[phenixbb] How to model domain-wide disorder in Phenix.refine (turn off bump interactions) ?

Jon Schuermann schuerjp at anl.gov
Fri Feb 8 08:52:37 PST 2013


A much simpler way (if resolution permits) is to use SHELXL with the 
PART keywords. I had a similar issue a couple of years ago and this 
worked fine, even at 2.5A. At the time, this was the only way to handle 
disorder. The problem then becomes modeling into intertwined electron 


Jonathan P. Schuermann, Ph. D.
Beamline Scientist, NE-CAT
Argonne National Laboratory, 436E
9700 S. Cass Ave.
Argonne, IL 60439

Email: schuerjp at anl.gov
Tel: (630) 252-0682

On 02/01/2013 03:15 PM, Pavel Afonine wrote:
> Hi Phil,
> the only way to do it phenix.refine is to assign different altlocs to 
> overlapping atoms, say A to one domain and B to another one. Then they 
> will not "see" each other via non-bonded interactions.
> Also, in this case phenix.refine will refine occupancies of these 
> atoms (which you can turn off if you wish). I guess by default it will 
> group occupancies such that A+B=1 per residue frame (may be not, I 
> forgot how I implemented it). That is for instance adjacent residues 
> within A conformer may have different occupancies; same for B.
> Perhaps in your case you don't want this: having all occupancies to be 
> equal within each conformer would make more sense. You can do it by 
> using this syntax:
> refinement.refine {
>     occupancies {
>       constrained_group {
>         selection = chain A and resseq 1:100 and altloc A
>         selection = chain B and resseq 1:100 and altloc B
>       }
>     }
> }
> In this case all atoms in (chain A and resseq 1:100 and altloc A) will 
> have the same occupancy between 0 and 1, and same for (chain B and 
> resseq 1:100 and altloc B); and constraint occupacy_of(A) + 
> occupancy_of(B)=1 will be used.
> Let me know if you need any help with this.
> Pavel
> On 2/1/13 12:58 PM, Phil Jeffrey wrote:
>> Hi,
>> I've got a pernicious problem where the electron density for one 
>> domain appears to extensively interpenetrate another similar domain.  
>> I'm in the process of trying to work out things like: MR solution in 
>> the wrong space group courtesy of pseudo-centering. In the meanwhile 
>> I want to model it as interpenetrating domains, and need to turn off 
>> VdeW bumps at the domain (chain) level of structure.  I can't just 
>> model it as a infinite list of alternate locations.
>> I (think) I remember how to do this in CNS (constraints interaction), 
>> but is there a way to do this in phenix ?  I could not track down a 
>> particularly promising section of either the manual or the .def/eff 
>> file(s).
>> Thanks
>> Phil Jeffrey
>> Princeton
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