<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">That works well, thanks Eric. Is there any way to reassign the ramaProbs to the bfactor column on the command line, without using the attribute calculator? That way I can set the whole sequence of commands as an alias.<div><br></div><div>Cheers,</div><div>Oliver.<br><div><div>On Aug 26, 2014, at 1:45 PM, Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu">pett@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><meta http-equiv="Content-Type" content="text/html charset=us-ascii"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Aug 26, 2014, at 10:27 AM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi Oliver,<br>The more direct way I tried used Attribute Calculator (in menu under Tools.. Structure Analysis) to calculate attribute "bfactor" for "atoms" using the formula:<br><br>residue.ramaProb<br><br>(after assignment using Ramachandran). It currently generates an error, which seems buglike. I could create a new atom attribute with that formula, but not overwrite "bfactor". We'll look into that .</blockquote><br></div><div>The problem here is that bfactors <i>must</i> be numeric, but some residues have a ramaProb of "None" (e.g. they are terminal residues or non-peptides and lack either a phi or a psi). You can assign such residues a ramaProb of -1.0 with this command:</div><div><br></div><div>setattr r ramaProb -1.0 :/^ramaProb</div><div><br></div><div>You could then use the Attribute Calculator to assign the ramaProbs to the bfactors.</div><div><br></div><div>--Eric</div><br><div apple-content-edited="true">
<span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px; font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;"><div style="margin: 0px;"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>Eric Pettersen</font></div><div style="margin: 0px;"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>UCSF Computer Graphics Lab</font></div><div style="margin: 0px;"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> </span><a href="http://www.cgl.ucsf.edu/">http://www.cgl.ucsf.edu</a></font></div><br class="Apple-interchange-newline"></span>
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