Re: [phenixbb] Optimal settings for finding NCS from density

5 Jul 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" mailto:[email protected]>
Date: Friday, 3 July 2015 18:08
To: William Chao mailto:[email protected]>
Cc: "[email protected]mailto:[email protected]" mailto:[email protected]>, "Terwilliger, Thomas Charles" mailto:[email protected]>
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 [[email protected]mailto:[email protected]] on behalf of William Chao [[email protected]mailto:[email protected]]
Sent: Friday, July 03, 2015 10:24 AM
To: [email protected]mailto:[email protected]
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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