<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=us-ascii"><meta name=Generator content="Microsoft Word 12 (filtered medium)"><style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri","sans-serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal-compose;
font-family:"Calibri","sans-serif";
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal>Hi Meng,<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>I’ve run into this problem a few times when I wanted to calculate and show the surface of a pdb model. <o:p></o:p></p><p class=MsoNormal>I got the following on my reply log:<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>C:\Chimera\bin\mscalc.exe 1.400000 2.000000 1<o:p></o:p></p><p class=MsoNormal>Calculation of some surface components failed.<o:p></o:p></p><p class=MsoNormal>Falling back to single-component calculation.<o:p></o:p></p><p class=MsoNormal>C:\Chimera\bin\mscalc.exe 1.400000 2.000000 0<o:p></o:p></p><p class=MsoNormal>Surface calculation failed, mscalc returned code 5<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Sometimes I managed to go around it by resaving the pdb file in Chimera, or removing some irrelevant chains. but other times it just doesn’t work. Any suggestions?<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>One particular file that gives me the problem is 1IGT from PDB. I’ve tried removing all the heteroatoms and water molec, for I only need the chains A, B, C and D. but still the problem persists.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Thanks!<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Cheers,<o:p></o:p></p><p class=MsoNormal>Sumitro<o:p></o:p></p></div>
<DIV>
Institute for Infocomm Research disclaimer: "This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you."<BR>
</DIV></body></html>