<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear Dr. Li,<div><span class="Apple-tab-span" style="white-space:pre"> </span>I'm sorry, but that would not be feasible. It is not a "plug and chug" situation, where the exact series of tasks you need is already known. As mentioned previously, the structures would first need to be superimposed before Match->Align is used to calculate similarity scores. Although Chimera provides several ways to superimpose structures (<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html">Superimposing Structures</a>), you would need to evaluate which method and parameters work on your structures of interest, using your own knowledge of this family of proteins. After superimposing, getting the scores, and building a phylogeny, if there were any discrepancies from what you were expecting, you would probably want to re-evaluate some of the superpositions and possibly recalculate them, again based on your own detailed knowledge of these proteins.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>We are willing to provide tools for your research, but actually performing this part of your study with Chimera would go far beyond that role. It sounds like you may need to take a simpler approach, such as using some other program that both superimposes proteins and provides a similarity score in the same step (as opposed to the decoupled approach in Chimera, which would also require python scripting knowledge). However, I'm not aware of any program that will do all pairwise comparisons automatically, so you would need to find a program that you can download for local use and then somehow (shell or other) script looping through all the pairs.<br><span class="Apple-tab-span" style="white-space:pre"> </span>Here is an informal list of superposition programs, some of which are available for download: <a href="http://www.cgl.ucsf.edu/home/meng/grpmt/structalign.html">Online Structure Alignment Resources</a><br><div><div><span class="Apple-tab-span" style="white-space:pre"> </span>If you recruit someone familiar with Python to your team, I'd be willing to make the scriptability improvements to Match->Align that I mentioned previously and provide guidance on the basic scripting outline you would need.</div><div><br></div><div>--Eric</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>On Apr 3, 2010, at 2:09 PM, Minming Li wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div><br>Dear Dr. Pettersen and Dr. Meng,<br><br>Thank you for your last email. I'm sorry that I am not so familiar with<br>Python, so could you help me to use the Chimera to produce the distance <br>matrix of the listed 45 pdbs below? Otherwise, is there any easy way to do this <br>just by running the program instead of using the Match->Align by hand? Thank <br>you so much! <br><br>The list of the 45 pdbs: <br>1il2a,1asza,1kmmc,1adyb,1adjb,1b76b,1efwa,11asb,1j5wb,1bbwa,<br>1lylb,1e1oa,1pysa,1b8aa,1httb,1kmna,1qe0b,1g51a,1evlc,1evka,<br>1nj8d,1kmmb,1c0aa,1j5wa,1serb,1h4qa,1eqrc,1sera,1nj1a,1h4sb,<br>1atib,1h4vb,1b70a,1eqra,1kmnb,1adya,1adjc,1hc7a,1httc,1eqrb,<br>1g51b,1qe0a,1b76a,1atia,1efwb.<br><br>Best regards!<br><br>sincerely,<br>Minming Li<br><br>--------------------------<br>Minming Li<br>PhD student,<br>Interdisciplinary Life Science Program (PULSe Program), <br>Purdue University, <br>West Lafayette, IN. USA.<br>Email: <a href="mailto:li362@purdue.edu">li362@purdue.edu</a><br><br><br>Quoting Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu">pett@cgl.ucsf.edu</a>>:<br><br><blockquote type="cite">On Mar 30, 2010, at 9:04 PM, Elaine Meng wrote:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">However, there are some issues that may affect whether you decide to <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">use Chimera to calculate these values for your structures:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">(1) You would need to run Match->Align for each pair. There is no <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">option to do all pairwise comparisons on multiple structures. You <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">would need to script looping through all pairs (with python or shell <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">scripting).<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">(2) There is no Chimera command for Match->Align. Thus Match->Align <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">would also need to be run via python. I don't have scripting <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">expertise, so someone else would have to provide more details if you <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">decide to try this.<br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Given that you said you wanted a complete pairwise matrix of ~50 <br></blockquote><blockquote type="cite">structures, that would be ~1200 unique pairs, which is obviously way <br></blockquote><blockquote type="cite">too many to do by hand. Currently Match->Align is awkward to script, <br></blockquote><blockquote type="cite">even in Python, since all the important code is internal to the Match- <br></blockquote><blockquote type="cite"><blockquote type="cite">Align dialog and basically impossible to call externally. If you <br></blockquote></blockquote><blockquote type="cite">are sure that you would like to use Chimera for this computation I can <br></blockquote><blockquote type="cite">reorganize the Match->Align code so that it could be called <br></blockquote><blockquote type="cite">externally. I don't think the reorganization will be difficult. You <br></blockquote><blockquote type="cite">would still need to resort to a Python script to make the Match->Align <br></blockquote><blockquote type="cite">calls and loop through your models, so you would need some rudimentary <br></blockquote><blockquote type="cite">familiarity with Python. Let me know.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">--Eric<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> Eric Pettersen<br></blockquote><blockquote type="cite"> UCSF Computer Graphics Lab<br></blockquote><blockquote type="cite"> <a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote></div></blockquote></div></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>