<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Sumitro,<div><span class="Apple-tab-span" style="white-space:pre"> </span>The shortest answer is no, there is no way (barring some Python shenanigans). You could clear SS assignments afterward with:</div><div><br></div><div>setattr r isHelix false #</div><div>setattr r isStrand false #</div><div><br></div><div>Can you describe <i>why</i> you want to turn off the SS computation? We might make it optional somehow if it was of general use.</div><div><br></div><div>--Eric</div><div><br><div><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> Eric Pettersen</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> UCSF Computer Graphics Lab</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> <a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></div><div><br></div></div></span></div><div><div>On Mar 14, 2010, at 6:54 AM, Sumitro Harjanto wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div lang="EN-SG" link="blue" vlink="blue" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div class="Section1"><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span lang="EN-US" style="font-size: 10pt; font-family: Arial; color: navy; ">Hi,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span lang="EN-US" style="font-size: 10pt; font-family: Arial; color: navy; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span lang="EN-US" style="font-size: 10pt; font-family: Arial; color: navy; ">Is there any way to turn off automatic secondary structure assignment upon opening a pdb file that does not contain secondary assignments?<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span lang="EN-US" style="font-size: 10pt; font-family: Arial; color: navy; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span lang="EN-US" style="font-size: 10pt; font-family: Arial; color: navy; ">Cheers,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span lang="EN-US" style="font-size: 10pt; font-family: Arial; color: navy; ">Sumitro<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span lang="EN-US" style="font-size: 10pt; font-family: Arial; color: navy; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span lang="EN-US" style="font-size: 10pt; font-family: Arial; color: navy; ">---------------------------------------------------------------------------------------------------------------------------------------------<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span lang="EN-US" style="font-size: 10pt; font-family: Arial; color: navy; ">…<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span lang="EN-US" style="font-size: 10pt; font-family: Arial; color: navy; ">Opening B-7301_SRWGYQVKH_1K5N.pdb...<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span lang="EN-US" style="font-size: 10pt; font-family: Arial; color: navy; ">Computing secondary structure assignments...<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span lang="EN-US" style="font-size: 10pt; font-family: Arial; color: navy; ">Computed secondary structure assignments (see reply log)<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span lang="EN-US" style="font-size: 10pt; font-family: Arial; color: navy; ">Model 2 (B-7301_SRWGYQVKH_1K5N.pdb) appears to be a protein without secondary structure assignments.<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span lang="EN-US" style="font-size: 10pt; font-family: Arial; color: navy; ">Automatically computing assignments using 'ksdssp' and parameter values:<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span lang="EN-US" style="font-size: 10pt; font-family: Arial; color: navy; "> energy cutoff -0.5<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span lang="EN-US" style="font-size: 10pt; font-family: Arial; color: navy; "> minimum helix length 3<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span lang="EN-US" style="font-size: 10pt; font-family: Arial; color: navy; "> minimum strand length 3<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span lang="EN-US" style="font-size: 10pt; font-family: Arial; color: navy; ">Use command 'help ksdssp' for more information.<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span lang="EN-US" style="font-size: 10pt; font-family: Arial; color: navy; ">…<o:p></o:p></span></font></div></div></div></div></span></blockquote></div><br></div><div apple-content-edited="true"><span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><span class="Apple-style-span" style="font-size: medium;"><br class="Apple-interchange-newline"></span></div></span> </div><br></body></html>