<div dir="ltr"><div><div>Hi Pavel,<br><br></div>Yes, you can see it in the original map, of course, but it is still useful as a visual aid while building, and to do rigid body fitting of ligands into the difference density (where otherwise they might stray into the protein density at low resolution).<br><br></div><div>Cheers,<br></div><div>Oli<br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Mar 15, 2016 at 2:20 PM, Pavel Afonine <span dir="ltr"><<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
Hi Oliver,<br>
<br>
something I'm not quite sure I understand.. if you can see the
ligand in the difference map you should be able to see it in the
original experimental map too (at appropriate contour level). <br>
<br>
It's different from crystallography, I think. In crystallography we
almost always use model phases to compute usual maps, meaning we
have to deal with model bias and other artifacts. In cryo-EM the
reconstructed map is your primary data for atomic modeling. If there
is signal you should be able to see it in this map.<span class="HOEnZb"><font color="#888888"><br>
<br>
Pavel</font></span><div><div class="h5"><br>
<br>
<div>On 3/15/16 12:03, Oliver Clarke wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div>
<div>Hi Pavel, Thanks! Such maps can definitely be helpful, I
calculate them quite often - to identify bound ligands it is
certainly helpful, or to highlight regions of the model that
have poor fit to the map, similar to their use in
crystallography.<br>
<br>
</div>
Cheers,<br>
</div>
Oliver.<br>
<div>
<div><br>
</div>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Tue, Mar 15, 2016 at 12:47 PM, Pavel
Afonine <span dir="ltr"><<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Oliver,<br>
<br>
why not.. I think we can compute map from model and then
subtract it from the experimental input map (after scaling
them somehow).<br>
<br>
No I did not have that plan because it wasn't clear to me
how such map can be helpful (especially since we don't do
best possible job on B factor refinement).<br>
<br>
I will add this option.<span><font color="#888888"><br>
<br>
Pavel</font></span>
<div>
<div><br>
<br>
On 3/15/16 10:25, Oliver Clarke wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hello,<br>
<br>
is there any possibility of (or current plan for)
including the capacity in a future PHENIX release to
calculate a residual map automatically after
phenix.real_space refine, (i.e. simulating a map from
the model incorporating corrections for B-factor
variation and calculating a difference map with the
experimental map)? This would be very convenient when
building into EM maps.<br>
<br>
Cheers,<br>
Oli<br>
</blockquote>
<br>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</blockquote>
<br>
</div></div></div>
</blockquote></div><br></div>