<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Yeping,<div class=""><br class=""></div><div class=""> As Elaine says the tutorial</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="http://ncmi.bcm.edu/ncmi/software/segger/docs_fitting" class="">http://ncmi.bcm.edu/ncmi/software/segger/docs_fitting</a></div><div class=""><br class=""></div><div class="">is out of date. But it is easy to place copies of the molecule to get the last image in the tutorial. Just fit each selected region (you can select them all by ctrl-clicking one, then press the up arrow key). Then select all the lines in the fit list and use menu entry Fit / Place Molecule Copies.</div><div class=""><br class=""></div><div class=""> It might help you to read the Chimera documentation on the Fit to Segments tool which describes menu entry Place Molecule Copies.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/segger/fitsegments.html" class="">http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/segger/fitsegments.html</a></div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Apr 7, 2015, at 6:51 AM, sunyeping wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="__aliyun_email_body_block"><div style="font-family: Tahoma, Arial, STHeiti, SimSun; font-size: 14px;" class=""><div style="margin: 0px; padding: 0px; border: 0px; outline: 0px; font-family: Tahoma, Arial, STHeiti, SimSun; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 23px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">Dear <span class="Apple-converted-space"> </span><span style="margin: 0px; padding: 0px; border: 0px; outline: 0px; font-family: Tahoma, Arial, STHeiti, SimSun; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 23px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); float: none; display: inline !important;" class="">Elaine,</span></div><div style="margin: 0px; padding: 0px; border: 0px; outline: 0px; font-family: Tahoma, Arial, STHeiti, SimSun; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 23px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br class=""></div><div style="margin: 0px; padding: 0px; border: 0px; outline: 0px; font-family: Tahoma, Arial, STHeiti, SimSun; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 23px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="margin: 0px; padding: 0px; border: 0px; outline: 0px; font-family: Tahoma, Arial, STHeiti, SimSun; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 23px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); float: none; display: inline !important;" class=""><span style="margin: 0px; padding: 0px; border: 0px; outline: 0px; font-family: Tahoma, Arial, STHeiti, SimSun; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 23px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); float: none; display: inline !important;" class="">I have read the link provide. However the "Fitting Options" section and the last paragraph of "Fittint models to segments" tutorial still tells us to "<span style="color: rgb(206, 219, 223); font-family: Helvetica, Arial, Verdana, sans-serif; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 20px; orphans: auto; text-align: left; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(59, 95, 123); float: none; display: inline !important;" class="">check the button to the left of<span class="Apple-converted-space"> </span></span><em style="color: rgb(206, 219, 223); font-family: Helvetica, Arial, Verdana, sans-serif; font-size: 12px; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 20px; orphans: auto; text-align: left; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(59, 95, 123);" class="">Save each fit when doing multiple alignments</em>". I cannot find this botton and so cannot follow this tutorial. Could you just tell me in this GroEL example how to align the structure to multiple regions and get the last figure of this tutorial?</span></span></div><div style="margin: 0px; padding: 0px; border: 0px; outline: 0px; font-family: Tahoma, Arial, STHeiti, SimSun; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 23px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="margin: 0px; padding: 0px; border: 0px; outline: 0px; font-family: Tahoma, Arial, STHeiti, SimSun; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 23px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); float: none; display: inline !important;" class=""><span style="margin: 0px; padding: 0px; border: 0px; outline: 0px; font-family: Tahoma, Arial, STHeiti, SimSun; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 23px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); float: none; display: inline !important;" class=""><br