<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class=""><br class=""><blockquote type="cite" class=""><div dir="ltr" class=""><div class="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div style="margin: 0px;" class=""><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif;" class=""><b class="">From: </b></span><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif;" class="">Sarder Arifuzzaman <<a href="mailto:arifpharmju@gmail.com" class="">arifpharmju@gmail.com</a>><br class=""></span></div><div style="margin: 0px;" class=""><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif;" class=""><b class="">Subject: </b></span><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif;" class=""><b class="">Inquiry for new/re-registration license key_Arifuzzaman Sarder</b><br class=""></span></div><div style="margin: 0px;" class=""><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif;" class=""><b class="">Date: </b></span><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif;" class="">July 31, 2018 at 9:08:53 AM PDT<br class=""></span></div><div style="margin: 0px;" class=""><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif;" class=""><b class="">To: </b></span><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif;" class=""><a href="mailto:chimera-announce-owner@cgl.ucsf.edu" class="">chimera-announce-owner@cgl.ucsf.edu</a><br class=""></span></div><br class=""><div class=""><div dir="ltr" class=""><div class="">Hi</div><div class="">Greetings.</div><div class="">This is Arifuzzamman Sarder. I am an earlier user of chimera software tool. Recently I installed the updated version (v1.13). However, I could not draw any chemical structure by inputting canonical smiles or any other chemical ID in this tool. Even it can not capture any chemical structure from PDB, unlikely it is giving us only <span class="">protein structure. Could you please let me know how can I revive this tool, so that I can use it for molecular docking and chemical structure as well. </span></div><div class=""><span class="">Thank you very much in advance. I am looking forward for your response please. </span></div><div class=""><span class="">Sincerely<br class=""></span></div><div class="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><strong class="">Arifuzzaman, Sarder</strong></div><div dir="ltr" class=""><strong class=""><strong class=""><span lang="EN-US" class="" style="color: rgb(136, 136, 136);"><span lang="EN-US" class="" style="font-size: 10pt;"><font face="Times New Roman" class="">PhD research fellow</font></span></span></strong></strong></div><div class=""><strong class=""><span lang="EN-US" class="" style="color: rgb(136, 136, 136);"><span lang="EN-US" class="" style="font-size: 10pt;"><font face="Times New Roman" class="">Chung-Ang University</font></span></span></strong></div><div dir="ltr" class=""><strong class=""><span lang="EN-US" class="" style="color: rgb(136, 136, 136);"><span lang="EN-US" class="" style="font-size: 10pt;"><font face="times new roman,serif" class="">Mobile: 010-2654-2606</font></span></span></strong></div><div dir="ltr" class=""><span lang="EN-US" class="" style="color: rgb(136, 136, 136);"><span lang="EN-US" class="" style="font-size: 10pt;"><span lang="EN-US" class="" style="font-family: "맑은 고딕"; font-size: 10pt;"><font face="times new roman,serif" class="">E-mail: <a href="mailto:arifpharmju@gmail.com" target="_blank" class=""><font color="#1155cc" class="">arifpharmju@gmail.com</font></a></font></span></span></span></div><div dir="ltr" class=""><span lang="EN-US" class="" style="color: rgb(136, 136, 136);"><span lang="EN-US" class="" style="font-family: "맑은 고딕"; font-size: 10pt;"><font face="Times New Roman" class="">Web: <a href="https://sarderarifuzzaman.wixsite.com/arif" target="_blank" class="">https://sarderarifuzzaman.wixsite.com/arif</a></font></span></span></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></blockquote></div><div class=""><div dir="ltr" class=""><div class="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div class=""><div dir="ltr" class=""><div class="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><span lang="EN-US" class="" style="color: rgb(136, 136, 136);"><span lang="EN-US" class="" style="font-family: "맑은 고딕"; font-size: 10pt;"><br class=""></span></span></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div><div class=""><br class=""></div>HI Arifuzzamman Sarder,<div class="">(forwarding to the proper address for asking Chimera questions: <a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a> )</div><div class=""><br class=""><div class="">There is no reason it should not work as before. Chimera does not use a license key.</div><div class=""><br class=""></div><div class="">For example, in Chimera 1.13, command:</div><div class=""><br class=""></div><div class="">open pubchem:12123</div><div class="">(- or -)</div><div class="">open smiles:C1CCNC1</div><div class=""><br class=""></div><div class="">…shows a small molecule in sticks, and command:</div><div class=""><br class=""></div><div class="">open 2gbp</div><div class=""><br class=""></div><div class="">… shows PDB entry 2GBP; protein ribbons with ligand (glucose) as sticks and nearby sidechains as sticks.</div><div class=""><br class=""></div><div class="">If you mean that your Chimera 1.13 is not showing small molecules, or not showing sticks, I only have two ideas: (A) graphics/rendering problem of your computer or (B) New Molecules preferences was set to show only ribbons. To check (B), show Preferences from the Favorites menu, then change to category: New Molecules and check that the settings are what you want, and then click Save.</div><div class=""><br class=""></div><div class="">The behavior I described is for the default, “smart initial display” true. If you had it false, and also had “show atoms” false, it would not show atoms when you open a structure.</div><div class=""><br class=""></div><div class="">If you feel it is a bug, you can use menu: Help… Report a Bug and describe in detail what you did and what the problem is. However, if it is a graphics problem of your computer, it is not something we can fix.</div><div class=""><br class=""></div><div class="">I hope this helps,</div><div class="">Elaine<br class=""><div class="">
<span class="Apple-style-span" style="border-collapse: separate; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; line-height: normal; border-spacing: 0px; -webkit-text-decorations-in-effect: none;"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">-----</div><div class="">Elaine C. Meng, Ph.D. </div><div class="">UCSF Chimera(X) team</div><div class="">Department of Pharmaceutical Chemistry</div><div class="">University of California, San Francisco</div><div class=""><br class=""></div></div></span></div><br class=""></div></div></body></html>