[phenixbb] Refinement with partial model - question

Alexandre Urzhumtsev sacha at igbmc.fr
Thu Apr 1 08:40:21 PDT 2010

Hi, Pavel and Peter,

>>Alternatively, is there a program that will build dummy atoms (zero 
>>occupancy) automatically in a map in all peaks above a certain sigma 
>>(i.e. atoms just for mask calculation).
>I'm not aware of such program although it's a couple of hours to write 
>one. I would probably even write it if I ever see a clear need for it or 
>evidence for its usefulness. So far I don't understand why you really need it?

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.
         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. Would it be 
easier and faster ?

         I understand that any solution requires your personal time (as 
usually, your initial time estimations multiplied by 10 :-)

Best regards,


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