[ccp4bb] tricky molecular replacement III

- Protein crystallography

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

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Subject: MacPro Xeon NVIDIA Quadro FX4500 Stereo Nuvision problem
From: Gretchen Meinke gretchen {- dot -} meinke {- at -} TUFTS {- dot -} EDU
Date: 2007-11-09

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Subject: Re: Torsion angle restraints
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-11-11

Subject: tricky molecular replacement III
From: Jan Abendroth jan {- dot -} abendroth {- at -} GMAIL {- dot -} COM
Date: 2007-11-10

Hi all,
thanks to several tremendously helpful replies I got the molecular
replacement, which I bugged the ccp4bb with during the last weeks, under
control. Thanks for all the input, I'll send out a summary soon.

One question remains, though:

With an improved search model, the molecular replacement in Phaser got much
stronger. This time, the correct rotation solution was on top of the list,
and translation Z-scores were >10. ARP/wARP could not build into these maps,
even after cross crystal averaging. In the end, no utter surprise given the
low homology of the search model with my protein of interest.
Molrep also succeeded with this model . After the standard sequence
rotation/translation/rigid body, Molrep reported R-factors of 31% and 41%
for data up to 4AA or 3AA, respectively. However, when I used the Molrep
output for a rigid body refinement in Refmac, R-factors were at 55% for 4AA
data.

This huge gap of R-factors from Molrep and Refmac is really puzzling to me.
Any ideas?

Cheers
Jan

CCP4bb navigation

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

Previous message:
Subject: MacPro Xeon NVIDIA Quadro FX4500 Stereo Nuvision problem
From: Gretchen Meinke gretchen {- dot -} meinke {- at -} TUFTS {- dot -} EDU
Date: 2007-11-09

Next message:
Subject: Re: Torsion angle restraints
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-11-11