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Hi Ashu,<br>
<br>
2mFobs-DFmodel synthesis that phenix.refine outputs is not
sharpened. High overall atomic B (maximal common B-factor that can
be subtracted from all individual atomic B-factors that will still
leave them non-negative) is what makes the map blurred. <br>
If we subtract this common B from individual atomic B-factors,
recompute Fcalc and then recompute Fmodel, which is<br>
<br>
Fmodel = k_total * (Fcalc + Fbulk)<br>
<br>
and then compute the new synthesis with amplitudes
(2mFobs-DFmodel)/k_total it will be sharpened (and likely similar to
what you used to build the model). Note, noise will be upscaled too
(this is the main reason why it is not done by default!). <br>
<br>
We are thinking of making this map available as part of
phenix.refine output.<br>
<br>
For now try this: <br>
<br>
phenix.pdbtools shift_b_iso=SOME_NEGATIVE_VALUE model.pdb<br>
<br>
where SOME_NEGATIVE_VALUE is negative B-factor, like -10 or so,
chosen such that subtracting it from atomic B will not leave them
negative. <br>
<br>
Then compute maps using modified PDB file:<br>
<br>
phenix.maps model.pdb data.mtz<br>
<br>
Pavel<br>
<br>
<br>
<div class="moz-cite-prefix">On 9/8/14 7:57 AM, Ashu S wrote:<br>
</div>
<blockquote
cite="mid:1410188242.21089.YahooMailNeo@web140304.mail.bf1.yahoo.com"
type="cite">
<div style="color:#000; background-color:#fff;
font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial,
Lucida Grande, sans-serif;font-size:12pt">
<div id="yiv9543139437">
<div>
<div style="color: rgb(0, 0, 0); background-color: rgb(255,
255, 255); font-family: HelveticaNeue, 'Helvetica Neue',
Helvetica, Arial, 'Lucida Grande', sans-serif; font-size:
12pt;">
<div id="yiv9543139437yui_3_16_0_6_1410186871429_10">Dear
all,</div>
<div id="yiv9543139437yui_3_16_0_6_1410186871429_10"><br>
</div>
<div id="yiv9543139437yui_3_16_0_6_1410186871429_10"
style="color: rgb(0, 0, 0); font-size: 16px;
font-family: HelveticaNeue, 'Helvetica Neue', Helvetica,
Arial, 'Lucida Grande', sans-serif; background-color:
transparent; font-style: normal;">I am working on a 3.6A
Se SAD data. Autosol followed by autobuild gave a decent
map (as expected at this resolution) with a moderate
trace. After building poly ala trace and assigning few
resides in and around Se positions when I refine the
model, all the sharp features of the electron density
map are lost. For example, a nice looking helical
density becomes a tube. I presume that this happens
because wilson B is high (~110 A2) and the map requires
modification, sharpening etc. Is there a way to get the
map with similar sharp features after model building
�and refinement as auto build gives? How could I follow
exactly the same steps of density modification etc which
auto build does?</div>
<div id="yiv9543139437yui_3_16_0_6_1410186871429_10"
style="color: rgb(0, 0, 0); font-size: 16px;
font-family: HelveticaNeue, 'Helvetica Neue', Helvetica,
Arial, 'Lucida Grande', sans-serif; background-color:
transparent; font-style: normal;"><br
id="yiv9543139437yui_3_16_0_1_1410186871429_2821">
</div>
<div id="yiv9543139437yui_3_16_0_6_1410186871429_10"
style="color: rgb(0, 0, 0); font-size: 16px;
font-family: HelveticaNeue, 'Helvetica Neue', Helvetica,
Arial, 'Lucida Grande', sans-serif; background-color:
transparent; font-style: normal;">Thanks,</div>
<div id="yiv9543139437yui_3_16_0_6_1410186871429_10"
style="color: rgb(0, 0, 0); font-size: 16px;
font-family: HelveticaNeue, 'Helvetica Neue', Helvetica,
Arial, 'Lucida Grande', sans-serif; background-color:
transparent; font-style: normal;"><br
id="yiv9543139437yui_3_16_0_1_1410186871429_2823">
</div>
<div id="yiv9543139437yui_3_16_0_6_1410186871429_10"
style="color: rgb(0, 0, 0); font-size: 16px;
font-family: HelveticaNeue, 'Helvetica Neue', Helvetica,
Arial, 'Lucida Grande', sans-serif; background-color:
transparent; font-style: normal;">Ashu</div>
</div>
</div>
</div>
</div>
<br>
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