Where do these files come from? The mol2 format does not allow for anything between the number and the element symbol on that atom line.
http://www.tripos.com/tripos_resources/fileroot/mol2_format_Dec07.pdf Bob Reichsman Frieda wrote: > Hi Bob, > > I have some mol2 files wherein Jmol cannot read the embedded EPS (or > are they more correctly called partial charge) values, and also Jmol > fails to render one atom in the file. An example file is attached, > along with one that Jmol reads fine: ala-problem.mol2 (Jmol won't > read EPS) and ala.mol2 (Jmol does read EPS), > > Comparing the two mol2 files, the format is slightly different. I am > not sure if the file is formatted incorrectly (generated by the > program AtomSmith), or if Jmol is too strict. The differences are as > follows. > > In the ala-problem.mol2 file, > 1. The eps values from are offset by one additional space from the > coordinates, and > 2. the three-letter abbreviation for the amino acid is missing in > each row from inbetween the number "1" and the EPS values. > > When I change both these aspects to mimic the file ala.mol2, Jmol can > read the eps values. > > 3. In the ala-problem.mol2 file I also had to remove the ALA that > appears as characters 4, 5 and 6 in the line for atom #1, in order > for Jmol to be able to render that particular atom. > > > Frieda > > > ////////////////////////////////////// > > Frieda Reichsman, PhD > Molecules in Motion > Interactive Molecular Structures > http://www.moleculesinmotion.com > 413-253-2405 > > ////////////////////////////////////// > > > > > ////////////////////////////////////// > > Frieda Reichsman, PhD > Molecules in Motion > Interactive Molecular Structures > http://www.moleculesinmotion.com > 413-253-2405 > > ////////////////////////////////////// > > > > >------------------------------------------------------------------------ > >------------------------------------------------------------------------- >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 > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 ------------------------------------------------------------------------- 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
