[Ifeffit] Atoms restraints

[Kelly, Shelly D.]

Hi Matt,

My program for rotating a phosphate group can be easily modified to
rotate any group of atoms.  The problem being that you need to know a
little bit of perl to do it.  The top part of the perl script has a lot
of comments showing you where you would want to make these changes.
Basically you have to tell the program where all the atoms are and how
you want to rotate them.  I could easily modify the script to run from
an input file, but it seems like I should write a gui interface to the
program so that it would be more user friendly...hum..?  I wonder if
PGplot could be used to display a ball and stick model and then be used
to transfer information back and forth from perl?  Would anyone be
interested in helping me figure that part out?

Shelly

> -----Original Message-----
> From: Stefano Ciurli [mailto:stefano.ciurli at unibo.it] 
> Sent: Sunday, June 27, 2004 12:41 PM
> To: XAFS Analysis using Ifeffit
> Subject: Re: [Ifeffit] Atoms restraints
> 
> 
> 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 
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