[phenixbb] Error in sequence assignment

Tom Terwilliger tterwilliger at newmexicoconsortium.org
Sun Nov 17 16:32:18 PST 2019

Hi Nicholas,

I'm afraid there isn't a way to say which sequence goes with which chain.

I would suggest using the tool phenix.replace_side_chains.  Give it 1 chain
and 1 sequence and if they have the same length it should just put it in.
If it doesn't work, try phenix.sequence_from_map which can do the same

Let me know if that doesn't do it!
All the best,
Tom T

Date:    Sun, 17 Nov 2019 17:07:16 -0500
From:    Nicholas Gao <dominion146 at GMAIL.COM>
Subject: Specify chain assignment in sequence file for rebuild-in-place of

Dear CCP4,

I currently have an MR solution that has the wrong sequence.  The pdb file
of the solution contains 3 chains, and I'd like to use the rebuild-in-place
functionality within phenix.autobuild to correct the sequence of all 3
chains.  Phenix allows me to supply a sequence file as input for this job,
it's not clear to me how I tell the program which sequence should be
assigned to which chain.  Anyone know how to do this?

Nicholas Gao

Thomas C Terwilliger
Laboratory Fellow, Los Alamos National Laboratory
Senior Scientist, New Mexico Consortium
100 Entrada Dr, Los Alamos, NM 87544
Email: tterwilliger at newmexicoconsortium.org
Tel: 505-431-0010
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