[phenixbb] Questions about sequence file vs pdb model file in Autobuild

sbiswas2 at ncsu.edu sbiswas2 at ncsu.edu
Thu Jul 22 07:10:42 PDT 2010

How does your density look? I had similar issues with one of my
structures, I think there is no solution at this moment in autobuild. This
happens when your density is poor. It just randomly puts side chains not
corresponding to your sequence also the numberings are not OK.

> Dear All,
> Facts:
> -input: a sequence file, a pdb model file, an mtz file; the sequence file
> is
> the same as the pdb model except that the sequence file has 6 more
> residues
> at N-terminal; the pdb model is almost the same as my protein structure.
> (In a word, I just want to add a few more residues to the current pdb
> model. Of course I can do it in coot by manually placing residues at
> the N-terminal, but why not autobuild?)
> -problem: the output chain sequence is not the same as the sequence file
> (not the same as the input model file either). It misses some residues at
> the N-terminal and it adds some residues at the C-terminal (but
> disconnected
> from the C-terminal). Is it normal in autobuild? How to correct it?
> Thanks.
> Jason
> U Pitt
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