[phenixbb] (no subject)

Petr Kolenko Petr.Kolenko at fjfi.cvut.cz
Thu Jul 29 10:34:27 PDT 2021

Dear Smita,
Pavel is right. However, if you want do to it the optimal way, use paired refinement. Select conservative resolution first (e.g. cut your data at I/sigma equals 2). Build a reasonable model of your structure and run paired refinement afterwards using higher and higher resolution data. For that purpose, you may use program PAIREF (https://pairef.fjfi.cvut.cz/). PAIREF also works for PHENIX users and it is very easy to install.
If you wanted to know more about the program in general, read here: https://journals.iucr.org/m/issues/2020/04/00/mf5044/index.html
We had a webinar from which we made video available: https://pairef.fjfi.cvut.cz/dokuwiki/doku.php?id=webinar_2021-03
PHENIX contains paired refinement as well. It should be somewhere in the most advanced version of the refinement? It does the same thing, but the report from the job is focused differently. We report merging data statistics and some other parameters. Moreover, PHENIX itself does not allow complete cross-validation that we strongly recommend to the users.
In any case, feel free to contact me directly. ;-) Best regards,

From: phenixbb-bounces at phenix-online.org <phenixbb-bounces at phenix-online.org> on behalf of Pavel Afonine <pafonine at lbl.gov>
Sent: Wednesday, July 28, 2021 9:10:36 PM
To: Smita Yadav; phenixbb at phenix-online.org
Subject: Re: [phenixbb] (no subject)

Hi Smita,

>               Can someone suggest to me, how we can decide the
> resolution range in the outer shell during the protein crystal data
> set.

the choice is pretty arbitrary. Typically the software chooses it for
you and it is fine most of the time.


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