Hi Dmitry,

The Phenix find_ncs tool sorts chains into groups that have similar structures. It has a default value of 2 A for chain_max_rmsd, the threshold for separating chains into different groups.

In your case, this resulted in two ncs groups instead of one. In your version of Phenix, you can't change that value of 2 A in find_ncs. I have just made a fix so that you can change it in the GUI with the "NCS finding parameters" button. This version will be available tomorrow at:

https://phenix-online.org/download/phenix/nightly/?version=1.21rc1-4975

If you want to get the same result now, you can do it from the command line with simple_ncs_from_pdb:

phenix.simple_ncs_from_pdb my_pdb.pdb chain_max_rmsd=3

This should find 14 ncs operators for your model (no map needed).

Let me know if that does not do it!

All the best,

Tom T

On Sun, May 21, 2023 at 10:42 PM Pavel Afonine <pafonine@lbl.gov> wrote:

Hi Dmitry,

finding out what's happening in cases like this almost always requires us having the files and being able to reproduce the issue at our end. So.. Would you mind sending me the files (off-list)? -Thanks!

Pavel

On 5/17/23 05:03, Dmitry A. Semchonok wrote:

Dear colleagues,

I have a cryo-em 3D map // full model // a monomer.

I run the FIND NCS parameters for my model – Homo 14-mer.

When I ran Applied the NCS operators with the monomer I received a 12-mer model instead of a 14-mer.

So 2 subunits are missing.

Could you please prompt how to fix that?

Thanks in advance

Sincerely,

Dmitry

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