[buster-discuss] Temp factors for solvent refining to very low values?

[Ashley Pike]

Yes - data far from ideal so not an issue with any particular processing pipeline per se. Crystal probably drifted out of the beam a little bit during collection sweep. This, combined with the anisotropic nature of diffraction,  presents challenges for data scaling and impacts data quality (data predates autoPROC pipeline at Diamond). With STARANISO have tried using either merged or unmerged data - either from Diamond autoprocessing or manually processed data. Either way, STARANISO treatment exacerbates Bfactor problem in this case. BUSTER RSCC plots show nothing out of the ordinary (at least with my relatively uneducated eye).
Thanks again,
Ashley
 
-----Original Message-----
From: Clemens Vonrhein [mailto:vonrhein at globalphasing.com] 
Sent: 21 April 2017 16:51
To: Ashley Pike
Cc: buster-discuss at globalphasing.com
Subject: Re: [buster-discuss] Temp factors for solvent refining to very low values?

Hi Ashley,

On Fri, Apr 21, 2017 at 01:27:23PM +0000, Ashley Pike wrote:
> Thanks for taking time to respond (the first response to this 
> enquiry!). For info - got to the bottom of the problem. Only appeared 
> to occur when data processed in a certain way - odd behaviour observed 
> with DIALS processed data (DIAMOND auto pipeline) and/or data run 
> through STARANISO truncation process.

Was that DIAMOND/DIALS processed data then given to the STARANISO webserver? Or something else?

Depending when you collected the data, our processing pipeline autoPROC [1] is also available and run at DIAMOND. Or you could re-process the data via autoPROC there - which will include the STARANISO analysis of anisotropy as well.

Of course, if there is something peculiar about data processing (with one or several programs/pipelines), there could be something problematic with the crystal, the data collection or the processing itself. The output from autoPROC (summary.html) can be very useful in highlighting those issues [2].

> Dataset is mildly anisotropic (3.1 x 3.7A) so suspect something going 
> wrong with scaling/compensation carried out by these processes.

Scaling wouldn't really completely compensate for that: if the crystal diffracts anisotropically the correction applied e.g. in STARANISO [3] could help yes. What do the plots from STARANISO look like?

> Solution was to simply re-process (XDS then aimless)

That is what autoPROC would/will do by default as well.

> and resulting dataset gives OK results (no atoms with B's at 3 
> although some are or the lower than expected side).

Another diagnostics plot comming out of BUSTER is the Reciprocal Space Correlation Coefficients Plot[4]. Does that give any indications of problems with the data and/or model?

You can find those plots in the buster-report output (or when running "graph_autobuster_recipCC" on the command-line).

> PS. Waters are 'high confidence' - manually placed based +fofc peaks 
> and environment although there is no higher resolution structure to 
> fall back on to confirm existence for sure.

Sounds like a sensible approach, yes.

Cheers

Clemens, Claus & Gerard (for buster-develop)

[1] http://www.globalphasing.com/autoproc/
[2] http://www.globalphasing.com/autoproc/manual/autoPROC7.html
[3] http://staraniso.globalphasing.org/
[4] http://www.globalphasing.com/buster/wiki/index.cgi?BRrecipCCplot