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<div>No I wanted the structure alignment RMSD but thank you. </div><br><br><blockquote style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #0000ff 2px solid; MARGIN-RIGHT: 0px"><div class="msgHeaders">-----Original Message-----<br><b>From:</b> nwmoriarty@lbl.gov<br><b>Sent:</b> Wed, 1 Oct 2014 15:47:09 -0700<br><b>To:</b> patrick.cossins@inbox.com<br><b>Subject:</b> Re: [phenixbb] Off Topic: Calculating accurately RMSD<br><br></div><div class="oldBody"><div><div dir="ltr">Patrick<div><br></div><div>If you do a refinement in Phenix you get a .geo which contains the geometry restraints information. It's a simple matter to calculate the rmsd of the geometry restraints given that the model and ideal values are all listed.</div><div><br></div><div>Do you want a geometry restraints rmsd or a structure alignment rmsd?</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 3:21 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>
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<div>Hi Nigel,</div><div><br></div><div>Could you tell me how you used the .geo file?</div><div><br></div><div>In this I case I don't have a geo file but this might be useful in the future </div><div><div _class="h5"><br><br><blockquote _style="PADDING-LEFT:5px;MARGIN-LEFT:5px;BORDER-LEFT:#0000ff 2px solid;MARGIN-RIGHT:0px"><div>-----Original Message-----<br><b>From:</b> <a href="mailto:nwmoriarty@lbl.gov" target="_blank">nwmoriarty@lbl.gov</a><br><b>Sent:</b> Wed, 1 Oct 2014 15:04:54 -0700<br><b>To:</b> <a href="mailto:patrick.cossins@inbox.com" target="_blank">patrick.cossins@inbox.com</a><br><b>Subject:</b> Re: [phenixbb] Off Topic: Calculating accurately RMSD<br><br></div><div><div><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>elbow.refine_geo_display model.geo</p>
<p>Time to parse 1.43</p>
<p><br></p>
<p>RMS results for model</p>
<p><br></p>
<p>RMS(D/Z)</p>
<p> d-all d-none d-alt z-all z-none z-alt </p>
<p> bond 0.001( 3550) 0.001( 3550) 0.000( 0) 0.051( 3550) 0.051( 3550) 0.000( 0)</p>
<p> angle 0.532( 6399) 0.532( 6399) 0.000( 0) 0.182( 6399) 0.182( 6399) 0.000( 0)</p>
<p><br></p>
<p><br></p></div></div><div><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 : <a href="tel:510-486-5709" value="+15104865709" target="_blank">510-486-5709</a> Email : NWMoriarty@LBL.gov<br>Fax : <a href="tel:510-486-5909" value="+15104865909" target="_blank">510-486-5909</a> Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a></div></div></div></div>
<br><div>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><u></u>
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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="">
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