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 /
>
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