<div style="line-height:1.7;color:#000000;font-size:14px;font-family:Arial"><div>Dear Pavel,</div><div> </div><div>For the input, the last line of PDB is as followng,</div><div>ATOM 21953 HH22 ARG H 295 53.862 115.032 84.116 1.00100.56 H</div><div>For the run=ADP of the phenix.real_space_refine, the last line of the first model of all states pdb is,</div><div>ATOM 21953 HH22 ARG H 295 53.862 115.032 84.116 1.00194.44 H</div><div>and the last line of the second model of all states pdb is</div><div>ATOM 21953 HH22 ARG H 295 53.862 115.032 84.116 1.00164.47 H.</div><div><br>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.</div><div><br>Thus will you please explain why there are 2 states pdbs which seems both are refined pdbs?</div><div> </div><div>In addition, is it normal that the single state refined pdb cannot be opended?</div><div> </div><div>Next, will you please explain based on what of the mrc file, the phenix.real_space_refine run=ADP function got the b-factors?</div><div> </div><div>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?</div><div><br>Best regards.</div><div> </div><div>Smith<br><br><br><br></div><div style="position: relative; zoom: 1;"></div><div id="divNeteaseMailCard"></div><div><br></div><div id="isForwardContent">-------- Forwarding messages --------<br>From: "Pavel Afonine" <pafonine@lbl.gov><br>Date: 2015-05-23 00:48:00<br>To: "Smith Liu" <smith_liu123@163.com>,"phenixbb@phenix-online.org" <phenixbb@phenix-online.org><br>Subject: Re: Fw:Re: [phenixbb] on B-factor refine of the phenix.real_space_refine<br>
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<blockquote cite="mid:7a74ce2e.18152.14d796a00d7.Coremail.smith_liu123@163.com" type="cite">
<div style="color: rgb(0, 0, 0); line-height: 1.7; font-family: Arial; font-size: 14px;"> For
the all states PDB, it contains the input pdb for the
phenix.real_space_refine and the real spaced refined PDB<br>
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Yes I think so.. Is it not?<br>
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Pavel<br>
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