[phenixbb] AUTOBUILD: sequence file for multiple chains

Gino Cingolani Gino.Cingolani at jefferson.edu
Sun Feb 3 07:18:41 PST 2013


Hi All, 

my model contains multiple chains and I would like Autobuild to build them all.
What is the correct way to give multiple sequences (in FASTA format) to Autobuild?

In my 'seq.dat' file, shall I leave one (or two) spaces in between one sequence and the other?

Thanks,

Gino

******************************************************************************
Gino Cingolani, Ph.D.
Associate Professor
Thomas Jefferson University
Dept. of Biochemistry & Molecular Biology
233 South 10th Street - Room 826
Philadelphia PA 19107
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E-mail:   gino.cingolani at jefferson.edu
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"Nati non foste per viver come bruti, ma per seguir virtute e canoscenza"
("You were not born to live like brutes, but to follow virtue and knowledge") Dante,
The Divine Comedy (Inferno,  XXVI, vv. 119-120)


________________________________________
From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Terwilliger, Thomas C [terwilliger at lanl.gov]
Sent: Saturday, February 02, 2013 9:55 PM
To: PHENIX user mailing list
Subject: Re: [phenixbb] autosol MIR with more than one native?

Hi Ed,
Unfortunately, autosol only has a way to deal with one native, so you'd need to average them together or run 2 runs, one with each.
All the best,
Tom T

________________________________________
From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Edward A. Berry [BerryE at upstate.edu]
Sent: Saturday, February 02, 2013 10:39 AM
To: PHENIX user mailing list
Subject: [phenixbb] autosol MIR with more than one native?

Is it possible to run phenix.autosol MIR problem with two "native" datasets?
And does this make sense, or would it be better to scale the two natives
together to make a single dataset before running autosol?
eab
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