[phenixbb] clashscore discrepancies

[Pavel Afonine]

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 
> <mailto: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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