[ccp4bb] w average & riding hydrogens

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

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Subject: Re: c-terminus modification in crystals
From: Dale Tronrud det102 {- at -} UOXRAY {- dot -} UOREGON {- dot -} EDU
Date: 2008-01-02

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Subject: Re: w average & riding hydrogens
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-01-02

Subject: w average & riding hydrogens
From: Roni Gordon rgordon {- at -} UHNRESEARCH {- dot -} CA
Date: 2008-01-02

Hi all,

I observed a very strange phenomenon with a high-resolution dataset
phased via rigid-body refinement (using the apo target); the "generate
all hydrogens" option seems to throw w_average out of whack:

========================
Without riding hydrogens:
========================

CGMAT cycle number = 1

w_average 0.320431173
GRID VALUES:
0.109375 Angstrom for D
5.18181801 Angstrom^2 for B

R/Rfree: 0.3210/0.3262
Overall FOM: 0.6653
ML based su of positional parameters = 0.3351
ML based su of thermal parameters = 14.0097

After 10 rounds:
R/Rfree = 0.225/0.283, FOM = 0.755
RMSD B/A/C = 0.016/1.579/0.107

========================
With riding hydrogens:
========================

CGMAT cycle number = 1

w_average 7.62235823E-6
GRID VALUES:
0.109375 Angstrom for D
5.133333321 Angstrom^2 for B

R/Rfree: 0.3184/0.3261
Overall FOM: 0.0023
ML based su of positional parameters = 30945.4297
ML based su of thermal parameters = *************

After 10 rounds:
R/Rfree = 0.529/0.551, FOM = 0.012
RMSD B/A/C = 1.558/49.687/10.240

I've never seen such drastic behaviour before, especially with something
so benign as riding hydrogens. Toggling this parameter alone seems to
cause the aforementioned effects (i.e. success vs utter failure).

I'm using Refmac v5.2.0019 from CCP4 6.0.2.

Any thoughts/suggestions?

Thanks,

Roni Gordon

CCP4bb navigation

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

Previous message:
Subject: Re: c-terminus modification in crystals
From: Dale Tronrud det102 {- at -} UOXRAY {- dot -} UOREGON {- dot -} EDU
Date: 2008-01-02

Next message:
Subject: Re: w average & riding hydrogens
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-01-02