Francesco Pietra wrote:
OK, although the issue of non correspondence of SEQRES and ATOM list remains, five models were built. I'll check the quality. On Chimera the structures are, at first sight, as expected.
Modeller does not read the SEQRES records. It only reads the structure (ATOM and HETATM records). It says this in the log file you posted originally.
A question: of the homomer in the pdb I have modeled a subunit only. Should I had best modeled all chains for the homomer? On using Chimera to get the homomer from the homology model, can the BIOMT transformation matrix given in the pdb file (for both crystallographic and non-crystallographic operation) be used with the model?
Modeller certainly has no methods for applying such matrices. I think Chimera does, but you'd be better off asking that on the Chimera mailing list.
Ben Webb, Modeller Caretaker
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