[phenixbb] clashscore discrepancies

[Jeff Headd]

Hi Alex,

Yes, you need to use 1.8.2-1309 or later. We've made changes to how both
Phenix and MolProbity handle x-H bond lengths, as well as vdW radii, which
effect how clashscores are calculated. They should be in sync now, but if
you do run into discrepancies please let us know.

Jeff


On Thu, Apr 25, 2013 at 1:16 AM, Pavel Afonine <pafonine at lbl.gov> wrote:

>  Hi Alex,
>
> please try recent (1.8.2-1309 or later) version of Phenix and I hope that
> should eliminate the discrepancy. If not please let us know.
>
> Pavel
>
>
> On 4/24/13 8:38 PM, Alex Theodossis wrote:
>
>  Dear phenixbb,
>
>  Have refined a 1.05A structure with riding hydrogen model in phenix
> v1.8.1-1168 and doing final validation.
>
>  The molprobity statistics output by phenix include:
> all atom clashscore = 4.12
> Rotamer outliers = 0.71%
> Overall score = 1.2
>
>  Put through the molprobity server I am given the option of analysing
> with existing hydrogen model, or replacing with the 'electron-cloud
> parameters' they recommend for X-ray crystal structures. The results end up
> being very different:
>
>                                           existing H model:
>      electron-cloud model:
> All atom clash score:            4.66 (78th percentile)             3.72
> (85th percentile)
> Poor rotamers:                      1.14%
>  1.14%
> Overall score:                        1.28 (88th percentile)
>  1.20 (92nd percentile)
>
>  While all three scenarios give acceptable statistics, I am surprised by
> the inconsistency in the results given by molprobity, even when using the
> same hydrogen model.
> I am also wondering whether I am using a suboptimal riding model in my
> refinement (generated using phenix ready-set).
>
>  Can anyone advise on the reason for these inconsistencies (is it just
> due to differences in the version of molprobity being run in each case). Is
> there anything I should be doing differently?
>
>  Thanks in advance.
>
>
>
>
>
>
>
> On 18 November 2012 12:36, Alex Theodossis <alex.theodossis at monash.edu>wrote:
>
>> Hi,
>>
>>  I'm attempting to install the latest version of phenix on mac 10.5.8,
>> using the command line installer.
>>
>>  Installation proceeds well until towards the end, where it hangs on:
>>
>>  precompiling .py files
>>
>>  I can leave it for up to an hour without any further progress, but upon
>> typing:
>>
>>  ctrl+c
>>
>>  The installation comes back to life and proceeds to completion.
>>
>>  Can anyone advise as to what might be causing this and on how reliable
>> this installation is going to be?
>>
>>  Thanks in advance.
>>
>>
>>
>
>
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