Thread View: sci.techniques.xtallography
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Started by Lachlan Cranswick
Wed, 16 Aug 2000 01:20
Example why Platon/Addsym should be mandatory for crystallographers?
Author: Lachlan Cranswick
Date: Wed, 16 Aug 2000 01:20
Date: Wed, 16 Aug 2000 01:20
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I hope this isn't considered too "hyped up" but there is
a new Platon/Addsym tutorial on the CCP14 site titled:
"An example of why Platon/Addsym should be considered a mandatory
program for all crystallographers"
http://www.ccp14.ac.uk/tutorial/platon/addsymb.htm
This is based on the structure and spacegroups involved with the
recent Short Communication in Acta Cryst "P1 or P-1? Corrigendum",
Acta Cryst B56 (2000) 744 from Richard E. Marsh
------
As posted before: "Addsym (building on Yvon LePage's powerful
published MISSYM (C) algorithm) allows the identification of missed
symmetry; which thus minimizes the chances of publishing structures
in the wrong spacegroup. It can also identify miss-fitting atoms for
the benefit of the crystallographer who can then check if these
are legitimately breaking a possible better symmetry."
The above tutorial includes all the NIXQAM related files in
Shelx format that people can try out for themselves if in
the mood.
The Original Triclinic P1 structure (published 1997)
The revised Monoclinic C2 structure (1999)
The Platon/Addsym Orthorhombic Fdd2 solution (2000)
It also shows how easy Platon can be used to routinely check
for missing symmetry in structure files - and output an
updated Shelx file if some extra symmetry is found.
-----
Platon by Ton Spek is available off the internet for UNIX
and Windows:
Homepage:
http://www.cryst.chem.uu.nl/platon/
Mirrors:
UK http://www.ccp14.ac.uk/ccp/web-mirrors/platon-spek/platon/
CA http://ccp14.sims.nrc.ca/ccp/web-mirrors/platon-spek/platon/index.html
AU ftp://ftp.minerals.csiro.au/pub/xtallography/ccp14/ccp/web-mirrors/platon-spek/platon/index.html
FTP Download of Platon for UNIX:
ftp://xraysoft.chem.uu.nl/pub/
Mirrors:
UK http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/platon-spek/pub/
ftp://ftp.ccp14.dl.ac.uk/ccp14/ftp-mirror/platon-spek/pub/
CA http://ccp14.sims.nrc.ca/ccp/ccp14/ftp-mirror/platon-spek/pub/
AU ftp://ftp.minerals.csiro.au/pub/xtallography/ccp14/ccp/ccp14/ftp-mirror/platon-spek/pub/
======
Platon for Windows (ported by Louis Farrugia)
http://www.chem.gla.ac.uk/~louis/platon97/
Mirrors:
UK http://www.ccp14.ac.uk/ccp/web-mirrors/farrugia/~louis/platon97/
CA http://ccp14.sims.nrc.ca/ccp/web-mirrors/farrugia/~louis/platon97/index.html
AU ftp://ftp.minerals.csiro.au/pub/xtallography/ccp14/ccp/web-mirrors/farrugia/~louis/platon97/index.html
======
Any corrections, suggestions, etc for the above tutorial greatfully
accepted.
Lachlan.
-------
Lachlan M. D. Cranswick
Collaborative Computational Project No 14 (CCP14)
for Single Crystal and Powder Diffraction
Daresbury Laboratory, Warrington, WA4 4AD U.K
Tel: +44-1925-603703 Fax: +44-1925-603124
E-mail: l.cranswick@dl.ac.uk Ext: 3703 Room C14
http://www.ccp14.ac.uk
Re: Example why Platon/Addsym should be mandatory for crystallographers?
Author: Pedro M. Matias
Date: Wed, 16 Aug 2000 00:00
Date: Wed, 16 Aug 2000 00:00
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Lachlan Cranswick wrote:
> I hope this isn't considered too "hyped up" but there is
> a new Platon/Addsym tutorial on the CCP14 site titled:
>
> "An example of why Platon/Addsym should be considered a mandatory
> program for all crystallographers"
>
> http://www.ccp14.ac.uk/tutorial/platon/addsymb.htm
>
> This is based on the structure and spacegroups involved with the
> recent Short Communication in Acta Cryst "P1 or P-1? Corrigendum",
> Acta Cryst B56 (2000) 744 from Richard E. Marsh
>
> ------
>
...
I just tried out the example and it's really awesome what the program can do. However,
I don't like loose ends so I tried the triclinic cell on the CAD-4 software and TRANS C
gives the following results:
CD7>trans
M, R or C? [C]
Nr FOM Lattice Bra
44 .000000 TRICLINIC P OBTUSE ( .000)
Solutions rejected on FOM:
Nr FOM Lattice Bravais Type
26 .005315 ORTHORHOMBIC F ACUTE ( .305)
29 .003778 MONOCLINIC C ACUTE ( .216)
27 .005315 MONOCLINIC C ACUTE ( .305)
28 .005315 MONOCLINIC C ACUTE ( .305)
Transformation-number?26
Orientation matrix:
R11= .201961 R12= -.024318 R13= -.005776
R21= -.036941 R22= .004454 R23= -.032756
R31= .131892 R32= .038298 R33= .000000
S11= 16.7936 S22= 481.2467 S33= 903.9512
S32= 2.3606 S31= -.6605 S21= .1967
A = 4.0980 B = 21.9373 C = 30.0658
Alp = 89.7949 Bet = 90.3072 Gam = 89.8746 Vol= 2702.8269
Reciprocal axes:
A*= .2440 B*= .0456 C*= .0333
Alp*= 90.2057 Bet*= 89.6924 Gam*= 90.1265
In my opinion, this may mean one of two things:
1. not enough reflections for getting a good initial orientation matrix (insufficient sampling
of reciprocal space);
2. poorly aligned diffractometer.
There are probably other possibilities but these are the two that come to my mind...
Cheers,
Pedro Matias
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