<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<style type="text/css" style="display:none;"> P {margin-top:0;margin-bottom:0;} </style>
</head>
<body dir="ltr">
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<span style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">Dear Chimera users, </span><br>
</div>
<div>
<div dir="ltr">
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
I'm attempting to write a chimera script to automate the process of calculating the relative exposure of residues as per this tutorial: <a href="https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfnorm.html" id="LPlnk">https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfnorm.html</a> </div>
<div class="x__Entity x__EType_OWALinkPreview x__EId_OWALinkPreview x__EReadonly_1">
</div>
<br>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
The script I have is as follows: </div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
<div style="color:#d4d4d4; background-color:#1e1e1e; font-family:Consolas,'Courier New',monospace; font-weight:normal; font-size:14px; line-height:19px">
<span><span>rc(</span><span style="color:#ce9178">'surface'</span><span>) </span><span style="color:#6a9955"># defines areaSES of residues </span></span>
<div><span>rc(</span><span style="color:#ce9178">'defattr C:/Users/Admin/Downloads/areaSESgxg.txt log 0'</span><span>) </span><span style="color:#6a9955"># define attribute using areaSESgxg.txt</span></div>
<div><span style="color:#c586c0">for</span><span> m </span><span style="color:#c586c0">in</span><span> chimera.openModels.list(</span><span style="color:#9cdcfe">modelTypes</span><span>=[chimera.Molecule]):</span></div>
<div><span> </span><span style="color:#c586c0">for</span><span> r </span><span style="color:#c586c0">in</span><span> m.residues:</span></div>
<div><span> r.relSESA = r.areaSES/ r.areaSESgxg</span></div>
</div>
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
However, when I run this script, I am receiving this error: </div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
<img size="107152" tabindex="-1" style="max-width: 100%; height: auto;" data-outlook-trace="F:2|T:2" src="cid:39cc50d4-a627-494c-b0f5-411a7785a9a2"><br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
When I run the process using the UI I can successfully calculate relSESA</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
By using the command: "surface" </div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
Then using the assign attribute function to assign areaSESgxg.txt</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
Followed by using the calculate attribute function to calculate per residue: residue.areaSES/ residue.areaSESgxg</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
<span style="color:rgb(0,0,0); font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt"><br>
</span></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
<span style="color:rgb(0,0,0); font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">Could you advise on any methods I could use to fix this script to produce the output I am receiving from the UI. </span></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
<span style="color:rgb(0,0,0); font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt"><br>
</span></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
<span style="color:rgb(0,0,0); font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">Kind regards, </span></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
<span style="color:rgb(0,0,0); font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">David</span></div>
</div>
</div>
</body>
</html>