<div dir="ltr"><div><div><div><div><div>Hi Pavel<br><br></div>I have two more questions:<br><br></div>1. If I see a small drop in R/Rfree when I request solvent update (I over-rode the default cut-off of 2.8 A), should I keep those waters?<br><br></div>2. Where can I find the values for favored phi/psi values for Ramachandran? Using the FEM map, I can see some residues flagged as outliers but when they are fixed in Coot (real space refine tool) to a favored region, they actually come out of the density. This makes me suspect that those outliers are real. When I use Ramachandran restraints, obviously the outliers are 'fixed' but clashscore increases. In other cases, the tweak needed to fix them are quite small.<br><br></div>3. For publication, do I need to make an image of each outlier that was not fixed?<br><br></div> Thanks.<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, May 21, 2015 at 11:32 PM, Tristan Croll <span dir="ltr"><<a href="mailto:tristan.croll@qut.edu.au" target="_blank">tristan.croll@qut.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<div>> <span style="background-color:rgba(255,255,255,0)">So, it seems weight optimization is trying to lower the clashes and outliers at the expense of R factor.</span></div>
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</span><div>That's certainly not a bad thing. Remember, the object of refinement is to get the best possible model, not the best possible R-factor. I suspect that what these results are trying to tell you is that there's something fundamentally wrong somewhere in
your model - something out of register, perhaps? Some close inspection of regions where lots of outliers appear may be in order.<br>
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<div>Tristan Croll</div>
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<div><br>
On 22 May 2015, at 8:27 am, mohamed noor <<a href="mailto:mohamed.noor34@gmail.com" target="_blank">mohamed.noor34@gmail.com</a>> wrote:<br>
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<div>Hi Pavel<br>
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Just to let you know, I ran phenix.refine with and without weight optimization and I summarize the results below (R, clashscore, Ramachandran and rotamer outliers)<br>
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without - 27.9/32.1, 21.9, 4.71, 11.08<br>
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with - 32.8/35.1, 8.6, 3.89, 6.44<br>
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<div>without (torsion-angle NCS) - 27.9/31.0, 26.5, 4.1, 10.82<br>
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So, it seems weight optimization is trying to lower the clashes and outliers at the expense of R factor.<br>
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<div class="gmail_extra"><br>
<div class="gmail_quote">On Wed, May 20, 2015 at 11:39 AM, 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 Mohamed,<span><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I am refining a low resolution structure (3.8 A). After I fix most of the outliers (red bars) in Coot, phenix.refine is causing my structure to be worse than the start with 13 % Ramachandran outlier and 13 % rotamer outlier.<br>
</blockquote>
<br>
</span>could you please send me data and model (before refinement) files then I will have a look. Refinement at low resolution is generally tricky and often requires using beyond the default settings such as secondary structure, rotamer and Ramachandran plot
restraints, NCS (at 3.8A Cartesian NCS or even NCS constraints might be a better option).<br>
<br>
If you send me files I will try plausible options to see what can be done.<span><font color="#888888"><br>
<br>
Pavel<br>
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