[phenixbb] autobuilding homomers

Ingemar Andre ingemar.andre at biochemistry.lu.se
Sun Oct 28 05:35:04 PDT 2012

I have a question about the proper procedure for building homomers. My  
test case is a trimeric coiled-coil with 3-fold symmetry (trimer in  
assymetric unit). My input model is a trimer with three chains (A,B,C)  
with identical sequence. If I run phenix autobuild  
(rebuild_in_place=False) with this model I get a structure with decent  
R/Rfree. However, there are some issues:

1) Helix 1 consists of chain A in the output structure. There is a  
jump in the sequence number for chain A at the end. However,  
disregarding this chain break the full sequence is correct for helix 1.
2) Helix 2 consists of chain B + C in the output structure. The chain  
B has the correct sequence for helix 2. Chain C has partly the right  
sequence for helix 2.
3) Helix 3 consists of chain C in the output structure. Chain C has  
partly the correct sequence for helix 3. Lots jumps in the sequence  

GIven that I know its has three subunits with identical sequences I  
gather it should be possible to have autobuild generate structures  
with three chains with identical sequences. I have tested a few  
things. With and without giving it the sequence file corresponding to  
the sequence of a monomer. With and without enforcing ncs based on the  
input model (find_ncs=False input_ncs_file=find_ncs.ncs_spec). I am  
never able to build sequence-symmetric structures with  
rebuild_in_place=False for any homomer I have tried to build. I have  
limited experience with phenix so it is likely I am missing something  
obvious. In any case, I would appreciate your input on this.

Best regards,


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