[phenixbb] Partially occupied side chains in special position

Pavel Afonine pafonine at lbl.gov
Wed Sep 5 20:32:57 PDT 2012

Hi Nick,

could you please try using "custom_nonbonded_symmetry_exclusions" 
parameter to specify selections for involved atoms to be excluded from 
non-bonded interactions. If this does not help, please send me PDB file 
(and optionally data file) and specify which atoms do not behave as 


custom_nonbonded_symmetry_exclusions="(chain A and resseq 123 and altloc 
A) or (chain B and resseq 345 and sidechain) or (chain Z and element Zn)"

See phenix.refine command-line manual for more examples illustrating 
atom selection syntax. You can do it from the command line or using the GUI.

I will not have email from a few hours from now till mid of next week, 
so I may not respond very quickly.


On 9/4/12 8:02 AM, Nicholas Keep wrote:
> I have an ARG which has nice density for its guanadinium group on a 2 
> fold. This is the same conformer from the two copies.  The occupancy 
> of this chain is set to 0.5 and a second conformer that does not cross 
> the two fold is provided.
> There is clearly a repulsion term in phenix refines that moves the 
> quanadinium away from the two fold.  Do the atoms of the guanadinum 
> group need to have an occupancy of 0.25? Can I specify no repulsion 
> between these symmetry elements?
> Best wishes
> Nick

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