[phenixbb] NCS operators

[Tom Terwilliger]

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 at 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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-- 
Thomas C Terwilliger
Laboratory Fellow, Los Alamos National Laboratory
Senior Scientist, New Mexico Consortium
100 Entrada Dr, Los Alamos, NM 87544
Email: tterwilliger at newmexicoconsortium.org
Tel: 505-431-0010
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