[phenixbb] Molprobity percentile statistic

[hari jayaram]

Thanks Nat and Pavel for your emails,
Thanks for the suggestion of using phenix.polygon. The comparative
analysis of my structure relative to others at my resolution was what
I was after.

And thats the reason I liked the molprobity statistics expressed as
percentile since it helped me realize how far I have to go relative to
other structures at the PDB. If its not too difficult can I cast my
vote to report it inside the phenix GUI. Its just that running the
full analysis inside of phenix is significantly faster than running it
on the duke webservers.

In molprobity If I  remember correctly the overall score is some
weighted average,  and the molprobity paper also cautions against
taking it too literally. Also If I remember the molprobity percentiles
are absolute and not only composed of structures at similar
resolutions .

Regardless  thanks for the hint about phenix.polygon .
I just looked at my phenix.polygon report and I am afraid its a little
asymmetric.

Hari


On Mon, Oct 19, 2009 at 9:58 PM, hari jayaram <harijay at gmail.com> wrote:
> Thanks Nat and Pavel for your emails,
> Thanks for the suggestion of using phenix.polygon. The comparative
> analysis of my structure relative to others at my resolution was what
> I was after.
>
> And thats the reason I liked the molprobity statistics expressed as
> percentile since it helped me realize how far I have to go relative to
> other structures at the PDB. If its not too difficult can I cast my
> vote to report it inside the phenix GUI. Its just that running the
> full analysis inside of phenix is significantly faster than running it
> on the duke webservers.
>
> In molprobity If I  remember correctly the overall score is some
> weighted average,  and the molprobity paper also cautions against
> taking it too literally. Also If I remember the molprobity percentiles
> are absolute and not only composed of structures at similar
> resolutions .
>
> Regardless  thanks for the hint about phenix.polygon .
> I am attaching  a snapshot of my polygon ..I an afraid its a little
> asymmetric.
>
> Hari
>
> On Mon, Oct 19, 2009 at 7:48 PM, Pavel Afonine <PAfonine at lbl.gov> wrote:
>> Hi Hari,
>>
>> if you run phenix.model_vs_data you will get those numbers (namely:
>> Ramachandran outliers, clashscores, CB-deviations; although you will not
>> get "Molprobity score" simply because I don't know what it is and so I
>> didn't add it):
>>
>> phenix.model_vs_data model.pdb data.mtz
>>
>> Nat: every time time you run model_vs_data for whatever purpose (getting
>> fmodel, etc...) you get an object that contains all these numbers.
>>
>> Pavel.
>>
>>
>> On 10/19/09 3:32 PM, hari jayaram wrote:
>>> Hi i just started using the phenix GUI front-end to Molprobity . Its
>>> really nice the way it plugs into coot and displays all the statistics
>>> etc.
>>> Is there any place that it also reports the percentile clashscore and
>>> percentile Molprobity score for overall model quality  a la the
>>> webserver at molprobity.biochem.duke.edu
>>>
>>> Thanks
>>> Hari
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>