data-mce-bogus="1" class=""></span></span></div><div style="margin: 0px; padding: 0px; border: 0px; outline: 0px; font-family: Tahoma, Arial, STHeiti, SimSun; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 23px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="margin: 0px; padding: 0px; border: 0px; outline: 0px; font-family: Tahoma, Arial, STHeiti, SimSun; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 23px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); float: none; display: inline !important;" class=""><span style="margin: 0px; padding: 0px; border: 0px; outline: 0px; font-family: Tahoma, Arial, STHeiti, SimSun; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 23px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); float: none; display: inline !important;" class="">Best regards, <span style="color: rgb(206, 219, 223); font-family: Helvetica, Arial, Verdana, sans-serif; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 20px; orphans: auto; text-align: left; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(59, 95, 123); float: none; display: inline !important;" class=""><br class=""></span></span></span></div></div><div style="font-family: Tahoma, Arial, STHeiti, SimSun; font-size: 14px;" class=""><br class=""></div><div class="__aliyun_signature_wrap"><p class="">Yeping Sun</p><p class="">Institute of Microbiology, Chinese Academy of Sciencesalign</p></div><div style="font-family: Tahoma, Arial, STHeiti, SimSun; font-size: 14px;" class=""><br class=""></div><blockquote style="margin-right:0;margin-top:0;margin-bottom:0" class=""><div style="font-family: Tahoma, Arial, STHeiti, SimSun; font-size: 14px;" class="">------------------------------------------------------------------</div><div style="font-family: Tahoma, Arial, STHeiti, SimSun; font-size: 14px;" class="">From:Elaine Meng </div><div style="font-family: Tahoma, Arial, STHeiti, SimSun; font-size: 14px;" class="">Send Time:2015年4月7日(星期二) 07:19</div><div style="font-family: Tahoma, Arial, STHeiti, SimSun; font-size: 14px;" class="">To:孙业平 </div><div style="font-family: Tahoma, Arial, STHeiti, SimSun; font-size: 14px;" class="">Cc:Mailing List <<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a>></div><div style="font-family: Tahoma, Arial, STHeiti, SimSun; font-size: 14px;" class="">Subject:Re: [Chimera-users] where is "Save each fit when doing multiple alignments" button</div><div style="font-family: Tahoma, Arial, STHeiti, SimSun; font-size: 14px;" class=""><br class=""></div>P.S. I see that NCMI has newer Segger documentation at<br class=""><br class=""><<a href="https://sites.google.com/site/electronmicroscopyportal/tools/segger/user-guide" class="">https://sites.google.com/site/electronmicroscopyportal/tools/segger/user-guide</a>><br class=""><br class="">I'll add this link to the Chimera documentation.<br class="">Elaine<br class=""><br class=""><br class="">On Apr 5, 2015, at 10:34 AM, Elaine Meng wrote:<br class=""><br class="">> Dear Yepin Sun,<br class="">> I don’t know of any such option either, so I’m just guessing that the tutorial at NCMI is slightly out of date. However, I believe the “Fit to Segments” tool will already list all the fits, subject to any clustering options you might also have checked, so you would not need such an option anyway.<br class="">> Best,<br class="">> Elaine<br class="">> -----<br class="">> Elaine C. Meng, Ph.D. <br class="">> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br class="">> Department of Pharmaceutical Chemistry<br class="">> University of California, San Francisco<br class="">> <br class="">> On Apr 5, 2015, at 7:33 AM, sunyeping wrote:<br class="">> <br class="">>> Dear all,<br class="">>> I am studying the chimera tutorial "fitting to segments" of Segger segmentation tutorials from Greg Pintilie at NCMI (<a href="http://ncmi.bcm.edu/ncmi/software/segger/docs_fitting" class="">http://ncmi.bcm.edu/ncmi/software/segger/docs_fitting</a>). In the last paragraph, the tutorial states that to align the structure to multiple regions, one needs to check the "Save each fit when doing multiple alignments" button. But where is this button? I cannot find it in the "Fit to Segments", "Segment Map" or other dialogue boxes. Could you tell me where I can find it?<br class="">>> Best regard,<br class="">>> Yeping Sun<br class="">>> Institute of Microbiology, Chinese Academy of Sciences<br class="">> </blockquote></div>_______________________________________________<br class="">Chimera-users mailing list<br class=""><a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<br class=""></div></blockquote></div><br class=""></div></div></body></html>