Francois,
The bad news: Looks like we have a file format issue here. Angel has it
right, that the mol2 format as specified uses SYBYL atom types. The AMBER
team has co-opted that file format for their own purposes, still calling it
"mol2" but using non-SYBYL atom types. Jmol expects a mol2 file to have mol2
format.
The good news: Jmol is very flexible, and we have a rapid development cycle.
So we should be able to get it to do just about anything anyone wants it to
do. I'd particularly like to see the AMBER community embrace Jmol as an
alternative visualization tool. So let's get this working for you.
The solution: For example, the AMBER, GAFF atom type list is small. Perhaps
we could have the mol2 reader map that list to element symbols. All this
would be easier if there were some identifying characteristic within the
mol2 file that clearly identified it as not being "true" mol2 format. But we
can work with just about anything.
Bob
On Thu, Oct 30, 2008 at 5:15 AM, Angel Herraez <[EMAIL PROTECTED]> wrote:
> OK, I've got it
>
> Jmol is not using the atom name for element identification; mol2 has
> an "atom type" field which seems to be both the cause and the cure.
> http://www.tripos.com/data/support/mol2.pdf
>
> In your DMSO file, the atom type for the offending atoms is CT and
> H1.
>
> This is not supported by mol2 spec. See
> http://www.tripos.com/mol2/atom_types.html
> http://www.sdsc.edu/CCMS/Packages/cambridge/pluto/atom_types.html
>
> If you cahnge that to just C and H, Jmol behaves. You should maybe
> use the proper types, which seem to be C.3, H, S.o, O.2
> They also work in Jmol.
>
> > > I guess it is because the name of
> > > the atoms are the following: C1 H11 H12 H13 S O C2 H21 H22 H23
>
> As I said, not that name, but the type at column 50.
>
>
>
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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
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If nature does not answer first what we want,
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