<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><div>On Feb 8, 2012, at 8:27 AM, Ahir Pushpanath 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-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-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; font-size: medium; ">Eric, although the script is highly useful for what I previously asked, I have come to the realisation that simply copying all the apo chi angles to the holo form may not be ideal for me in this particular situation. I noted that of around 200 residues modelled, around 90 of them are modelled different to the apo, the rest are modelled similar to the apo form. Of these 90, only around half are truly changed in the holo form(literature evidence from homolog), therefore I do require a script that is able to accept an input of which residues to copy the chi angles for, I think this will be useful for other users who want to copy chi angles from apo-holo forms and other applications, and probably could be included in later build versions of chimera, under structure editing.<br><br>Do you think you could help me with this? I am only learning python now, so my scripting is not at a good level for these types of things.<br></span></blockquote><div><br></div>I've attached a modified script that will only copy the chi angles for residues that are selected in the lowered-numbered model. It's up to you to select them somehow. :-)</div><div><br><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-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; font-size: medium; ">On another note, do you have any experience with using chimera to model apo-holo transitions any other way without using Modeller?</span></blockquote><div><br></div>I don't. Maybe others on the list will have suggestions... ?</div><div><br><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-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; font-size: medium; ">Also, does chimera have the ability to do docking of ligands, i.e. given you know the apo crystal structure, can you tell it to dock a ligand and change conformation of protein,(similar to autodock)?<br></span></blockquote><br></div><div>Currently Chimera cannot dock ligands. If our next 5 years of funding gets approved by the NIH, we have proposed interfacing Chimera to an Autodock Vina web service that would allow docking to be carried out directly from Chimera. Right now all you can do is prepare the input for / analyze the output of external docking programs in Chimera</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><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><br></font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"></font></p></div></span></div></body></html>