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I don't know what exactly you have done and how, so I can't offer
meaningful comments. Why don't yo just refine against the map
directly? <br>
<br>
Also, it sounds like you juts try things out to learn.. It may be a
good idea to attend a Phenix workshop that we have occasionally in
different places. From you email "163.com" I figure you are in
China. Chances are that we may be doing a Phenix workshop in
Shanghai beginning of next year, so if you are nearby or keen to
attend regardless the travel distance - you are welcome. <br>
<br>
Pavel<br>
<br>
<br>
<br>
<div class="moz-cite-prefix">On 7/10/15 19:20, Smith Liu wrote:<br>
</div>
<blockquote
cite="mid:14b2cd42.33cf.14e7ae9de66.Coremail.smith_liu123@163.com"
type="cite">
<div
style="line-height:1.7;color:#000000;font-size:14px;font-family:Arial">
<div>Dear Pavel,</div>
<div><br>
</div>
<div>The other question is, if we convert mrc file to mtz file
by phenix.map_to_structure_factors and then run the GUI phenix
refine, in the refilne output, it indicates the FOFCWT map is
much much stronger than then 2FOFCWT map, as shown by Coot,
for this reason I doubt the correctness of the GUI phenix
refine for this purpose. Can you explain why?</div>
<div><br>
</div>
<div>Smith</div>
<div><br>
<br>
<br>
<br>
<br>
</div>
<div><br>
</div>
At 2015-07-11 09:41:48, "Pavel Afonine" <a class="moz-txt-link-rfc2396E" href="mailto:pafonine@lbl.gov"><pafonine@lbl.gov></a>
wrote:<br>
<blockquote id="isReplyContent" style="margin: 0px 0px 0px
0.8ex; padding-left: 1ex; border-left-color: rgb(204, 204,
204); border-left-width: 1px; border-left-style: solid;"> <br>
<blockquote
cite="mid:614fae2a.1d06.14e7a683871.Coremail.smith_liu123@163.com"
type="cite">
<div style="color: rgb(0, 0, 0); line-height: 1.7;
font-family: Arial; font-size: 14px;"> Is any software
convert mtz file into mrc file (for viewing in chimera)?</div>
</blockquote>
<br>
phenix.mtz2map .<br>
<br>
<blockquote
cite="mid:614fae2a.1d06.14e7a683871.Coremail.smith_liu123@163.com"
type="cite">
<div style="color: rgb(0, 0, 0); line-height: 1.7;
font-family: Arial; font-size: 14px;">
<div> In addition, by mrc file I can run
phenix,real_space_refine very nicely. But for knowledge
gaining purpose, I convert a mrc file to a mtz file by
phenix.map_to_structure_factors, and then run the
GUI phenix refine with the
phenix.map_to_structure_factors converted mtz file (from
mrc) file and a model PDB (from mrc), first the
GUI phenix refine will give very high Rwork and Rfree,
secondly the mtz output density by GUI phenix looks does
not fit the initial mrc density at all, thus the pdb
models given by phenix,real_space_refine and GUI phenix
refine seem strongly different. </div>
<div> </div>
<div>Is any way to get similar pdb models by
phenix,real_space_refine and GUI phenix refine?<br>
</div>
</div>
</blockquote>
<br>
Results should be similar, in general without doing anything
special.<br>
<br>
Pavel<br>
<br>
</blockquote>
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<br>
<br>
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