Angel, Please check me on the syntax of what I'm suggesting below. I usually do
this with molfiles - not mol2
Birgit,
I'm not sure why you want to store the Jmol mep data in the mol2 file, but here
is an approach that will work. You can store jmol script in a mol2 file that
will automatically run when the file is loaded. You simply add a comment at the
beginning of the mol2 file with this format:
# jmolscript: YourScript
Below is an example with methanol that simply calculates the charges, but the
script can be more complex. The jmolscript must be lower case.
# Created by: Discovery Studio
# Creation time: Wed Oct 07 19:16:15 Central Daylight Time 2009
# jmolscript: select *; calculate partialcharge
@<TRIPOS>MOLECULE
methanol.mol
6 5 0 0 0
SMALL
USER_CHARGES
@<TRIPOS>ATOM
1 C1 -0.6666 0.0000 0.1880 C.3 1 SUBUNIT 0.0321
2 O2 0.7369 0.0000 -0.0343 O.3 1 SUBUNIT -0.3995
3 H3 -1.1484 0.0000 -0.8131 H 1 SUBUNIT 0.0526
4 H4 -0.9079 0.9530 0.7055 H 1 SUBUNIT 0.0526
5 H5 -0.9079 -0.9530 0.7055 H 1 SUBUNIT 0.0526
6 H6 1.1484 0.0000 0.8131 H 1 SUBUNIT 0.2096
@<TRIPOS>BOND
1 1 2 1
2 1 3 1
3 1 4 1
4 1 5 1
5 2 6 1
@<SCITEGIC>ATOM_PROPERTY
Formal Charge
SciTegic.value.StringValue
1 0
2 0
3 0
4 0
5 0
6 0
@<SCITEGIC>ATOM_PROPERTY
pdb_tempFactor
SciTegic.value.DoubleValue
1 0.00
2 0.00
3 0.00
4 0.00
5 0.00
6 0.00
@<SCITEGIC>ATOM_PROPERTY
pdb_occupancy
SciTegic.value.DoubleValue
1 1.00
2 1.00
3 1.00
4 1.00
5 1.00
6 1.00
Otis
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