Re: [ccp4bb] practical limits of MR?

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

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From: Peter Adrian Meyer pam52 {- at -} CORNELL {- dot -} EDU
Date: 2007-03-08

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Subject: Re: practical limits of MR?
From: Peter Adrian Meyer pam52 {- at -} CORNELL {- dot -} EDU
Date: 2007-03-08

> Anyway, with the improvements in software we may have reached a stage
> where the limitation of the search model is not whether or not you can
> find a MR solution, but whether or not that solution is going to help
> you determine the structure. What you can and can't get away with
> depends on the resolution of your native dataset and the power of
> density modification, in particular the presence/absence of NCS.

I'll second this (although I'm a bit late to the conversation). When I
was doing some test runs on phaser (using a known structure with
experimental amplitudes), I got good solutions using a partial model that
was only 10% of the total mass (which I only tested because I had my
script incorrect...I wouldn't have expected this to work). These agreed
with the known position, allowing for origin shifts. Even allowing for
the fact that this is with 100% sequence identity, I was very impressed by
phaser.

> It's always worth a try but if finding a MR solution is a challenge you
> should consider how useful a solution, if found, is going to be.

An MR solution that's very incomplete could still be very useful for
anomalous/heavy atom site location (no issues with alternative origins or
handedness), particularly with weak sites. 10% total mass would probably
give too much noise in anomalous difference fourier, but ~40-50% seems to
work fine.

Pete

Pete Meyer
Fu Lab
BMCB grad student
Cornell University

CCP4bb navigation

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

Previous message:
Subject: summary: questions on SF likelihood
From: Peter Adrian Meyer pam52 {- at -} CORNELL {- dot -} EDU
Date: 2007-03-08

Next message:
Subject: resolution and hydrogen bonds
From: Jacqueline Vitali jackie {- dot -} vitali {- at -} GMAIL {- dot -} COM
Date: 2007-03-09