[phenixbb] Overlapping ligand-protein side chain density

Pavel Afonine pafonine at lbl.gov
Thu Mar 1 14:59:37 PST 2018

Hi Jason,

Oleg is correct, you can assign the ligand and PHE different non-blanc 
altlocs (say A and B). In this case PHE and ligand will not 'see' each 
other via repulsion term of restraints. Also, their occupancies will be 
refined independently and will be constrained to be within 0 and 1, but 
it will not make sure that they add up to 1. If you want them to add up 
to 1, then make a parameter file with a constrained group as described 
in one of examples here:

"13 typical occupancy refinement scenarios and available options in 

You can do it in the GUI too.

Let us know if you more questions or problems!


On 3/2/18 02:57, Oleg Sobolev wrote:
> Hi Jason,
>     The ligand and APHE got pushed away from one another and off of
>     their respective densities. Occupancies for both were reduced to
>     0.5 for the refinement. What am I doing wrong here? Does the
>     ligand need to have an altloc as well? But I don’t see an
>     alternative conformation.
> Yes, the ligand also needs an altloc, and it should be different from 
> PHE altloc. This way the refinement will know that these atoms don't 
> see each other. You don't have to put two alternative conformations 
> for the ligand, you can have just one with partial occupancy (<1.0) 
> which will mean that the ligand is not always there.
> Best regards,
> Oleg Sobolev.
>>     On Feb 28, 2018, at 5:35 PM, van den Bedem, Henry
>>     <vdbedem at slac.stanford.edu <mailto:vdbedem at slac.stanford.edu>> wrote:
>>     If the phe is a gatekeeper, shouldn’t the ligand be refined at
>>     partial occupancy; i.e. occupancies not necessarily have to ‘add
>>     up’ as you suggest? Maybe this link is helpful
>>     too:www.biorxiv.org/content/early/2018/01/24/253419
>>     <http://www.biorxiv.org/content/early/2018/01/24/253419>
>>     H
>>     *From:*<phenixbb-bounces at phenix-online.org
>>     <mailto:phenixbb-bounces at phenix-online.org>> on behalf of "Phan,
>>     Jason" <jason.phan at vanderbilt.edu <mailto:jason.phan at vanderbilt.edu>>
>>     *Date:*Wednesday, February 28, 2018 at 1:30 PM
>>     *To:*"phenixbb at phenix-online.org
>>     <mailto:phenixbb at phenix-online.org>" <phenixbb at phenix-online.org
>>     <mailto:phenixbb at phenix-online.org>>
>>     *Subject:*[phenixbb] Overlapping ligand-protein side chain density
>>     All,
>>     A piece of a ligand and the side chain of a “gate-keeper” Phe
>>     occupy the same space with well-defined features observed for
>>     both (resolution is 1.7 A). It looks about 50:50. How do you
>>     refine both ligand and protein side chain in this case? A couple
>>     of phenixbb suggestions for dealing with ligand-ligand
>>     overlapping density have been considered. With the first
>>     suggestion, the two entities still clashed and moved apart off of
>>     their respective densities. The second suggestion is not
>>     applicable in this case since the other molecule is not a ligand
>>     but part of the protein but it was tested anyway. Although there
>>     was no bumping, the occupancies don’t add up, resulting in a big
>>     blob of negative density around the ligand piece.
>>     ------------------------------
>>     Only two comments:
>>      1. At that resolution, constrained group occupancy refinement
>>         should work reasonably well (provided you can model the 2
>>         entities). Then you also do not have clashes between the
>>         molecules, because Occ(A)+Occ(B)=1, meaning when one (A) is
>>         there, the other one (B) is not. This works with refmac
>>         (external keyword file); if you need more sophisticated
>>         occupancy re/constraints SHELXL may offer more opportunities.
>>      2. There is no necessity for the two NCS copies of the binding
>>         site to look exactly the same (non-equivalent). Maybe there
>>         is a good reason/story (accessibility, contacts etc) for one
>>         site to be occupied differently than the other one.
>>     Best, BR
>>     ——————————————
>>     Modeling two molecules that occupy overlapping binding sites in a
>>     structure simply involves designating them as alternate
>>     conformers, with the same chain and residue number, and an
>>     occupancy that sums to 1.0. For example, if you have an AMP and
>>     an ADP that occupy the same binding site, you would define them as
>>     AAMP B 501
>>     BADP B 501
>>     and initially set the occupancies for the atoms in each conformer
>>     to the ratio (50:50, 30:70, etc.) that you observe in the density.
>>     Refinement in this manner is straightforward in PHENIX.
>>     Diana
>>     ----------------------------
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