[phenixbb] RMS angles and comprehensive validation in phenix

[George Devaniranjan]

If the RMS of angles are so deviant and the structure is high resolution
then wouldn't it show up in COOT density fitting?

On Fri, Sep 19, 2014 at 12:50 PM, Katherine Sippel <
katherine.sippel at gmail.com> wrote:

> This is from Phenix's FAQ page...
>
> *"My resolution is X Angstroms; what should RMS(bonds) and RMS(angles) be?*
>
> This is somewhat controversial, but absolute upper limits for a
> well-refined protein structure at high resolution are typically 0.02 for
> RMS(bonds) and 2.0 for RMS(angles); usually they will be significantly
> lower. As resolution decreases the acceptable deviation from geometry
> restraints also decreases, so at 3.5 Angstrom, more appropriate values
> would be 0.01 and 1.0."
>
> If the histogram shows that the RMS(angles) average higher than 2 then I
> think that would be a result of poorly refined structures skewing the graph
> rather than a reflection of what the RMS should be.
>
>
>
> On Fri, Sep 19, 2014 at 1:57 AM, Pavel Afonine <pafonine at lbl.gov> wrote:
>
>>  Hi,
>>
>> if you make sure these values are not caused by a handful of atoms that
>> flew a distance apart for whatever reason then values like ok to me. This
>> is why looking at a histogram of deviations (bond, angles etc) is way more
>> useful than looking at just one number!
>>
>> Pavel
>>
>>
>> On 9/18/14 1:32 PM, C wrote:
>>
>> Hi,
>>
>>  Refining using phenix I find the RMS angle drifting towards 2.3-2.7
>> range when validating the resulting structure.
>>
>>  These are high resolution structures and I was wondering if someone
>> could comment on whether 2.3-2.7 values are worrisome?
>> Thank you
>>
>>
>>
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>>
>>
>
>
> --
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