Dear Max,
I'm a new user of the Feffit package and I have a question about atom restraints for the fitting.
I'm dealing with metal binding protein, and somehow I need to keep some atoms in a fixed structure (mainly histidine rings) while leaving a certain degree of freedom to the remaining atoms of the environment.
I'd like to know if there is a library containing histidine structure restraints or if exists any input file of a similar matter.
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
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
Good morning! Max asked about histidine rings and Stephano said:
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.
Perhaps I should clarify. I used the word "easy" in the sense that physicists often use that word -- that is, I see it as a solvable math problem. That doesn't mean that I know the solution off the top of my head, just that it is no harder than solving a geometry problem. Shelly mentioned a bit of code she has written for rotating a phosphate group. I haven't seen this code, but I would guess that it is the sort of "easy" solution I was refering to. The central point here is that Ifeffit (and by extension, Artemis) allows you to write such things as the distance between atoms in the form of an almost arbitrary algebraic expression. Given that handling a rigid group like a histidine ring is no more than a geometry problem and given that geometry problems are solved by algebra, Ifeffit (and by extension, Artemis) are completely up to this task. For the sake of complete disclosure, I should say that I have never, not even once in my career, measured or analyzed data on a sample containing a histidine ring. That should provide the complete context for my assertion that the problem is "easy". ;-) HTH, B -- Bruce Ravel ----------------------------------- ravel@phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
participants (3)
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Bruce Ravel -
Matt Newville -
Stefano Ciurli