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
ala-problem.mol2
Description: Binary data
ala.mol2
Description: Binary data
////////////////////////////////////// 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 //////////////////////////////////////
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