<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On May 4, 2010, at 10:56 AM, Kim, Sunghoon 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 ocsi="x"><div style="font-family: Tahoma; direction: ltr; color: rgb(0, 0, 0); font-size: 13px; "><div></div><div dir="ltr"><font color="#000000" size="2" face="Tahoma">Hi all,</font></div><div dir="ltr"><font size="2" face="tahoma"></font> </div><div dir="ltr"><font size="2" face="tahoma">I would like to do the bump checking for the various rotameric states of a specific side chain generated by the rotation about dihedral angles. Bumps were detected by chimera command 'rotation' and 'findclash' and at first the script seemed working OK, but I'm not sure if the chi angles were correctly defined. When we look at the 'clashes/contacts' panel in Chimera, there are atom options for "Near" and "Far" positions in the rotating bonds. How can I specifying the 'Near' and 'Far' atoms in my 'rotation' command line in my python script to define my chi angles ?</font></div><div dir="ltr"> </div><div dir="ltr"><font size="2" face="tahoma">Thanks in advance for any info that you can provide.</font></div></div></div></span></blockquote><br></div><div>Hi Sunghoon,</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>'rotation' is a generic command and doesn't know anything specific about chi angles, phi/psi angles, etc. It simply changes the angle by the amount you specify <i>from its current position</i>. So if you want a chi angle of 180, "rotation 180" about the appropriate bond won't get you there -- it will simply turn that bond by 180 degrees from where it started.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>However, in recent versions of Chimera Residues have phi/psi/chi attributes. Therefore the easy way to set the chi1 angle of a residue to 180 in a Python script would be:</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>r.chi1 = 180</div><div><br></div><div>the equivalent Chimera command is:</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>setattr r chi1 180 #0:<residue you want></div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>I hope this helps.</div><div><br></div><div>--Eric</div><br><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>