<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On May 7, 2010, at 6:27 AM, Tom Duncan wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>On May 6, 2010, at 6:32 PM, Elaine Meng wrote:<br><blockquote type="cite">At first I thought you meant you ran DSSP yourself. How do you know that the secondary structure in the PDB file of 1aqt came from DSSP? I thought that PDB structure depositors were at liberty to define secondary structure as they wished, which could be done with several different programs or even based on subjective opinions. In that case, it is not at all surprising for there to be differences, within reason. I could be mistaken about the PDB protocol, however.<br></blockquote><br><br>Sorry for the lack of details. I was referring the annotated sequence info for the PDB entry.<br>Example that I mentioned: <a href="http://www.pdb.org/pdb/explore/remediatedSequence.do?structureId=1AQT">http://www.pdb.org/pdb/explore/remediatedSequence.do?structureId=1AQT</a><br>It shows a DSSP cartoon of secondary structure above the sequence. I tried tweaking the parameters for ksdssp in Chimera (1.4) and could not get the same as shown with the PDB sequence.<br></div></blockquote></div><br><div>I can't get them to be identical either, thought they're awfully close:</div><div><br></div><div><img height="449" width="747" apple-width="yes" apple-height="yes" src="cid:5D3EFB81-159A-49F8-AC5B-41ED5B6DCAED@cgl.ucsf.edu"></div><div><br></div><div>The only difference I see is the tyrosine at position 35 (PDB numbering). Is this what you're referring to? Chimera has it as strand and the PDB does not. Looking at the structure it looks like the PDB might be correct in that the tyrosine doesn't seem to form any backbone hydrogen bonds with the neighboring strand. I'll have to look into this.</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 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; "><p style="margin: 0.0px 0.0px 0.0px 0.0px"><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></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><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></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><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></p><br class="Apple-interchange-newline"></div></span> </div><br></body></html>