<html>
<head>
<meta content="text/html; charset=utf-8" http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
Hi Oliver, <br>
<br>
ok, this makes sense! I will add option to output difference map and
let time prove its usefulness!<br>
<br>
All the best,<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 3/15/16 12:26, Oliver Clarke wrote:<br>
</div>
<blockquote
cite="mid:CAPghYOqq=qHkgfcDgvRiqcGfdbW7ypff5_gmtS1CxKugGCaWmQ@mail.gmail.com"
type="cite">
<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 moz-do-not-send="true"
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
moz-do-not-send="true"
href="mailto:pafonine@lbl.gov"
target="_blank"><a class="moz-txt-link-abbreviated" href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a></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>
</blockquote>
<br>
</body>
</html>