Re: [ccp4bb] The importance of USING our validation tools

- Protein crystallography

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

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Subject: Re: The importance of USING our validation tools
From: Dominika Borek dominika {- at -} WORK {- dot -} SWMED {- dot -} EDU
Date: 2007-08-16

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Subject: Re: The importance of USING our validation tools
From: "Dunten, Pete W {- dot -} " pete {- at -} SLAC {- dot -} STANFORD {- dot -} EDU
Date: 2007-08-16

A few thoughts following on Richard Baxter and George Sheldrick . . .

Re: gaps in the lattice – see the tyr-tRNA synthase structures (1tya for example). Fersht has written a whole book full of insights from these structures.

Re: Phaser Z scores. For some MR work with two xtal forms of a structure, I got Z scores of 4.0 and 4.3 for the rotation and translation searches in one form, and 8.7 and 3.5 for the other, using a model with 18% sequence identity. So you don't need great Z scores for the solution to be right. The map calculated with MR phases had a correlation coefficient of 0.22 with the final model.

Re: confusing columns in an mtz file. I had the same thought. If the column types were different for experimental versus calculated F's, and refmac only allowed you to refine against an experimental F, could this kind of trouble be avoided? Of course you'd want an option to override the default, for people doing weird things. Dunno about cns or phenix, but didn't we recently see messages about how hard it was to work with cns reflection files, leading to a new conversion program from Kevin? It seems possible to get the wrong column there as well.

Re: images. Be careful what you sign - the user agreements with synchrotron facilities in the USA may state that the data are public, and not private (as the funding is from the public).

Pete

CCP4bb navigation

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

Previous message:
Subject: Re: The importance of USING our validation tools
From: Dominika Borek dominika {- at -} WORK {- dot -} SWMED {- dot -} EDU
Date: 2007-08-16

Next message:
Subject: nature cb3 response
From: Bernhard Rupp bernhardrupp {- at -} SBCGLOBAL {- dot -} NET
Date: 2007-08-16