[phenixbb] Restraining altloc related atoms during refinement

Nathaniel Echols nechols at lbl.gov
Thu May 20 10:34:23 PDT 2010

On Thu, May 20, 2010 at 8:54 AM, John Pascal
<John.Pascal at mail.jci.tju.edu>wrote:

> I would like to restrain the positions of ribose/phosphate atoms of
> altloc 'A' to the positions of those in altloc 'B'.  Problem is,
> altloc A and altloc B are different residue types, so phenix.refine
> exits stating that there are no common atoms when I enter the
> following NCS-type restraint:

Wild guess - do you have a non-palindromic DNA helix bound in two different

You can use the custom bond definitions to do this, but it's going to be
messy.  The documentation is here:


You would need separate entries for each pair of atoms.  I guess you'll want
a distance_ideal of zero, and a small sigma (and perhaps slack).  In the
GUI, open Settings->Geometry restraints->Edit geometry restraints to add
bonds.  Might be easier to just write them out in a file and add that to the
inputs list, however.

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