I have adjusted the MOL2 reader so that
1) it displays (in this case) "14 1 *" as the spacegroup -- "*" here
will mean "no symmetry operations available"
2) Jmol does autobonding even when symmetry is present, provided the
spacegroup has no symmetry operations other than (x y z)
This should do the trick. Aidan, you can then enter:
load "t.mol2" {2 2 2}
connect (?1*) (?2*) delete
display (?1* and not x*)
or you could
set defaultloadscript "define model1 (?1* and not x*);define model2 (?2*
and not x*);connect (model1) (model2) delete;display model1"
load "t.mol2" {2 2 2}
and only the first model will be shown. Then you can use
display model2
or
display model1 or model2
at your convenience.
This will be part of Jmol 11.1.14, out later today, I expect.
Bob
Aidan Heerdegen wrote:
>>>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
>
>
>
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