Dear Frieda I've never tried that. From the doc http://www.tripos.com/data/support/mol2.pdf it seems that atoms can have IDs and residue IDs; they quote an example: 1 CA -0.149 0.299 0.000 C.3 1 ALA1 0.000 BACKBONE|DICT|DIRECT 1 CA -0.149 0.299 0.000 C.3 [...] the atom is named CA and is [...] It belongs to the substructure with ID 1 which is named ALA1.
So, Jmol should be able to interpret that, but maybe the file reader has not been set for that. As far as I know, the "protein" is determined based on bonding and key atom names (N, CA, C) within the same residue. Similarly for residue names. A quick test with a pdb file read into Accelrys DS Viewer 1.7 and saved into mol2 shows that the atom IDs are read in Jmol (example: select *.CA works), but not recognized as protein. "select ala" doesn't work either. So maybe it's just the residue ID part that is not being interpreted. Notably, that goes after the coordinates, rather than before them as in pdb. ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
