[phenixbb] Optimal settings for finding NCS from density

William Chao William.Chao at crick.ac.uk
Sun Jul 5 11:42:20 PDT 2015


Hi Tom,

Thanks very much for the tips. I wonder if I need to increase peak separation in case of a long protein?

Best,

William
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From: "Terwilliger, Thomas Charles" <terwilliger at lanl.gov<mailto:terwilliger at lanl.gov>>
Date: Friday, 3 July 2015 18:08
To: William Chao <william.chao at crick.ac.uk<mailto:william.chao at crick.ac.uk>>
Cc: "phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>" <phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>>, "Terwilliger, Thomas Charles" <terwilliger at lanl.gov<mailto:terwilliger at lanl.gov>>
Subject: RE: Optimal settings for finding NCS from density

Hi William,

For find_ncs_from_density the shape of the molecule itself is not so important. What matters is if there is some local part of the molecule that is recognizable in both copies.  So I would try default parameters first.  I assume you did that and it didn't give you a useful answer...so then I would do these things:

1. try many locations :  n_center_use=20
This is the best option...it will try 20 times using density at 20 different locations to search.  If you have an older version of phenix you may need to download a nightly build to do this.

2. Try varying the resolution

3. Try varying the angular spacing of the search (delta_phi)

All the best,
Tom T

________________________________
From: CCP4 bulletin board [CCP4BB at JISCMAIL.AC.UK<mailto:CCP4BB at JISCMAIL.AC.UK>] on behalf of William Chao [William.Chao at CRICK.AC.UK<mailto:William.Chao at CRICK.AC.UK>]
Sent: Friday, July 03, 2015 10:24 AM
To: CCP4BB at JISCMAIL.AC.UK<mailto:CCP4BB at JISCMAIL.AC.UK>
Subject: [ccp4bb] Optimal settings for finding NCS from density

Dear all,

What would be the best settings to look for NCS using phenix.find_ncs_from_density on an elongated (~150A) molecule? No coordinate is available unfortunately and there should be 2 copies in a P21 space group.

Many thanks in advance!

William
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The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 215 Euston Road, London NW1 2BE.

The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 215 Euston Road, London NW1 2BE.
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