[ccp4bb] SUMMARY: Getting started with twin refinement with SHELXL

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

Previous message:
Subject: Re: twin fraction varies between crystals?
From: "Radisky, Evette S {- dot -} Ph {- dot -} D {- dot -} " Radisky {- dot -} Evette {- at -} MAYO {- dot -} EDU
Date: 2007-04-18

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Subject: Re: twin fraction varies between crystals?
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-04-18

Subject: SUMMARY: Getting started with twin refinement with SHELXL
From: "Radisky, Evette S {- dot -} Ph {- dot -} D {- dot -} " Radisky {- dot -} Evette {- at -} MAYO {- dot -} EDU
Date: 2007-04-18

Thanks to everyone for all the great suggestions.

Regarding which mtz to use as a starting point, advice was to either re-run scala selecting the option to output unmerged reflections, "scaled, unmerged & no outliers" under "Customize scala process" in ccp4i (Miguel Ortiz Lombardía), or to go ahead and use the merged intensities from the previous Truncate job (Carlos Frazao).

Regarding Free-R selection, the consensus was that it will be better to use the thin shells method to select a new set; SHELXPRO has an option to do this automatically (Miguel, Carlos, Artem Lyubimov). Of course, most pointed out that this will necessitate going back to the original MR model, rather than picking up from the refmac refined model.

Peter Zwart and Mark Mayer both suggested the new development version of phenix.refine as an alternative (and easy to use, they promise) refinement program that can deal with twinned data.

Thanks again,
Evette

Evette S. Radisky, Ph.D.
Assistant Professor and Associate Consultant II
Mayo Clinic Cancer Center
Griffin Cancer Research Building, Rm 310
4500 San Pablo Road
Jacksonville, FL 32224
(904) 953-6372 (office)
(904) 953-2857 (lab)

________________________________

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Radisky, Evette S. Ph.D.
Sent: Friday, April 13, 2007 4:23 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Twin refinement with SHELXL

Dear All,

I have 1.4 A data and a molecular replacement solution for a crystal indexed as C2, with beta approximately equal to 90. Refinement with refmac is progressing poorly, and intensity statistics (Truncate) and other twinning tests (xtriage) suggest pseudo-merohedral twinning with a twin fraction around 0.44. I want to try refining in SHELXL with a twin-specific target function, but I have some questions about how to get started.

SHELX documentation indicates that the reflection file should contain intensities rather than amplitudes, and preferably unmerged data. I have been refining against an mtz file that was integrated with MOSFLM, scaled and merged with SCALA, converted to amplitudes with TRUNCATE, then had freeR flags assigned. I am getting the mtz2various patch recently mentioned on the bb, that will make an mtz file into a proper SHELX hkl file, but which mtz file do I convert? The mtz output by TRUNCATE contains both F's and I's, so I could use that one to get measured intensities, or do I actually need to go back further to get my unmerged reflections?

A second question relates to Rfree flags - should I transfer the ones I've been using up until now? They were a randomly assigned 5%. Now I've read that using the "thin shell" method is better for twinned crystals and NCS, but I don't know exactly how that is done... any recommendations?

Thanks!
Evette

Evette S. Radisky, Ph.D.
Assistant Professor and Associate Consultant II
Mayo Clinic Cancer Center
Griffin Cancer Research Building, Rm 310
4500 San Pablo Road
Jacksonville, FL 32224
(904) 953-6372 (office)
(904) 953-2857 (lab)

CCP4bb navigation

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

Next message:
Subject: Re: twin fraction varies between crystals?
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-04-18