<div dir="ltr">Patrick<div><br></div><div>If you have a .geo (optionally from the end of phenix.refine) you can run a script I wrote to get the rmsd values for all, alt and not alt.</div><div><br></div><div>
<p class="">elbow.refine_geo_display model.geo</p>
<p class="">Time to parse 1.43</p>
<p class=""><br></p>
<p class="">RMS results for model</p>
<p class=""><br></p>
<p class="">RMS(D/Z)</p>
<p class=""> d-all d-none d-alt z-all z-none z-alt </p>
<p class=""> bond 0.001( 3550) 0.001( 3550) 0.000( 0) 0.051( 3550) 0.051( 3550) 0.000( 0)</p>
<p class=""> angle 0.532( 6399) 0.532( 6399) 0.000( 0) 0.182( 6399) 0.182( 6399) 0.000( 0)</p>
<p class=""><br></p>
<p class=""><br></p></div></div><div class="gmail_extra"><br clear="all"><div><div dir="ltr">Cheers<div><br></div><div>Nigel<div><br></div><div>---</div><div>Nigel W. Moriarty<br>Building 64R0246B, Physical Biosciences Division<br>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : 510-486-5709 Email : NWMoriarty@LBL.gov<br>Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov">CCI.LBL.gov</a></div></div></div></div>
<br><div class="gmail_quote">On Wed, Oct 1, 2014 at 2:36 PM, PC <span dir="ltr"><<a href="mailto:patrick.cossins@inbox.com" target="_blank">patrick.cossins@inbox.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><u></u>
<div>
Hi,<div>Off topic-sorry</div><div>Is there a way to calculate RMSD </div><div><br></div><div>1) Considering atoms in ALT conformations?</div><div>2) considering all atoms in the protein ?</div><div><br></div><div>PYMOL seems to be throwing atoms away.</div><div><br></div><div>Thank you</div><hr size="1px" noshade style="clear:both;margin-top:10px;min-height:1px">
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