[phenixbb] DTT mediated disulfide crosslink across a crystallographic two-fold! (Pavel Afonine)

Nathaniel Echols nechols at lbl.gov
Wed Aug 4 10:47:46 PDT 2010

On Wed, Aug 4, 2010 at 10:43 AM, Joseph Noel <noel at salk.edu> wrote:

> Thanks Pavel! I will wait and see what Ralf says regarding defining the
> symmetry operator. If I am using the GUI for phenix.refine should I create a
> new file with the bond definition you mention and include it as one of the
> starting files or should I edit the Refine_*.eff file that gets created and
> insert it somewhere there?

Either of these should work, but there is also a third option: open Settings
menu, select "Geometry restraints", then "Edit geometry restraints", and
define custom bonds there.  (FYI, if you're going to edit the .eff file
directly, you want to select "Edit parameters and run" when clicking the run
button - not sure if that's what you meant, but other methods involving the
GUI tend to not work, which has been a source of confusion for some
command-line users.)

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