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"
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
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