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 thing.

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@GMAIL.COM>
Subject: Specify chain assignment in sequence file for rebuild-in-place of phenix.autobuild

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?

Sincerely,
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@newmexicoconsortium.org

Tel: 505-431-0010