To: [email protected], [email protected]
From: "Roger M. Sullivan" [[email protected]]
Date: Sun, 07 Oct 2001 13:54:11 -500
Reply-To: [email protected]
Subject: [sdpd] (unknown)

Greetings All, 

Please help me with insertion of rigid bodies in GSAS.  I have been 
using Ian Swain's guide (for which I am very grateful) at:
 
http://www.ccp14.ac.uk/ccp/web-mirrors/ian-swainson/fireside_fuide_to_rigid_bodies.pdf

My difficulty is knowing the proper input to orient my rigid bodies.  
I chose a local cartesian coordinate system such that x//a  z//axb y//(axb)xc
and placed the origins at the atom which is always 0 0 0 in vector 
input (central atom in r.b. type 1, bent L-M-L; central atom of r.b. 
type 2 tetrahedral ML4) so my cartesian vectors are oriented with 
respect to the fractional coordinate system of the monoclinic cell 
(b unique).  When I enter zero angles I seem to be getting a random 
orientation.  Also why are there six rotation angles? Are these related 
to the six unique elements of the transformation matrix between the 
cartesian coordinate system and the fractional monoclinic coordinate 
system?

Further background on the problem.  I am trying to solve a structure 
from powder diffraction data.  I know the structure of some similar 
materials and have tried both EXTRA/SIRPOW and ESPOIR to generate 
models for refinement.  I believe I have the proper fragements (this 
is also supported by MAS NMR data), and a roughly correct orientation 
in the unit cell from ESPOIR (using HKL, Fobs generated by EXTRA).  
I wish to try and refine the orientation of the bent and tetrahedral 
fragments as rigid bodies.

Roger M. Sullivan
Department of Chemistry, Box 8204
North Carolina State University
Raleigh, NC 27695-8204

Phone:  919.515.8924
FAX:    919.515.8909

[email protected]

To: [email protected], [email protected]
From: "Swainson, Ian - NRC" [[email protected]]
Date: Tue, 9 Oct 2001 10:15:41 -0400
Subject: RE: [sdpd] (unknown)

Hi Roger,

I'm afraid the short notes were designed to be talked around, so they are an
annotated set of handouts on the absolute basics: not sure how well they
work as a "stand alone" document.

I have to confess to only ever having done relatively simple RBs myself, but
you always need to start with an _orthogonal_ Cartesian system for your
molecule (at least I believe this to be a requirement).  I wasn't sure from
your description whether you had done that or not. The closest example in my
short notes (I think) to your situation would be (ND4)2PdCl6, however the
notes are not as detailed on that one.  Suffice it to say that the
tetrahedra/octahedra I used can be set up basically irrespective of the
crystal frame. 

 It is only when you do the insertion (e.g. I 1 1 etc...) that your
orthogonal RB axes become linked to your crystal axes via the transforms you
describe. This is probably the "random" orientation you describe.

 I am not sure if it is a typo in your message, or my short notes, but Z
(not Y) // axb and Y (not Z) //(axb)xa not (axb)xc. Apologies if that is my
fault. I will check to see.

So for a std monoclinic system (I'm thinking while I'm typing so please
check!) , X//a, Z//axb (i.e. 1/c*) and Y//(1/c*)x a which would be b, I
think. You should therefore be able to relate your XYZ orthogonal Cartesian
description to a,b,1/c* of the crystal frame

(The examples I have done, I have not had to worry too much about the intial
orientations too much. I have actually found that for simple molecular
crystals, if you damp everything, GSAS actually manages to find the correct
orientation for you, once you start refining(!) However, that probably
depends heavily on the complexity of the problem.)

 As to 6 angles: I think Bob Vondreele once told me that three XYZ rotations
are provided for an initial guess and three more to refine (see how wrong
you were!). I have only ever used three for everything. Hope this is some
help.

Ian

Ian Swainson
Neutron Program for Materials Research, NRC
Chalk River Labs, Stn 18
Chalk River, ON, K0J 1P0
CANADA
Tel: +1 613 584 8811 ext 3995 Fax: +1 613 584 4040

Date: Tue, 09 Oct 2001 09:40:13 -0600
From: Allen Larson [[email protected]]
To: [email protected]
Subject: Re:[sdpd](unknown)   Re: 6 rotations in GSAS rigid bodies

I might insert a word or two here concerning rigid bodies in GSAS.

The reason for 6 rotations angles in GSAS is to provide flexibility to molecules
such as nitro methane permitting refinement of rotations of the methyl and nitro
groups about an axis that goes through the molecule origin. 

Three rotation angles are used to orient the complete rigid group and the other
three are available to allow up to secondary groups rotation about axes that go
through to group origin. In general you should not be using them for most rigid
bodies. 

Since much of the design work on GSAS rigid bodies was done about 30 years ago
(10 to 15 years before I met Bob Von Dreele), it might be worth while to
rethink some of the details again.

Allen C. Larson