[phenixbb] AutoMR:Multi-subunit model

S. Saif Hasan sshasan at purdue.edu
Tue Jun 22 08:16:08 PDT 2010


Hello,

Thanks. When I use the PDB structure with 8 polypeptides as the search model and
specify the 8 sequences together, I get this warning from AutoMR-

"ASYMMETRIC UNIT TOO FULL (scattering from ensembles =1.82 of total scattering)-
TOTAL SCATTERING INCREASED: To get rid of this warning message do one of the
following: (1) Increasing the scattering in the ASU (keyword COMPOSITION)
because you have more scattering than you thought (2) Decrease the number of
ensembles you are packing into the ASU (keywords SOLUTION and SEARCH)"

Could this be a problem in missing some additional prosthetic groups ? I did not
specify any non-protein groups but the search model has them.

-- 
S. Saif Hasan

Graduate Student
Department of Biological Sciences
Hockmeyer Hall of Structural Biology
Purdue University
240 S. Martin Jischke Drive
West Lafayette, IN 47907



Quoting "Thomas C. Terwilliger" <terwilliger at lanl.gov>:

> Hi Saif,
> 
> If I understand you correctly, you can specify the search model with 8
> polypeptides as one PDB file and all 8 sequences (separated by blank lines
> or lines starting with ">" in one sequence file.  Also component 1 can be
> all 8 polypeptides and copies=1.
> 
> All the best,
> Tom T
> 
>  >> Hello,
> >>
> >> I have a membrane protein complex made up of 8 different polypeptides
> >> present in
> >> two copies each (16mer). The asymmetric unit is the octamer, as
> determined
> >> from
> >> previous crystallographic studies. To carry out molecular replacement
> with
> >> the
> >> phases from the published structure in AutoMR, should I specify the
> >> coordinates
> >> of the search model and its overall sequence identity as one file or
> >> should I
> >> break it down for each subunit ? Also, for the asymmetric unit contents,
> >> should
> >> I specify the sequence or mass of each subunit separately (as component
> 1,
> >> 2 and
> >> so on) keeping the number of copies fixed at 1 ? There is no NCS.
> >>
> >> Thanks.
> >> --
> >> S. Saif Hasan
> >>
> >> Graduate Student
> >> Department of Biological Sciences
> >> Hockmeyer Hall of Structural Biology
> >> Purdue University
> >> 240 S. Martin Jischke Drive
> >> West Lafayette, IN 47907
> >>
> >>
> >>
> >>
> >>
> >> _______________________________________________
> >> phenixbb mailing list
> >> phenixbb at phenix-online.org
> >> http://phenix-online.org/mailman/listinfo/phenixbb
> >>
> 
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> 




More information about the phenixbb mailing list