Re: [Jmol-users] R: Re: Parsing JME string

[Angel H. <ang...@ua...>]

1)

> Does anyone every go into the code to see what really happening when 
> Jmol/JSmol parsing the JME format, cuz the JME format works 
> incredible well for the limited information containing in the JME 
> format. 

The relevant source must be in
http://chemapps.stolaf.edu/jmol/jsmol/j2s/J/adapter/readers/simple/Jme
Reader.js

as compared to
http://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/src/org/jmol/a
dapter/readers/simple/JmeReader.java


2)
Are you comparing JSmol to a recent version of Jmol (ideally the same 
version). I say so because formerly Jmol used the UFF force field for 
3D minimization, while more recently MMFF94 became available. There 
might be a difference there in performance.


3)
> When the molecule in MOL format passes onto JSmol, it works fine 
with 
> no EM. 

Note that when you transfer MOL data into Jmol, EM will (or may) be 
run too, to generate the 3D. When JME is passed that is automatic, 
since JME is really one-dimensional (text string) data, not 2D as MOL 
is.


4)
> Even so I still am trying to address the problem using mol format, 
as 
> the charge information (the number of H atoms) in the mol file is 
not 
> presented right in JSmol.

I have always had problems with 3-bonded carbons as Jmol refuses to 
add a H to them (assuming they are sp2 which is often not the case). 
Not sure if that's related to your problem.

There may be a limitation in dealing with charged atoms when 
calculating Hs. Or the charge field is not being recognized.


·
 Dr. Angel Herráez
 Biochemistry and Molecular Biology,
 Dept. of Systems Biology, University of Alcalá
 E-28871 Alcalá de Henares  (Madrid), Spain