Hi Angel, Thanks - your results are identical with my own--I thought perhaps Jmol could interpret the structure as protein but found it didn't. I wanted to be sure that that was the intended behavior of Jmol, not a flaw in the mol2 formating. Now I am satisfied on that point.
So Bob, would that be possible then, for Jmol's file reader to be able to read a mol2 file containing residue names and appropriate atom names, as protein? I don't know what else would need to be taken into consideration so I'm not sure if this is even a reasonable request. Frieda On Sep 10, 2008, at 9:51 AM, Angel Herraez wrote: > 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
