[phenixbb] unit cell dimesions

Pavel Afonine pafonine at lbl.gov
Wed May 13 12:23:43 PDT 2020

Hi Leonard,

reflection file editor has no other choice but the input data file you 
provide. If you provide multiple files with different crystal symmetry 
(SG and uc dimensions), it will pick one of the available and show it in 
Output options. This is your chance to check it and change it if 
necessary. If you don't do it, the choice may not be what you want.

phenix.refine will inspect all inputs for the crystal symmetry 
information (command line, parameter file, input model file, and input 
data files; note, data can come in different data file, like flags in 
one file and Fobs in another, for example), and choose the "working 
crystal symmetry", and then check it against crystal symmetry from the 
data. There are quite some complex logic behind that choice. It will 
show you that choice and you always can accept it or change to what you 

Clearly, to make things easier and not rely on programs guessing, it's 
best to supply inputs with consistent crystal symmetry inputs.


On 5/13/20 09:08, Thomas, Leonard M. wrote:
> Hello All,
> I have  run into something that has me a bit puzzled.  When finishing 
> up a structure we ended reprocessing the data to get nice statistics 
> for deposition, I don’t want to get into that discussion.  Upon 
> reprocessing the unit cell dimensions shifted slightly, 0.05 A or so. 
>  The PDB file used had the unit cell from the original 
> solution/refinement while the data set cell dimensions were different. 
>  I ran the newly processed reflection data set through the reflection 
> editor in order to transfer the Rfree set.  Now the really odd thing 
> is that I ended up reprocessing a couple times and transferring over 
> the Rfree set once more.  The cell dimensions on the final reflection 
> file is from not the original reflection file/PDB but one that was 
> used with an intermediate cutoff between the two, it is not the cell 
> dimensions in the input reflection either.  Just for completeness the 
> data were processed using XDS at SSRL.
> My question is where does phenix.refine pick up the unit cell 
> dimensions and were does the reflection file editor pick them up?
> Best Regards
> Len

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