Re: [ccp4bb] refined vs 'others'

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

Previous message:
Subject: Research Associate (team leader) and Post doctoral positions
From: Jinrong Min jinrong_min {- at -} YAHOO {- dot -} COM
Date: 2007-11-07

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Subject: Re: refined vs 'others'
From: Pavel Afonine pafonine {- at -} LBL {- dot -} GOV
Date: 2007-11-07

Subject: Re: refined vs 'others'
From: Bernhard Rupp bernhardrupp {- at -} SBCGLOBAL {- dot -} NET
Date: 2007-11-07

All right, one more peculiar question on the subject:
If that is true - that
> "others" in case means the bonds to the hydrogens added in riding
positions during refinement

then how comes that in example 2veh the restraint listing does not have
'others' but still says that hydrogens were added?

HEADER ISOMERASE 24-OCT-07 2VEH
REMARK 2 RESOLUTION. 2.19 ANGSTROMS.

REMARK 3

REMARK 3 REFINEMENT.

REMARK 3 PROGRAM : REFMAC 5.2.0019

REMARK 3 BOND LENGTHS REFINED (A): 2921 ; 0.026 ; 0.022

REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL

REMARK 3 BOND ANGLES REFINED (DEGREES): 3989 ; 2.131 ; 1.945

REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
.
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE

REMARK 3 RIDING POSITIONS.

I reran that (same refmac version) but I cannot reproduce the output.

a)If I select 'generate hydrogens' = HYRD ALL, then I get proper 'others'
and
the 'Hydrogens have been added' statement. Seems they were added and used.

c)If I select 'use when in file' = HYRD YES (there are none), then
the 'others' is missing as expected but the

REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE

REMARK 3 RIDING POSITIONS.

That is odd and seems illogical? If they ARE added but NOT used, it should
probably say exactly that and not the same when added AND used. Does 'added'

and 'used' mean different things indeed?

d) So......is 2veh refined with riding hydrogens used or not?

Best, br

CCP4bb navigation

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

Previous message:
Subject: Research Associate (team leader) and Post doctoral positions
From: Jinrong Min jinrong_min {- at -} YAHOO {- dot -} COM
Date: 2007-11-07

Next message:
Subject: Re: refined vs 'others'
From: Pavel Afonine pafonine {- at -} LBL {- dot -} GOV
Date: 2007-11-07