[phenixbb] assign multiple ligand conformations

Wei Shi wei.shi118 at gmail.com
Mon Feb 10 20:35:23 PST 2014

Hi everyone,
I am working with protein-ligand complex structure. For the head group in
one of the ligands in the structure, two more positions in addition to the
current position look possible according to the blue density in Coot. I am
thinking of assigning multiple occupancies/positions to this head group.
So, I am wondering what I should do to achieve this. Is the following
strategy right?
1. Fit the head group to the density at three different positions
separately in Coot and save them separately.
2. Find out the atoms that are different among the three ligand positions
and combine the same atoms with different positions and change the
occupancy of those atoms to something between 0 to 1.
3. Use Phenix. refine to refine. The occupancy refinement should be
automatically on, right?
Is this the best way to assign multiple occupancies/positions to the head
group? Thank you so much!
Also, anything to look after refinement which can tell me whether I am
assigning the right multiple conformations to the ligand?
Thank you so much!

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