On 01/29/2015 10:21 PM, Robert Hanson wrote: > My point was that you can easily create a CIF with Perl or anything else > that Jmol will parse *for the information in the ATOM/HETATM/CONECT lines*, > which is what it sounded like you were saying. You did not refer to > specific REMARK records. Some of those are more involved. > > Basically you just add a couple of single-character columns to keep values > separate, define your _loop keys, and you are done. > You were right with this. And if mmCIF currently is the only choice and the behaviour with CML is as intended and not a bug I can adapt to this and use mmCIF.
> What do you really want to do - exactly? Which records do you need? > I want to import network data (connection information and node type information) and then translate this within Jmol into hetero atom and bond information, determine suitable coordinates for the atoms, and build model data that Jmol can then load from a variable and that Jmol can save and that Jmol (and maybe also other programs) can reload. Essential for this would be to be able to specify the following atom properties: 1) atom number 2) atom name 3) residue name 4) model number 5) chain id 6) atom coordinates In the future maybe also the 'residue number' might be useful. But currently all residues will only have a single atom. So it wouldn't provide any extra information that the 'atom number' not already provides. > Is this your real question? > > *I am looking for a replacement for the mmCIF format that offers all of the > information that Jmol can read from mmCIF files, but isn't mmCIF.* No. Within Jmol I don't need any extra information. (see above) Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 ------------------------------------------------------------------------------ Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
