[phenixbb] Autobuild in to "extra density"

Flath, Ben bef206 at mail.usask.ca
Tue Jan 9 12:50:41 PST 2018

Hi All
I have a structure I am building/refining at 2.6 A resolution, there are three NSC molecules in P321 unit cell. Each monomer contains 150 aa and are at least 95% built. Here is where I need some help. There is extra density. Gel and Mass Spec data suggests that there is a smaller MW weight protein/band contained in the crystals which is most likely a fragment of my target protein. Basically I have 3 NCS copies plus a half a molecule that does not appear to have the same tertiary structure (LSQ & SSM do not align well) as the other 3 molecules. I have been able to build several poly-A helices in to this density and R/Rfree are now 0.25/0.31.

My Question is, how do I set up a phenix run (presumably autobuild) So that I can begin to dock my sequence in to these chains and have them extended? Does my sequence input file need to include more than one sequence string? Asking autobuild to find and build 4 NCS groups does not seem to build anything in to this extra density (Also the sigma level for the extra density chains seems to be somewhat less than the well-defined part) I am guessing this is a rebuild_in_place=false job? Can I specify only a certain chain only to be rebuilt? Also are there some special considerations with regard to density modification I should be aware of?

Any help would be much appreciated.


Benjamin Flath, M.Sc.
Research Assistant, Cygler Lab
University of Saskatchewan
Department of Biochemistry
Room 3D40 HSCI
Box 27, 107 Wiggins Road
Saskatoon, SK
S7N 5E5
Phone: 306 220-7355
email: benjamin.f at usask.ca<mailto:benjamin.f at usask.ca>

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