[phenixbb] positive density around heavy metals

Subhani Bandara ramssb17 at gmail.com
Wed Mar 28 09:05:50 PDT 2012

Hi everyone,

I have refined a protein with a metal-chelate complex at 1.4 resolution and
saw positive density around some metals that are on a two fold. I refined
those chelator complexes with fixed occupancy  to avoid the negative
density seen around it as they are partially occupied. Also I had to avoid
xyz refinement after fixing them on special position, to avoid moving away
from two fold. I have attached a figure of one of those complexes. If I
increase occupancy then it shows negative density. How can I get rid of
this positive density.

Thanks in advance for the help

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