Dear Jmol developers,

I have a request for the Jmol developers...

Jmol handles atom names, charge values, force field atom types & more;  
it recognizes among others the PDB & mol2 file formats.

With the R.E.D. tools & R.E.D. Server we have introduced a new file  
format named P2N file format.
See http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php
     http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#3

This P2N file format derives from the PDB file format; the main  
difference is that this P2N file format can handle two types of atom  
names:
- the first one reflects chemical equivalencing used in RESP input  
generation and RESP/ESP charge derivation
- the second one conserves atom naming conventions

Do you think Jmol could recognize this P2N file format i.e. could Jmol  
display these two types of atom names independently?

You can find an example of P2N file format @
http://q4md-forcefieldtools.org/Tutorial/P2N/Metal-complex/Mol_red1.p2n

The idea would be to allow displaying these two types of atom names as  
Jmol already does for the regular atom names, the charge values and  
the force field atom types using the mol2 file format - such as in the  
follow applet:
http://q4md-forcefieldtools.org/RED/popup/javaapplet.php
Atomic charges            -> displayed or not displayed
Force field atom types    -> displayed or not
Atom names                -> displayed or not

We could imagine the same approach for the P2N file format i.e. for  
the files with the .p2n and P2N extensions:
Atom names (1st column)   -> displayed or not displayed
Atom names (2nd column)   -> displayed or not

As this P2N file format is only used by the tools from  
q4md-forcefieldtools.org, I would understand Jmol developers would not  
be motivated by this request ;-) no problem with that.

Thank you,
regards, Francois



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