<div dir="ltr">I have a related question to this.<div><br></div><div>I have a PDB structure (not mine I downloaded it from RCSB) and wondered if I could improve some of the problems in it using Phenix. </div><div><br></div><div>The Rw/R-free for the downloaded structure was 0.1279/0.1390</div><div><br></div><div>After I improved (or so I think so) the Rw/R-free is 0.1326/0.1440</div><div><br></div><div>The structure I have seems better in many aspects including its fit to the map (COOT/RSCC) + RMS Angles </div><div><br></div><div>I am a little confused whether to accept it or think I might have to do more validation checks as something has gone wrong?</div><div><br></div><div>Thank you,</div><div>George</div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Jan 12, 2015 at 4:01 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 Tim,<br>
<br>
it is a shame that I can't remember that particular paper where I
think Randy Read or Axel Brunger have demonstrated that phase error
and Rfree are well correlated. So if you get best Rwork and Rfree
chances are you also get best map too.<br>
<br>
All the best,<br>
Pavel<div><div class="h5"><br>
<br>
<div>On 1/12/15 3:54 AM, Tim Gruene wrote:<br>
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<blockquote type="cite">
<pre>Dear George,
what are the reasons why are you trying to reduce the R/Rfree instead of
producing the best possible map?
Best,
Tim
On 01/11/2015 11:24 PM, George D wrote:
</pre>
<blockquote type="cite">
<pre>Hi Phenix users,
I was looking at the phenix-refine manual and it mentions running
optimize_mask=true
optimize_xyz_weight=true
optimize_adp_weight=true
I was wondering what else I could try to bring the Rw/Rf down by 1-2%
if possible, just wondering if there are any other strategies I could
try.
Thank you,
George
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