Re: [ccp4bb] RMSD

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

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Subject: refine phosphotyrosine
From: JINJIN ZHANG zhang {- dot -} 508 {- at -} OSU {- dot -} EDU
Date: 2007-03-14

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Subject: Re: RMSD
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-03-14

Subject: Re: RMSD
From: Edwin Pozharski epozh001 {- at -} UMARYLAND {- dot -} EDU
Date: 2007-03-14

Does anyone know if Refmac includes riding hydrogens in rmsd
calculation? Because if it does, then the rmsd will indeed be lower for
Refmac, since these bonds are kept at ideal length.

Ed.

john kryst wrote:
> Hi ccp4bb !!!
>
> Does the rmsd estimation (for eg. rmsd_bonds ) depends on the program
> we use ??
>
> Example : shifting from Refmac to CNS. There appears to be an increase
> in rmsd of bonds even without refining the structure in CNS. Is the
> estimation methods are different or am i doing something wrong !!
>
> Thanks for your valuable inputs.
>
> regards
> john

--
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
----------------------------------------------
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
------------------------------ / Lao Tse /

CCP4bb navigation

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

Previous message:
Subject: refine phosphotyrosine
From: JINJIN ZHANG zhang {- dot -} 508 {- at -} OSU {- dot -} EDU
Date: 2007-03-14

Next message:
Subject: Re: RMSD
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-03-14