<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Mar 7, 2010, at 10:13 AM, Elaine Meng wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div><br>On Mar 7, 2010, at 5:12 AM, Sumitro Harjanto wrote:<br><br><blockquote type="cite">Hi Meng,<br></blockquote><blockquote type="cite">I would like to use chimera to help me with a process of combining receptors and ligands that were modelled separately (in separate files)<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">So here is my intended framework:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">For each iteration:<br></blockquote><blockquote type="cite"><span class="Apple-tab-span" style="white-space:pre"> </span>• open “template.pdb” template file (which contains the receptor/ligand complex) I used to model the receptor and ligand<br></blockquote><blockquote type="cite"><span class="Apple-tab-span" style="white-space:pre"> </span>• open the receptor_model.pdb<br></blockquote><blockquote type="cite"><span class="Apple-tab-span" style="white-space:pre"> </span>• open the ligand_model.pdb<br></blockquote><blockquote type="cite"><span class="Apple-tab-span" style="white-space:pre"> </span>• match receptor to template<br></blockquote><blockquote type="cite"><span class="Apple-tab-span" style="white-space:pre"> </span>• match ligand to template<br></blockquote><blockquote type="cite"><span class="Apple-tab-span" style="white-space:pre"> </span>• close template.pdb<br></blockquote><blockquote type="cite"><span class="Apple-tab-span" style="white-space:pre"> </span>• save the models in their current position into a single new pdb file.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I was exploring the feasibility of using the command “write” but I am not too sure if it will allow me to save the complex as a single pdb file..?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">On a side note, if it’s possible, any suggestion on how to optimise the run time since I might be running this for a large number of iterations ..? I read somewhere about switching off the GUI to save time, does it help..?</blockquote></div></blockquote><div><br></div><div>Hi Sumitro,</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>I don't have any really great suggestions for making things faster. Using --nogui will probably speed things up since Chimera won't have to build display lists for your structures. Also, you should probably open your structures with the "noprefs" keyword so that Chimera doesn't do a lot of work figuring about what parts of your structure to ribbon, which to ball-and-stick, etc. (see the docs for the "open" command).</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Did you need help with the scripting itself? It wasn't really clear from your mail whether you had all that under control or not...</div><div><br></div><div>--Eric</div><div><br></div><span class="Apple-style-span" style="font-size: 16px; "><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></span><blockquote type="cite"><div>Hi Sumitro,<br>You can't save multiple models in one file with the "write" command, but you can use "write" multiple times, one for each model you want to save. If you make sure to save each model "relative" to the same model, they will be in the correct positions with respect to each other when you reopen the files. See the "relative" keyword:<br><<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/write.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/write.html</a>><br><br>Or, if you really need to have them in a single file, you can use the "combine" command to create a new single model from multiple models. You would do that after the matching, but before saving the PDB file.<br><<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html</a>><br><br>I can't answer about how to script for multiple models, or how much faster it might be to use noGUI, so I'm sending this to the chimera-users list.<br><br>In the future, please send Chimera questions to the <a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a> list, because I might be away from work or (like now) others may be better able to answer the question.</div></blockquote></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; "><p style="margin: 0.0px 0.0px 0.0px 0.0px"><br></p></div></span> </div><br></body></html>