[Ifeffit] Atoms restraints

[Stefano Ciurli]

Dear Matt,

I also had asked a similar question some time ago, and Bruce said 
that it should be easy to build such restraints using his programs. I 
asked the question because I have several colleagues working with 
EXCURVE, a program that implements the histidine ring as a group and 
modifies distance and orientation with respect to the scattering atom 
to which it is bound. I do not want to use EXCURVE for several 
reasons, and I like FEFF much better. There must be people out there 
in the mailing list that deal with biological samples, most often 
containing a histidine ring bound to a metal ion, and use ifeffit. I 
think the question that Max asked should be dealt with in detail. I 
think that many more people would use these programs if a routine for 
histidine ring would be implemented. Some time ago Shelly Kelly 
proposed one of her programs to rotate a phosphate group bound to a 
metal ion, and the program was made available. This is the kind of 
things, that, when implemented by experienced people like many in 
this list, would help many non-experienced people in this list.

Another possibility is of course to build several models of M(His)n, 
with varying the number of histidines and their distances and angles. 
So far, this is the best I could think of.

Stefano

>I don't know of any such library, though such constraints and
>restraints could be done -- at least in principle. (I)Feffit is
>very strongly tied to the Sum-Of-Paths approach to EXAFS, which is
>not particularly good at dealing with groups of atoms as aingle
>entities.
>
>I believe this would be a significant amount of work.  Since
>(I)Feffit uses a sum-of-paths and since paths (in the form of
>Feff's feffnnnn.dat files) do not necessarily come from a single
>cluster of atoms (this is by design and is a _benefit_ in many
>cases, though not here!), it will not necessarily be easy to
>identify the x,y,z coordinates of the individual atoms in a ring,
>let alone know that certain atoms belong together.  The path to
>each atom would have to be identified by hand.  Then, the
>mathematical constraints keeping the distances and angles between
>atoms within the ring fixed while allowing the group to move
>relative to the central atom would have to be worked out in terms
>of the allowed motions.  To be honest, I haven't really thought
>about how to do this in any detail.
>
>--Matt
>
>
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-- 
____________________________________________

Stefano Ciurli
Professor of Chemistry
Department of Agro-Environmental Science and Technology
University of Bologna
Viale Giuseppe Fanin, 40
I-40127 Bologna
Italy
Phone:	+39-051-209-6204
Fax:	+39-051-209-6203

"Fatti non foste a viver come bruti,
ma per seguir virtute e canoscenza"
Dante Alighieri - Inferno - Canto XXVI