[phenixbb] phenix.refine using anomalous concepts for neutron data?

Pavel Afonine pafonine at lbl.gov
Wed May 29 14:10:35 PDT 2013

Hi Derek,

>> Then how you ended up having anomalous data set for your neutron 
>> observations: FO,SIGFO,DANO,SIGDANO,ISYM ?
> As I mentioned in my original mail, I've discovered that SCALA always 
> outputs I+ and I- no matter what you do. From the manual:
> "Normally anomalous scattering is ignored during the scale 
> determination (I+ & I- observations are treated together), but the 
> merged file always contains I+ & I-, even if the ANOMALOUS OFF command 
> is used."
> Thus if you don't take special precautions, e.g. in TRUNCATE, these 
> will be converted to F+ and F- and (I now know) phenix.refine will use 
> them. However I've now discovered that the keyword ANOMALOUS NO in 
> TRUNCATE will prevent output of the anomalous columns altogether.

oh I see how this may be a problem. Though unfortunately I don't think 
there is a robust way of catching this in phenix.refine.. phenix.refine 
strives to do a good refinement job but obviously it can't make sure the 
user provides meaningful data. Any suggestions are welcome!

>> All in all, if you don't have anomalous data make sure your inputs 
>> files do not have spurious (anomalous) arrays: phenix.refine can't 
>> read your mind to see what you have done in your diffraction 
>> experiment - it's beyond the scope of what it's supposed to do!
> Fine, I've now learned an important lesson in input/output checking! 
> But could I politely suggest that an improvement in phenix.refine's 
> mind-reading capabilities: if the user mistakenly inputs a file as 
> neutron data with anomalous columns in, then these should be ignored, 
> as the concept is by default incompatible with neutron data?

Yes, this is doable: adding to my todo list now.

> Finally, it would also be nice if the neutron maps and not just the 
> X-ray maps were displayed in Coot during refinement and if the summary 
> panel at the end of refinement showed statistics for the neutron data 
> as well as for the X-ray data.

Let's see what Nat thinks (he is the main and only GUI developer).

Also, the concept of joint XN refinement may change as outlined in 
slides 28-32 here:


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