[Ifeffit] Atoms restraints

[Bruce Ravel]

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 at phys.washington.edu
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