<div dir="ltr">Hi Alex,<div><br></div><div style>Yes, you need to use 1.8.2-1309 or later. We've made changes to how both Phenix and MolProbity handle x-H bond lengths, as well as vdW radii, which effect how clashscores are calculated. They should be in sync now, but if you do run into discrepancies please let us know.</div>
<div style><br></div><div style>Jeff</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Apr 25, 2013 at 1:16 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">
<div bgcolor="#FFFFFF" text="#000000">
<div>Hi Alex,<br>
<br>
please try recent (1.8.2-1309 or later) version of Phenix and I
hope that should eliminate the discrepancy. If not please let us
know.<br>
<br>
Pavel<div><div class="h5"><br>
<br>
On 4/24/13 8:38 PM, Alex Theodossis wrote:<br>
</div></div></div>
<blockquote type="cite"><div><div class="h5">
<div dir="ltr">
<div class="gmail_extra">Dear phenixbb,</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">Have refined a 1.05A structure with
riding hydrogen model in phenix v1.8.1-1168 and doing final
validation.</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">The molprobity statistics output by
phenix include:</div>
<div class="gmail_extra">all atom clashscore = 4.12</div>
<div class="gmail_extra">Rotamer outliers = 0.71%</div>
<div class="gmail_extra">Overall score = 1.2</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">Put through the molprobity server I am
given the option of analysing with existing hydrogen model, or
replacing with the 'electron-cloud parameters' they recommend
for X-ray crystal structures. The results end up being very
different:</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">
existing H model: electron-cloud model:</div>
<div class="gmail_extra">All atom clash score: 4.66
(78th percentile) 3.72 (85th percentile) </div>
<div class="gmail_extra">Poor rotamers:
1.14% 1.14%</div>
<div class="gmail_extra">Overall score:
1.28 (88th percentile) 1.20 (92nd percentile)</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">While all three scenarios give
acceptable statistics, I am surprised by the inconsistency in
the results given by molprobity, even when using the same
hydrogen model.</div>
<div class="gmail_extra">I am also wondering whether I am using
a suboptimal riding model in my refinement (generated using
phenix ready-set).</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">Can anyone advise on the reason for
these inconsistencies (is it just due to differences in the
version of molprobity being run in each case). Is there
anything I should be doing differently?</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">Thanks in advance.</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 18 November 2012 12:36, Alex
Theodossis <span dir="ltr"><<a href="mailto:alex.theodossis@monash.edu" target="_blank">alex.theodossis@monash.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,
<div><br>
</div>
<div>I'm attempting to install the latest version of
phenix on mac 10.5.8, using the command line installer.</div>
<div><br>
</div>
<div>Installation proceeds well until towards the end,
where it hangs on:</div>
<div><br>
</div>
<div>precompiling .py files</div>
<div><br>
</div>
<div>I can leave it for up to an hour without any further
progress, but upon typing:</div>
<div><br>
</div>
<div>ctrl+c</div>
<div><br>
</div>
<div>The installation comes back to life and proceeds to
completion.</div>
<div><br>
</div>
<div>Can anyone advise as to what might be causing this
and on how reliable this installation is going to be?</div>
<div><br>
</div>
<div>Thanks in advance.</div>
<div><br>
</div>
<div><br>
</div>
</blockquote>
</div>
<br>
</div>
</div>
<br>
<fieldset></fieldset>
<br>
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</blockquote>
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