Just send them that documentation. Pretty clear that they have that wrong and will want to correct it.
Reichsman Frieda wrote: >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 > > -- 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
