<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>
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