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As a follow up,
If you also take into consideration the time that would be required to
check packing of the MR solution in O after using AMoRe or Molrep, then a
faster way might be to implement a script to run PHASER in non-GUI mode (just
the keyworded scripts from command line) by using the fast rotation and
translation function options, keeping all other parameters constant, and then
running the packing check.
I suppose all this is based on the assumption that you may have changes
in cell dimensions, etc. and would like to start from MR.
Debanu.
----- Original Message -----
From: Debanu Das <[EMAIL PROTECTED]>
Date: Wednesday, December 20, 2006 7:49 pm
Subject: Re: [ccp4bb]: Fastest Molecular Replacement Code?
To: Steven Muchmore <[EMAIL PROTECTED]>
Cc: [email protected]
> *** For details on how to be removed from this list visit the ***
> *** CCP4 home page http://www.ccp4.ac.uk ***
>
>
> 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:
>
> >*** For details on how to be removed from this list visit the ***
> >*** CCP4 home page http://www.ccp4.ac.uk ***
> >
> >
> >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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> >Tired of spam? Yahoo! Mail has the best spam protection around
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> >
> >
>
