[phenixbb] Restraining to existing model

Peter Zwart PHZwart at lbl.gov
Thu Oct 11 14:04:06 PDT 2007

I guess that you could do it the with the tools that are available,
but would require some scripting to get it going, and will be
relatively slow and possibly not recommended.

phenix.refine allows the possibility to add distance restraints
between any atom specified:


what you could do, is take the high resolution structure you have,
find all 1-4 distances that you think should (not around the active
site) be invariant (this is the scripting bit) and write them out as a
custom bond with an appropriate sigma and feed this into
phenix.refine. This scheme is similar to the NCS restraints in shelx i

Again, this is possible, but not sure if recommended.
There are probably other (possibly better) ways of doing it as well.


2007/10/11, Frank von Delft <frank.vondelft at sgc.ox.ac.uk>:
> Hi, this was discussed some time ago (a few years?) on ccp4:  is there a
> way (even a fudge) to restrain a refinement at low resolution to an
> existing (much) higher resolution model?
> The scenario:  you have a 1.9A structure, beautiful etc.  You do a
> ligand soak, get 2.6A data, and only really want to see what's in the
> active site.  This requires refinement (to improve phases), but most of
> the structure shouldn't change (often the case, especially if it's the
> the same crystal form).  So you only want things to change that really
> are different.
> Thanks
> phx
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