Sorry to meddle, but I thougth I would give my opinion in case it is interesting for you.
> - What if you check for this second column of atom names only for > files with the .p2n or .P2N extension. Jmol does not rely on file extensions for reading any format. > - or we can add a header in the P2N file to distinguish it from the > PDB file format; for instance: > REMARK P2N FILE FORMAT JMOL COMPATIBLE That would always be good, and probably the best way for Jmol to filter these files without confusion. I think that best is that you conform to PDB standard as much as possible. Other software will then be able to read the files without trouble, ignoring the extra information. I would advice putting the alternative atom names AFTER the 80th column. And also adding the element name in the proper place, columns 77-78. Relying on the atom name for deducting the element symbol usually works, but is risky (as demonstrated often with calcium as well as with H atoms with too long names/id/locators). It is much better to have the symbol without ambiguity. Current PDB specification enforces that; it's only old PDB files and files created by external software that omit this field. Since your software is creating the files, I think all this is easy to accomplish. ------------------------------------------------------------------------------ Centralized Desktop Delivery: Dell and VMware Reference Architecture Simplifying enterprise desktop deployment and management using Dell EqualLogic storage and VMware View: A highly scalable, end-to-end client virtualization framework. Read more! http://p.sf.net/sfu/dell-eql-dev2dev _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
