Hi Tom,
Thank you for your detailed answers. I did refinement with or without NCS restraints (But in both cases, I did not provide any NCS operator. So I assume what it does is C1 symmetry?). Without NCS restraints refinement always outperform with the NCS restraint, such as Ramachandra, bond, angle, rotamer outliers. However, the biggest issue I have right now is that after refinement, not every chain is identical since they were refined independently? From my understanding, at the resolution I have (~3.8 A), it is better to constrain them to be identical? Am I correct? I refined the monomer first and then I built the model based on refined monomer. Also, for the torsion angle, do I have to specify from the command line or it is already implemented in gui interface?
Best,
Yangqi
Sent from Mail for Windows 10
From: Tom Terwilliger
Sent: Tuesday, January 21, 2020 9:18 AM
To: Yangqi Gu; Thomas Charles Terwilliger
Cc: PHENIX user mailing list
Subject: Re: [phenixbb] How critical is ncs operator for real space refinement
Hi Yangqi,
You don't actually need the NCS relationships in order to refine with NCS restraints because the default is to use torsion-angle restraints which only use local relationships, not overall NCS matrices.
So you can go ahead and use your rigid-body-refined starting model with torsion-angle restraints in phenix.real_space_refine. That will not impose perfect helical restraints, but I am guessing that your map already has near-perfect helical symmetry so that should not matter very much.
Also you might first run with just one monomer which will be much quicker and give you almost the same answer.
Let us know if that does not do it!
All the best,
Tom T
On Mon, Jan 20, 2020 at 9:33 PM Yangqi Gu <[email protected]> wrote: