[phenixbb] RMS angles and comprehensive validation in phenix

Katherine Sippel katherine.sippel at gmail.com
Fri Sep 19 11:38:09 PDT 2014


The point I was trying to make was that, assuming that there are no large
outliers skewing the final RMS(angles), an overall RMS of 2.3-2.7 would be
worrisome.

On Fri, Sep 19, 2014 at 1:21 PM, Pavel Afonine <pafonine at lbl.gov> wrote:

> Hi Ed,
>
> yes, that's right. One is to detect severe outliers that may screw up the
> overall numbers. The other one is to compare these overall numbers with
> those derived from similar structures available in the data base.
>
> Pavel
>
>
> On 9/19/14 11:05 AM, Edward A. Berry wrote:
>
>> Two different histograms involved here?
>> For one structure, histogram of the deviations at all the different
>> bonds, angles
>> For the entire PDB, histogram of rmsd of all the different structures
>>
>> On 09/19/2014 12:50 PM, Katherine Sippel 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
>>> <mailto: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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>>>
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-- 
"Nil illegitimo carborundum"* - *Didactylos
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