[phenixbb] Optimal settings for finding NCS from density
Terwilliger, Thomas Charles
terwilliger at lanl.gov
Fri Jul 3 10:08:11 PDT 2015
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,
From: CCP4 bulletin board [CCP4BB at JISCMAIL.AC.UK] on behalf of William Chao [William.Chao at CRICK.AC.UK]
Sent: Friday, July 03, 2015 10:24 AM
To: CCP4BB at JISCMAIL.AC.UK
Subject: [ccp4bb] Optimal settings for finding NCS from density
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!
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