[phenixbb] Partially occupied side chains in special position
pafonine at lbl.gov
Wed Sep 5 20:32:57 PDT 2012
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
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