Questions about sequence file vs pdb model file in Autobuild
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
The same problem shows up when I use the new function phenix.phase_and_build
(version 1.6.3).
On Thu, Jul 22, 2010 at 10:01 AM, J J
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
Hi, 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. Shya
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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
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