Well, I don't know.
1) There's no header information that distinguishes this from PDB files
2) The atom name field overlaps with the B-Factor field. (Kind of amazing to
me that you
would just invalidate that field that way instead of using the
available columns just after it.)
3) There's no element listed in columns 77-78
We don't particularly need (3), but I certainly need (1). I'm not going to
have Jmol check the B-Factor field for a non-number just to do this!
Bob
On Wed, Nov 10, 2010 at 9:51 AM, FyD <f...@q4md-forcefieldtools.org> wrote:
> 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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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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
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