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Hi,<br>
<br>
<blockquote
cite="mid:b067a26.22b4.14d7e6681c6.Coremail.smith_liu123@163.com"
type="cite">
<div
style="line-height:1.7;color:#000000;font-size:14px;font-family:Arial">For
the input, the last line of PDB is as followng,
<div>ATOM 21953 HH22 ARG H 295 53.862 115.032 84.116
1.00100.56 H</div>
</div>
</blockquote>
<br>
I would not recommend having H given that you are likely refining
against >4A resolution map.<br>
<br>
<blockquote
cite="mid:b067a26.22b4.14d7e6681c6.Coremail.smith_liu123@163.com"
type="cite">
<div
style="line-height:1.7;color:#000000;font-size:14px;font-family:Arial">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><br>
Thus will you please explain why there are 2 states pdbs which
seems both are refined pdbs?</div>
</div>
</blockquote>
<br>
Not sure I understand this. I would say they are different because
they went through refinement, so why it is unexpected to you?<br>
<br>
<blockquote
cite="mid:b067a26.22b4.14d7e6681c6.Coremail.smith_liu123@163.com"
type="cite">
<div
style="line-height:1.7;color:#000000;font-size:14px;font-family:Arial">
<div> In addition, is it normal that the single state refined
pdb cannot be opended?</div>
</div>
</blockquote>
<br>
No. It must be a bug in your system.<br>
<br>
<blockquote
cite="mid:b067a26.22b4.14d7e6681c6.Coremail.smith_liu123@163.com"
type="cite">
<div
style="line-height:1.7;color:#000000;font-size:14px;font-family:Arial">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?<br>
</div>
</blockquote>
<br>
If you do not provide resolution in input using keyword
"resolution=.." it will try to estimate it given model and map. This
may or may not be accurate, and the way it is estimated is different
from any available software.<br>
<br>
Hope this answers some of your questions!<br>
<br>
Pavel<br>
<br>
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