[phenixbb] Special position ambiguity

Pavel Afonine pafonine at lbl.gov
Mon Oct 5 15:15:11 PDT 2015

Hi Sarath,

you need to use

custom_nonbonded_symmetry_exclusions="chain B and resname ..."

as I explained in my email to you earlier this morning. This will 
exclude the ligand from clashing with its symmetry mate.

Let me know if you have questions.


On 10/2/15 01:23, R Sarath wrote:
> Hi,
> I have to place two carbon atoms (C3 and C6 - in para positions) of a 
> cyclohexane ring from a ligand in special positions (I4122 
> space-group), with C6' from the symmetry generated molecule 
> overlapping on C3 of the ligand. Can someone please suggest me a way 
> to do so. I tried changing the occupancies of C3 and C6 to 0.5. After 
> refinement, I observe that they don't overlap but instead spoil the 
> fitting of neighbouring atoms of the ligand.
> Thanks in advance,
> Regards,
> Sarath
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