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Hello,<br>
<br>
just to point out that CC alone may not be adequate measure, as we
show here:<br>
<br>
Acta Cryst. (2014). D70, 2593-2606.<br>
Metrics for comparison of crystallographic maps<br>
<br>
In addition, a histogram of per-atom correlations along with a
histogram of actual map values per-atom may be useful.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 10/9/14 10:30 AM, Tim Gruene wrote:<br>
</div>
<blockquote cite="mid:5436C631.3040300@shelx.uni-ac.gwdg.de"
type="cite">
<pre wrap="">Dear S,
a CC of 0.49 is quite strong, unless you mean 0.49% - did you take a
look at the resulting pdb-file?
Best,
Tim
On 10/09/2014 06:56 PM, Sneha Rangarajan wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hello everyone,
I have a question about ligand fitting into density.
At this point my maps look quite good with decent density for the peptide (ligand)[Rfactprs 26/31].
I tried using ligandfit by giving it the pdb and mtz of the ligand free model along with peptide.pdb (peptide stripped from a pdb where it was complexed with a homologous protein).
However the output was a ligand.pdb file with a CC of 0.49. I am not sure how to interpret this. Does this mean it could not find the density for the ligand?
Is there a better way to fit the peptide into density?
Thanks,
S
From: <a class="moz-txt-link-abbreviated" href="mailto:phenixbb-bounces@phenix-online.org">phenixbb-bounces@phenix-online.org</a> [<a class="moz-txt-link-freetext" href="mailto:phenixbb-bounces@phenix-online.org">mailto:phenixbb-bounces@phenix-online.org</a>] On Behalf Of Sneha Rangarajan
Sent: Wednesday, October 08, 2014 10:30 AM
To: Nathaniel Echols
Cc: <a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>
Subject: Re: [phenixbb] (no subject)
This was a great idea. My Rfactors after a second round of autobuild are now 25/32. I think it might be getting there afterall ☺
S
From: Nathaniel Echols [<a class="moz-txt-link-freetext" href="mailto:nechols@lbl.gov">mailto:nechols@lbl.gov</a>]
Sent: Friday, October 03, 2014 3:08 PM
To: Sneha Rangarajan
Cc: Pavel Afonine; <a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><a class="moz-txt-link-rfc2396E" href="mailto:phenixbb@phenix-online.org"><mailto:phenixbb@phenix-online.org></a>
Subject: Re: [phenixbb] (no subject)
On Fri, Oct 3, 2014 at 11:58 AM, Sneha Rangarajan <<a class="moz-txt-link-abbreviated" href="mailto:rsneha@umd.edu">rsneha@umd.edu</a><a class="moz-txt-link-rfc2396E" href="mailto:rsneha@umd.edu"><mailto:rsneha@umd.edu></a>> wrote:
I did another round of refinement with default settings (XYZ,realsp, IndB and occ) with and without weight optimization.
Without weight opt, the Rfactors are 23/36 with RMSbonds-0.0108 and RMSangles-1.750
One idea would be to run AutoBuild again. I've seen cases before where it didn't converge using the default settings, and feeding a previous result back into the program for a second run produced significantly better models. It might help get rid of the overfitting.
-Nat
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