Re: [ccp4bb] RMSD

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

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

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From: "Sabini, Elisabetta" sabini {- at -} UIC {- dot -} EDU
Date: 2007-03-14

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

When there are riding hydrogens then refmac gives rmsd for them
seperately (like rmsd for others. That is atoms not included in
refinement)

Garib

On 14 Mar 2007, at 17:02, Edwin Pozharski wrote:

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

Next message:
Subject: B-factors in Shelxl
From: "Sabini, Elisabetta" sabini {- at -} UIC {- dot -} EDU
Date: 2007-03-14