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.

Pavel

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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