[phenixbb] Apply NFC operators to get identical 14 homo oligomeric model

[Tom Terwilliger]

Hi Dmitry,

Normally you can just supply a symmetry file with N operators produced by
Phenix (ends in .ncs_spec) and a model with one chain to ApplyNCS and it
should create a new model with N copies of your chain.

The output model may indeed be missing the header information. You can copy
that from your original model if you like.

As this did not work for you, can you possibly try this example which I
have just tested:

in the Phenix GUI, go to "New Project", and select "Set up Tutorial Data".
Then scroll down and choose "Docking and Refinement" of GroEL and hit ok to
set up tutorial data.

1.Superpose 1ss8_A.pdb on chain A of 5w0s.pdb
Under "Models: superpose, search...", select sequence-based superposition.
Enter a title like "Superpose 1ss8_A.pdb on chain A of 5w0s.pdb"
Load the 5w0s.pdb as your fixed model
Load the 1ss8_A.pdb model as your moving model
Enter 1ss8_A_superposed.pdb as your output model
Add "ChainA" under selection for fixed model
Hit Run to superpose 1ss8_A.pdb on chain A of 5w0s.pdb

2. Get NCS operators from 5w0s.pdb
Under Models: superpose, search...", select "Find NCS operators"
Enter at title like "Get NCS operators from 5w0s.pdb"
For PDB file, select 5w0s.pdb
Hit run to get your NCS operators.

3.  Apply the NCS operators from 5w0s.pdb to 1ss8_A_superposed.pdb
The FindNCS GUI will put up a button called "Apply NCS operators".  Hit
that button and a FindNCS window appears with the symmetry file filled in.
You can also open FindNCS directly and select your
"groel_dock_refine/FindNCS_2/find_ncs_2.ncs_spec" or similar file.
Enter 1ss8_A_superposed.pdb as your input pdb file and hit Run.
Hit Open in Coot to show your expanded PDB file.  You can also load in
5w0s.pdb and see that they are similar.

If that does not work, please let us know!  If it does, then you can follow
the same steps for your case.  If your case does not work, it would be
great if you can send in a bug report and attach your files so that we can
reproduce the result, and we will fix it!

I hope that helps!

All the best,
Tom T






On Wed, Jun 28, 2023 at 4:10 AM Dmitry Semchonok <semchonok at gmail.com>
wrote:

> Dear colleagues,
>
>
>
> I use the «Apply NFC operators» tool and would like to use the option
> described under the "Configuration" sign.
>
> But when I follow these instructions, the outcome model is still a single
> subunit.
>
>
>
> Initially, I want to get 14mer (with D7 symmetry) with identical 14
> monomers.
>
>
>
> Could you please prompt how to get it with the «Apply NF operators»?
>
>
> Additionally, the resulting model doesn't contain description information
> in the newly created PDB file.
>
> Would you happen to know how to get the correct PDB file?
>
>
>
> Thanks in advance.
>
>
> Kind regards,
>
> 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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