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Hi,
After having played around extensively with PHASER, EPMR, BEAST
(replaced by PHASER), MOLREP, and AMoRe (although not by a systematic
study),
I would vote for the fast rotation and translation searches in AMoRe as
the quickest way to obtain solutions for easy and repetitive MR cases
(especially after taking into account all the parameters, file names,
etc. that have to be entered in some of the GUIs). I have been able to
go through sorting--> tabling-->rot-->trans-->fitting-->shifting to
final solution, faster in a stand alone version of AMoRe than it takes
to finish running any of the other programs.
With an easy MR case in which the correct solution will show up as the
top peaks in the rot & trans searches, it should be fairly simple to
write a script to automatically take the top solution from each step and
feed it to the next to obtain the final solution.
AMoRe's rot and trans searches literally take only a few seconds to run,
which is not surprising since the whole concept is based on breaking up
the 6D search into 2x 3D searches using the fast rotation and
translation functions.
I would choose this over writing something................
Debanu.
--
Debanu Das
University of California
Berkeley
Steven Muchmore wrote:
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All;
What's the hands down, fastest gun in the west,
A-numero uno, Speedy Gonzalez, speediest molecular
replacement code in existence?
I know that's a strange question, since most molrep
codes aren't optimized as much for speed but for
getting the correct answer.
But what if you have a real easy MR problem, but you'd
like to do it a whole bunch of times? What's the
fastest single-threaded canned app out there?
What stripped-down code would you use? Should I just
break down and steal^H^H^H^H^H write something myself?
Heavens forbid!
Just wondering...
Steve
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