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<blockquote
cite="mid:2232f6a7.9166.14d7513b719.Coremail.smith_liu123@163.com"
type="cite">
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<div>I have a EM map (.mrc), with fitting and based on a crystal
structure I got the fitted PDB file. I convert the mrc map to
the CCP4 map， </div>
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<br>
no need to convert .mrc into .ccp4 (isn't it the same thing?).
Anyways, phenix.real_space_refine can use both.<br>
<br>
<blockquote
cite="mid:2232f6a7.9166.14d7513b719.Coremail.smith_liu123@163.com"
type="cite">
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<div>and I run phenix.real_space_refine model.pdb map.mtz
run=adp, with phenix-dev-2034, in order to get my own
b-factors for my fitted PDB based on my EM map. However after
the above phenix.real_space_refine, I checked the refined PDB,
and I find phenix.real_space_refine neither change the
coordinates, nor change the b-factors for each atom.</div>
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<br>
I need to see the files to be able to comment. If you share the
files (off list and not sending directly via email but using things
like Dropbox instead) then I will be happy to have a look.<br>
<br>
<blockquote
cite="mid:2232f6a7.9166.14d7513b719.Coremail.smith_liu123@163.com"
type="cite">
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<div> Thus will you please introduce to me how can I get my own
b-factors for my fitted PDB in order to deposit my map and
fitte pdb to the EM database?<br>
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<br>
phenix.real_space_refine model.pdb map.mtz run=adp<br>
<br>
should just do what you want. If it didn't - see above (I need to
see the files).<br>
<br>
Pavel<br>
<br>
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