They come from AtomSmith, which is from Bitwixt software. The file that works in Jmol is included with the program; the file that does not work in Jmol is AtomSmith's output when it starts with a pdb file, puts an EP surface around it, and exports it as mol2. If it's their formatting needs changing, then I can urge them to deal with it - I have already emailed them about it twice.
Frieda On Aug 14, 2008, at 2:19 PM, Bob Hanson wrote: > 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 ------------------------------------------------------------------------- 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
