<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Jason,<div><br></div><div>Yes, the manual has some old text that goes with the now-unused GUI. Sorry about that. I fixed it just last week.</div><div><br></div><div>I think you want to say something very similar to what you have below. The key is: the entries in these 3 lists must all correspond (i.e., 2 numbers in each list). Try this:</div><div><br>rebuild_chain_list= " A B "<br>rebuild_res_end_list= "50 50"<br>rebuild_res_start_list="10 10"</div><div><br></div><div>or else:</div><div><br></div><div>rebuild_res_end_list= 50<br>rebuild_res_start_list=10</div><div><br></div><div>which should apply to all chains.</div><div><br></div><div>You should be able to use this approach to specify any number of regions to rebuild.</div><div><br></div><div>Let me know if that doesn't do it!</div><div>All the best,</div><div>Tom T</div><div><br><div><br></div><br></div><div><div><div>On Jul 14, 2010, at 11:42 AM, J J wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="font-family: Tahoma, 'Sans Serif', Arial; font-size: 11px; ">Dear All,</span><span class="Apple-style-span" style="font-family: Tahoma, 'Sans Serif', Arial; font-size: 11px; "><br></span><span class="Apple-style-span" style="font-family: Tahoma, 'Sans Serif', Arial; font-size: 11px; "><br></span><span class="Apple-style-span" style="font-family: Tahoma, 'Sans Serif', Arial; font-size: 11px; ">I am trying to use phenix.autobuild to rebuild some poor regions in my model.</span><span class="Apple-style-span" style="font-family: Tahoma, 'Sans Serif', Arial; font-size: 11px; "><br></span><span class="Apple-style-span" style="font-family: Tahoma, 'Sans Serif', Arial; font-size: 11px; ">Since I know which part should be rebuilt, I was thinking using rebuild_chain_list in combination with rebuild_res_end_list and rebuild_res_start_list.</span><span class="Apple-style-span" style="font-family: Tahoma, 'Sans Serif', Arial; font-size: 11px; "><br></span><span class="Apple-style-span" style="font-family: Tahoma, 'Sans Serif', Arial; font-size: 11px; "> The manual suggested: " You can specify more than one region by using the Parameter Group Options button to add lines." What is this Parameter Group Options button? I am running through an .eff file.</span><span class="Apple-style-span" style="font-family: Tahoma, 'Sans Serif', Arial; font-size: 11px; "><br></span><span class="Apple-style-span" style="font-family: Tahoma, 'Sans Serif', Arial; font-size: 11px; "><br></span><span class="Apple-style-span" style="font-family: Tahoma, 'Sans Serif', Arial; font-size: 11px; ">I have tried something like this:</span><span class="Apple-style-span" style="font-family: Tahoma, 'Sans Serif', Arial; font-size: 11px; "><br></span><span class="Apple-style-span" style="font-family: Tahoma, 'Sans Serif', Arial; font-size: 11px; "> </span><span class="Apple-style-span" style="font-family: Tahoma, 'Sans Serif', Arial; font-size: 11px; "><br></span><span class="Apple-style-span" style="font-family: Tahoma, 'Sans Serif', Arial; font-size: 11px; ">rebuild_chain_list= " 'A, 'B' "</span><span class="Apple-style-span" style="font-family: Tahoma, 'Sans Serif', Arial; font-size: 11px; "><br></span><span class="Apple-style-span" style="font-family: Tahoma, 'Sans Serif', Arial; font-size: 11px; ">rebuild_res_end_list= 50</span><span class="Apple-style-span" style="font-family: Tahoma, 'Sans Serif', Arial; font-size: 11px; "><br></span><span class="Apple-style-span" style="font-family: Tahoma, 'Sans Serif', Arial; font-size: 11px; ">rebuild_res_start_list=10</span><span class="Apple-style-span" style="font-family: Tahoma, 'Sans Serif', Arial; font-size: 11px; "><br></span><span class="Apple-style-span" style="font-family: Tahoma, 'Sans Serif', Arial; font-size: 11px; "><br></span><span class="Apple-style-span" style="font-family: Tahoma, 'Sans Serif', Arial; font-size: 11px; ">However, it does not work. It becomes more obscure to me what if I want to rebuild more than one region in a single chain? Thanks in advance.</span><span class="Apple-style-span" style="font-family: Tahoma, 'Sans Serif', Arial; font-size: 11px; "><br></span><span class="Apple-style-span" style="font-family: Tahoma, 'Sans Serif', Arial; font-size: 11px; "> </span><span class="Apple-style-span" style="font-family: Tahoma, 'Sans Serif', Arial; font-size: 11px; "><br></span><span class="Apple-style-span" style="font-family: Tahoma, 'Sans Serif', Arial; font-size: 11px; ">Jason</span><span class="Apple-style-span" style="font-family: Tahoma, 'Sans Serif', Arial; font-size: 11px; "><br></span><span class="Apple-style-span" style="font-family: Tahoma, 'Sans Serif', Arial; font-size: 11px; ">------------------------------------------------</span><span class="Apple-style-span" style="font-family: Tahoma, 'Sans Serif', Arial; font-size: 11px; "><br></span><span class="Apple-style-span" style="font-family: Tahoma, 'Sans Serif', Arial; font-size: 11px; ">University of Pittsburgh School of Medicine</span><span class="Apple-style-span" style="font-family: Tahoma, 'Sans Serif', Arial; font-size: 11px; "><br></span><span class="Apple-style-span" style="font-family: Tahoma, 'Sans Serif', Arial; font-size: 11px; ">3501 Fifth Avenue</span><span class="Apple-style-span" style="font-family: Tahoma, 'Sans Serif', Arial; font-size: 11px; "><br></span><span class="Apple-style-span" style="font-family: Tahoma, 'Sans Serif', Arial; font-size: 11px; ">Pittsburgh, PA 15261</span><span class="Apple-style-span" style="font-family: Tahoma, 'Sans Serif', Arial; font-size: 11px; "><br></span><span class="Apple-style-span" style="font-family: Tahoma, 'Sans Serif', Arial; font-size: 11px; ">------------------------------------------------</span> _______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>http://phenix-online.org/mailman/listinfo/phenixbb<br></blockquote></div><br><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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: 0; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div><div><div><div><br>Thomas C. Terwilliger<br>Mail Stop M888<br>Los Alamos National Laboratory<br>Los Alamos, NM 87545<br><br>Tel: 505-667-0072 email: <a href="mailto:terwilliger@LANL.gov">terwilliger@LANL.gov</a><br>Fax: 505-665-3024 SOLVE web site: <a href="http://solve.lanl.gov">http://solve.lanl.gov</a><br>PHENIX web site: http:<a href="http://www.phenix-online.org">www.phenix-online.org</a><br>ISFI Integrated Center for Structure and Function Innovation web site: <a href="http://techcenter.mbi.ucla.edu">http://techcenter.mbi.ucla.edu</a><br>TB Structural Genomics Consortium web site: <a href="http://www.doe-mbi.ucla.edu/TB">http://www.doe-mbi.ucla.edu/TB</a></div><div>CBSS Center for Bio-Security Science web site: <a href="http://www.lanl.gov/cbss">http://www.lanl.gov/cbss</a><br><br></div></div></div></div><br></div></div></span><br class="Apple-interchange-newline"> </div><br></div></body></html>