[phenixbb] on B-factor refine of the phenix.real_space_refine

[Smith Liu]

Dear Pavel,
 
For the input, the last line of PDB is as followng,
ATOM  21953 HH22 ARG H 295      53.862 115.032  84.116  1.00100.56           H
For the run=ADP of the phenix.real_space_refine, the last line of the first model of all states pdb is,
ATOM  21953 HH22 ARG H 295      53.862 115.032  84.116  1.00194.44           H
and the last line of the second model of all states pdb is
ATOM  21953 HH22 ARG H 295      53.862 115.032  84.116  1.00164.47           H.

Clearly in each PDB of each model of the all states pdb produced, the b-factor is different, and they are different with the b-factors of the input pdb.

Thus will you please explain why there are 2 states pdbs which seems both are refined pdbs?
 
In addition, is it normal that the single state refined pdb cannot be opended?
 
Next, will you please explain based on what of the mrc file, the phenix.real_space_refine run=ADP function got the b-factors?
 
Further, I have noticed that the phenix.real_space_refine run=ADP gave a resolution which is different from the mrc general resolution given by relion or some other software. Will you please explain base on what the phenix.real_space_refine run=adp gives the resolution?

Best regards.
 
Smith






-------- Forwarding messages --------
From: "Pavel Afonine" <pafonine at lbl.gov>
Date: 2015-05-23 00:48:00
To: "Smith Liu" <smith_liu123 at 163.com>,"phenixbb at phenix-online.org" <phenixbb at phenix-online.org>
Subject: Re: Fw:Re: [phenixbb] on B-factor refine of the phenix.real_space_refine


 For the all states PDB, it contains the input pdb for the phenix.real_space_refine and the real spaced refined PDB


Yes I think so.. Is it not?

Pavel
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