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</o:shapelayout></xml><![endif]--></head><body lang=ZH-TW link=blue vlink=purple style='text-justify-trim:punctuation'><div class=WordSection1><p class=MsoNormal><span lang=EN-US>To whom it may concern,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>I am willing to use Chimera for aligning several images from the structure illumination microscope (SIM).<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>Here is the surface maps generated by Chimera from two images. <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><img width=246 height=261 id="圖片_x0020_3" src="cid:image001.jpg@01D0EA0D.9317A860" alt="cid:image005.jpg@01D0E986.2CF5F370"></span><span lang=EN-US><o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>After alignment by the tool “Fit in Map”, they are aligned very well.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><img width=891 height=488 id="圖片_x0020_2" src="cid:image002.jpg@01D0EA0D.9317A860" alt="cid:image006.jpg@01D0E986.2CF5F370"></span><span lang=EN-US><o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>My next step is to average the intensity from two aligned images and generate a new map which will be used to fit other images.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>Can anyone tell me how to do it in Chimera? <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>By the way, please also tell me what the values mean in the reply log. <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><img width=595 height=351 id="圖片_x0020_1" src="cid:image003.jpg@01D0EA0D.9317A860" alt="cid:image007.jpg@01D0E986.2CF5F370"></span><span lang=EN-US><o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>It helps me to use another software to complete the mission, if I can get the rotation, voxel shift, or even scaling values from the alignment.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>Thank you!<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>All Best,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>Peggy Hsu, PhD<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>Institute of Cellular and Organismic Biology, Academia Sinica<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>128 Academia Rd Sec 2, Nankang, <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>Taipei 11529, Taiwan<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>Tel: 886-2-2787-1531 (O)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman","serif"'>email: <a href="mailto:peggyschsu@gate.sinica.edu.tw">peggyschsu@gate.sinica.edu.tw</a><o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p></div></body></html>