[phenixbb] Refinement with partial model - question

Pavel Afonine PAfonine at lbl.gov
Thu Apr 1 17:06:12 PDT 2010

> I think Peter touches the point that we discussed previously, and this 
> is one more reason to think about it in practical terms : it would be 
> nice if phenix has an alternative option NOT to build a mask from the 
> model but to read it outside. For example, it may be an EM envelope, 
> or a mask built by any automated procedure.

I still don't see why it is necessary / important.
Also, if you know a better way of mask calculation (or alternative way 
that sometimes may be better), then I would rather implement that then 
spend time on an option to allow a user-made mask.

>         An intermediate option is that indeed phenix gives a procedure 
> to fill an external mask by dummy atoms with occ=0 and then you add 
> them to you "regular" model and build the mask by your usual procedure. 

If I see a case where it really makes positive difference I will think 
of implementing it -:)


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