Re: [ccp4bb] brute force molecular replacement

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: brute force molecular replacement
From: Xie Jiabao xie {- dot -} jiabao {- at -} YAHOO {- dot -} COM
Date: 2009-02-01

Many thanks to all who responded to my earlier query (Drs. Paul Swepston, Randy Read and Nicholas Glykos). I am trying to determine the structure of a very long coiled
coil dimer (roughly 150 residues long) by molecular replacement. I don't know
if it forms a canonical coiled coil from end to end (it probably doesn't). I seem to get the right solution using
different lengths of polyala (and polygly and modeled ones with side-chains)
coiled coils as my search models (maps show some density for unmodeled parts of
the coiled coil structure). However, building a model accounting for the entire
sequence, getting the correct chain direction and placing residue side-chains
have proved difficult. And my R-facs have never improved beyond the low 50s
during different refinement attempts. At
the moment, I have 3 more or less contiguous 30 residue stretches of coiled
coil found by 3 independent molecular replacement attempts using epmr (This was
done to account for possible bends, stutters in the dimer). I am trying to get
the rest of the model by new rounds of molecular replacement using epmr. I have
carried out exhaustive runs using epmr. But I haven't found the rest of the
model. What are the options available to me
with molecular replacement? I have tried molrep, phaser and amore from the ccp4
suite. My diffraction data is quite good (data between 25 and 2 A with an Rsym
of 8%). I am currently using Qs on Dr. Glykos' advice. Can I run Qs when a partial structure is available?
Xie

--- On Sat, 1/24/09, Randy J. Read wrote:
From: Randy J. Read
Subject: Re: [ccp4bb] brute force molecular replacement
To: CCP4BB@JISCMAIL.AC.UK
Date: Saturday, January 24, 2009, 8:37 PM

Hi,

If you were desperate for BRUTE, I could probably dig out the source code. My
somewhat newer program BEAST also does a brute-force search, and you could get
that by downloading an older version of CCP4 or, again, directly from me.

Our new program Phaser also has brute-force rotation and translation search
options, in addition to the faster FFT-based searches. If you wanted to do a
full 6D brute-force search for a molecule, you'd have to use some tricks,
but it would be possible.

However, the reason we suggested to CCP4 that they should deprecate BEAST is
that we haven't found a case where doing a brute-force search solves a
structure that can't be solved faster with Phaser using the fast search
methods. (If anyone has such a case, we'd be delighted to learn what it has
to teach us!)

Is there a particular reason you'd like to try a brute-force search?

Regards,

Randy Read

On Jan 24 2009, Xie Jiabao wrote:

> Dear all,
>
> From where can I download the molecular replacement program BRUTE? What
are the other brute force programs for molecular replacement out there?
>
> Thanks in advance,
>
> Xie
>
>
>
>

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Google marks CCP4 web site as a potential security threat
From: Bernhard Rupp bernhardrupp {- at -} SBCGLOBAL {- dot -} NET
Date: 2009-01-31

Next message:
Subject: Re: Caution - 120 Hz LCDs: Not CRT killers yet...
From: Warren DeLano warren {- at -} DELSCI {- dot -} COM
Date: 2009-02-01