>> Ok. Would it help to have a lookup table in the Mol2Reader that will
>> convert from these numbers to a Hermann-Mauguin symbol?
> When I put this together I considered that, but on reflection decided
> that it was just too big a table. If you can show me that it is not so
> large, then we could talk about somehow making it loadable.
I'll get back to you if the CCDC folks get back to me ..
> What is the correct Hall symbol for "14 1", by the way?
This is what Mercury spat out when converting such a file to cif:
_symmetry_cell_setting monoclinic
_symmetry_space_group_name_H-M 'P 21/c'
_symmetry_Int_Tables_number 14
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 x,y,z
2 -x,1/2+y,1/2-z
3 -x,-y,-z
4 x,1/2-y,1/2+z
>> 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?
> not sure. It may be a mol2 reader bug.
It would be great if this worked like PDB and CIF.
> The CIF file format is better for disorder, and Jmol will display the
> disorder properly.
atom_disorder_group etc? Does anyone have a good reference for how
this should be used? To be honest we have a workflow which involves
cif -> mol2 using Mercury, as we're confident that all the space
group stuff is handled correctly, and we mostly source our structures
from the CCDC database.
>> 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.
> OK, I get it. That explains my problem above, and why the files are
> not
> fractional coordinates. Right, so "14 1" is just a reference. You
> don't
> need it. I've done a bit of an adjustment of the MOL2 reader:
>
> 1) If the @<TRIPOS>CRYSIN line is there, then it assigns P1 as the
> spacegroup
> 2) If that line is there, it automatically converts the nonfractional
> coordinates to fractional so that it can do the symmetry operations.
Sounds great for me, and acceptable for other people hopefully.
> In the mean time, you have to include P1 and the unit cell on the
> load line.
>
> Then just use
>
> load filename.mol2 {1 1 1}
> connect
> connect (?1*) (?2*) delete
>
> That third line deletes all bonds between the two disorder sets. It
> works because of the nice way that CSD assigns names; there could be
> some problems with this as a general method if two-letter atoms
> such as
> Ca are present because "?" stands for "just one letter." But in this
> case it is fine.
Thanks. You're right that it could get tricky (we do encounter Cl a
fair bit) and I don't really want a solution that relies on atom
labels -- this is bound to come to a sticky end. I want to use Jmol
in an application to be driven by naive users so I need a robust
solution.
With the fix above to bonding propagation all should be right with my
world.
Thanks again for your help Bob, and the great work on Jmol!
Cheerio
Aidan
--
Research School of Chemistry
Australian National University
ACT 0200, Australia
-------------------------------------------------------------------------
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
