[phenixbb] refining two chains into same density

Pavel Afonine pafonine at lbl.gov
Fri May 2 06:03:30 PDT 2014

Hi Scott,

you can do it in phenix.refine, please have a look at corresponding 
documentation page:


All you need to do is:
     1) Place two chains into density (which I figure you've already done)
     2) Make sure each chain has a non-blank altloc, say A and B
     3) Run phenix.refine.

If you need more help with this you can send me PDB file (and indicate 
chains in questions) and I will make sure it works correctly.


On 5/2/14, 5:50 AM, Scott Horowitz wrote:
> I have a strange case where I think there are two separate protein 
> chains that are partially occupying the same spot (i.e. two 
> proteins:one binding site=half of each bound). I'd really like to try 
> to simultaneously refine both chains at partial occupancy into this 
> density, but when I tried this (not surprisingly) it terminated 
> because there were some overlapping atomic coordinates between the two 
> chains. Is there a way to work around this?
> Thanks,
> Scott

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