> The mol2 file contains:
>
> @<TRIPOS>CRYSIN
> 9.88140 4.88480 12.02160 90.00000 90.49350 90.00000 14 1
>
> OK, here's the deal: This is not enough information, at least for
> Jmol.
> Jmol doesn't have a full library of all the possible spacegroups AND
> setting options (14 1 here) and generally prefers Hall symbols.
Ok. Would it help to have a lookup table in the Mol2Reader that will
convert from these numbers to a Hermann-Mauguin symbol?
I might be able to manage this .. I have just sent a letter to the
nice folks at CCDC asking for this information. Otherwise some sort
of manual reverse-engineering using Mercury would work (in a nasty
and long winded way).
> Note
> that the file does not include fractional coordinates, either. But you
> can still use the data. Just supply the needed information on the
> LOAD line:
>
> load "t.mol2" {1 1 1} spacegroup "P21/c" unitcell {9.88140 4.88480
> 12.02160 90.00000 90.49350 90.00000 }
Thanks. Works a charm.
> load "t.mol2" {1 1 1} spacegroup "P 21/n 1 1" unitcell {9.88140
> 4.88480 12.02160 90.00000 90.49350 90.00000 }
>
>
> By the way, with this file the following wildcards may be of use:
>
> connect; hide (?2*)
Very nice, but is there a reason the molecules that are produced by
applying cell translations aren't using the same bonding as the
molecules inside the cell?
I use mol2 files because I have disordered structures where molecules
overlap and mol2 is a useful file format for doing this. Auto bonding
doesn't work with overlapped disordered molecules, all sorts of
spurious bonds are created. The hide command above takes care of this
but doesn't allow disordered molecules to be viewed together.
I can concatenate two disordered structures together (and get frames/
models) but if I show more than one frame at a time the unit cell
disappears.
> I tried a couple of space groups, and none of them work properly.
> Let me
> know if there is still something wrong with Jmol in this regard. Maybe
> an origin problem?
Nope, just odd (wrong?) files. They are "pre-packed", so the symmetry
has already been applied, so they should have a spacegroup of P1. I
use mercury to produce these from the original file and this is how
they come out. For my purposes I think I will be ok just specifying a
space group on the command line, as I will use exclusively these
prepacked cells I think.
Cheers
Aidan
-------------------------------------------------------------------------
Take Surveys. Earn Cash. Influence the Future of IT
Join SourceForge.net's Techsay panel and you'll get the chance to share your
opinions on IT & business topics through brief surveys-and earn cash
http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
