Hi Phil, Thank you for the input. I would like to get CCP4ers input. I deal with multiple domain cytokine receptors in a manner very similar to antibody molecules.
Have people have more correct solutions searching for 1 domain sequentially and then other domains OR searching for multiple domains all at once? I am curious to hear peoples’ experiences on this topic? Cheers, Scott ************************************************ Scott T. R. Walsh, PhD Assistant Professor University of Maryland IBBR/CBMG 3127E CARB-2 9600 Gudelsky Drive Rockville, MD 20850 USA phone: (240) 314-6478 fax: (240) 314-6225 email: swals...@umd.edu On Oct 6, 2014, at 2:11 PM, Phil Jeffrey <pjeff...@princeton.edu> wrote: > 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
