[phenixbb] Add base pairing restraints between symmetric molecules

Nathaniel Echols nechols at lbl.gov
Mon Jan 28 15:30:55 PST 2013

On Mon, Jan 28, 2013 at 3:04 PM, Xiang Li <li338 at purdue.edu> wrote:
> I am trying to add base pairing restraint between the base from the model and its symmetry related molecule. I went through the tutorial but only found how to add a bond between symmetric molecules instead of the base pairing. Can anybody tell me how to do that please? Many thanks!

The automatic base pairing restraints don't work for symmetry-related
molecules at present.  Fixing this has been on our to-do list for a
while but no one has time to implement it, since it would require
significant changes to the way we detect the hydrogen bonds.  (It's
not actually that difficult to code, but actually testing and
validating the new procedure would be quite time-consuming.)  You can
still set up the base pairing one bond at a time using the custom bond
syntax, which is what I'd recommend.  The base pairs are simply
translated into this restraint type anyway.


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