<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=""><div class="">Dear Chimera developers,</div><div class=""><br class=""></div><div class="">I am a postdoc research associate working with Prof. Lev Kantorovich of King’s College London. I am currently a full time developer for the ab initio atomic simulation code CP2K, and as a part of our project funding, we are looking to develop a tool kit that would improve user friendliness that would allow the users to construct various bulk or molecular structures in an intuitive and graphically way.</div><div class=""><br class=""></div><div class="">We currently have a quite extensive tool-kit (tetr) developed by Prof. Kantorovich for generating, modifying structures—especially tailored for periodic systems, as well as post processing utilities on volume data (such as generating STM images etc). It is written in FORTRAN, and currently is command based only, with the user input being either interactive or by a batch file. The goal, is to be able to link to a visualisation package like Chimera, so that: </div><div class=""><br class=""></div><div class="">a) one is able to automatically update the visualisation when the user uses the tool interactively</div><div class="">b) allow the user to select atoms and fragments and use these selections as an input to the tool-kit.</div><div class=""><br class=""></div><div class="">Ideally, the took-kit can run as an independent code, with the extension providing an interface between Chimera and the tool-kit. The user would then control the tool-kit from within the Chimera command interface.</div><div class=""><br class=""></div><div class="">I have used Chimera a lot during my PhD, however, I have not yet written any extension for it. I do, however, have quite a number of years experiences with code development, especially in Fortran and in Python. I am wondering:</div><div class=""><br class=""></div><div class="">1) If you would mind if we develop an extension to link our took-kit with Chimera</div><div class="">2) If the functionalities I mentioned above would be possible to achieve</div><div class=""><br class=""></div><div class="">Any suggestions from you would be great. Thank you very much for your time, and I look forward to hearing from you soon.</div><div class=""><br class=""></div><div class="">Best regards,</div><div class=""><br class=""></div><div class="">Lianheng</div><div class=""><br class=""></div><div apple-content-edited="true" class="">
<span class="Apple-style-span" style="border-collapse: separate; line-height: normal; border-spacing: 0px;"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-stroke-width: 0px;"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; 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color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-stroke-width: 0px;"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-stroke-width: 0px;"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-stroke-width: 0px;"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""><div class="">====================================</div><div class="">Lianheng Tong</div><div class="">Room S4.02, Strand Building</div><div class="">Department of Physics</div><div class="">Kings College London</div><div class="">Strand, London WC2R 2LS, U.K.</div><div class="">Tel: +44 20 7848 2064</div><div class="">Fax: +44 20 7848 2420</div><div class=""><a href="mailto:lianheng.tong@kcl.ac.uk" class="">lianheng.tong@kcl.ac.uk</a></div><div class="">====================================</div></div></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span>
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