That document is fairly old and is in dire need of revision to reflect
the modern arsenal of programs.
Nevertheless:
Putting the hinge axis along Z was a trick told to me by Steven Sheriff
back in the days when we worked on Fab structures - which after all are
classical examples of hinged molecules. One would search with separate
domain fragments - split either side of the hinge - and the
Z-orientation trick makes it easier to spot pairs of peaks from each
search model that are related to each other. In the Fab world we
searched with Fv models (VH:VL heterodimer) and CH1:CL constant region
heterodimeric models. Peaks related solely by hinge motion would have
similar alpha and beta angles and potentially different gamma (Crowther
convention Eulerian angles). Historical note: this was back in the days
when it was possible to remember the names of all the Fab fragments that
were in PDB and their respective IDs.
This ploy was more important in the days before Phaser or Molrep, which
will now gleefully try a long list of rotation function peaks for you
quite quickly, so manually parsing the list of rotation function peaks
is rather unnecessary. And perhaps counter-productive.
Split your molecule apart at the hinge, giving fragment1 and fragment2.
Attempt to find both fragments independently. Choose the one that
gives the best results: TFZ score or LLG score or discrimination between
possible space groupr or whatever you like. Then, attempt to find the
*other* fragment in the context of that first solution.
Phil Jeffrey
Princeton
On 10/5/14 3:34 AM, Luzuokun wrote:
Dear all,
I’m doing molecular replacement using Phaser. My protein is predicted to
have two domain with a “hinge” linking them. The model sequence identity
is 0.27. But the MR result is poor. I’ve tried other programme (Molrep,
MrBump, Balbes,,,_.) But no improvement was observed. I think that this
is due to the “open” or “closed” conformation around the hinge. I was
told that I could place the Z axis along the hinge
(http://xray0.princeton.edu/~phil/Facility/Guides/MolecularReplacement.html),
could anyone tell me more details about how to do next?
Thanks!
Lu Zuokun
