystal that is essentially composed of two perfect unit cells related to each other in a particular way, sharing a common interface plane. Such situations are common in multi-phase materials. The concept of building such 'super-cells' is common in simulating HRTEM images of defects and interfaces. Being able to enter structures 'by-hand' adds a lot of flexibility into the program in terms of handling new structures that are models for defects or interfaces. But I do understand now that Jmol is built and specialised for handling organic large molecule structures, and not for crystal structures from materials science. Best Regards, Divakar --- Egon Willighagen <[EMAIL PROTECTED]> wrote: > On Monday 08 May 2006 08:06, [EMAIL PROTECTED] wrote: > > The Make crystal option under Edit menu is disabled. > > Looking through the mailing list archives I find a reply to > this > > which says that the feature has been removed since version > 10. > > Yes, Jmol 9 had the option to make crystals, starting from a > 3D structure. It > was not so much removed, but never ported to the Jmol 10 code > base. > > Can you explain how the building of crystal structures would > fit in, in your > daily practice? This normally helps others to think about > reintroducing this > feature... > > Egon > > -- > [EMAIL PROTECTED] > Cologne University Bioinformatics Center (CUBIC) > Blog: http://chem-bla-ics.blogspot.com/ > GPG: 1024D/D6336BA6 > > > ------------------------------------------------------- > Using Tomcat but need to do more? Need to support web > services, security? > Get stuff done quickly with pre-integrated technology to make > your job easier > Download IBM WebSphere Application Server v.1.0.1 based on > Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > Jmol-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-users > --------------------------------- [EMAIL PROTECTED] --------------------------------- __________________________________________________________ Yahoo! India Answers: Share what you know. Learn something new. http://in.answers.yahoo.com ------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
