<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="">Hi Evan,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>There are multiple possible approaches here. You can tightly couple your GUI to Chimera, which is what you are describing, you can more loosely couple your GUI to Chimera, or you could not use Chimera at all. Briefly:</div><div class=""><br class=""></div><div class=""><u class="">Tight Coupling</u></div><div class="">You write your GUI as a Chimera tool/extension, and starting your tool actually starts Chimera <i class="">and</i> your tool (possibly as “chimera —start “your tool” in a script).</div><div class=""><br class=""></div><div class=""><u class="">Loose Coupling</u></div><div class="">Your GUI starts Chimera as a subprocess when needed (“chimera —start <a href="https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/restserver/restserver.html" class="">RESTServer</a>”) and sends commands to it via HTTP in order to open and change the display of structures.</div><div class=""><br class=""></div><div class=""><u class="">Non-Chimera</u></div><div class="">One possibility is to use <a href="http://nglviewer.org/ngl/" class="">NGL Viewer</a> to show the structure in a web browser (that supports WebGL). The structure will be interactively manipulable.</div><div class=""><br class=""></div><div class="">Chimera citation info can be found via the Help->Citation Info menu item.</div><div class=""><br class=""></div><div class="">You other questions are only applicable if you go the “tight coupling” route. If you choose to go that route, then yes, all modules (including your own) would have to be installed using the Chimera interpreter. I am unaware of any module conflicts when this is done.</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Jan 28, 2018, at 9:45 AM, Evan Seitz <<a href="mailto:evan.e.seitz@gmail.com" class="">evan.e.seitz@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Eric, thank you for your detailed reply. I’m working on a project that analyzes user input data through a GUI, and at one point needs to open a 3d render of a specific protein mapping that can rotate, etc.<div class=""><br class=""></div><div class="">If we went with this option, our team would eventually have to compile our entire code using the Chimera Python interpreter, correct? Do you happen to know if this kind of thing is allowed, and if it is, what citations should be used? Also, are there any case you’ve heard of of the Chimera interpreter causing internal conflicts with other native Python modules and code?</div><div class=""><br class=""></div><div class="">Thank you so much for your time.</div><div class=""><br class=""></div><div class="">Best,</div><div class="">Evan<br class=""><div class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Jan 23, 2018, at 6:03 PM, Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Evan,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>That code only works in the context of <i class="">Chimera</i>’s Python interpreter, not a generic Python interpreter. So like it says in the example, “to execute the script, either open the script file with the File→Open menu item or with the open command”. </div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Third parties have developed modules to allow Chimera modules to be used in standard Python interpreters. One such package is <a href="https://pypi.python.org/pypi/pychimera/0.2.0" class="">pychimera,</a> which can be installed via pypi.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Chimera only supports Python2. ChimeraX uses Python3.</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""><div class="">
<div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div></div>
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<div class=""><br class=""><blockquote type="cite" class=""><div class="">On Jan 23, 2018, at 11:03 AM, Evan Seitz <<a href="mailto:evan.e.seitz@gmail.com" class="">evan.e.seitz@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi - I’m trying to follow Example 1 on <a href="http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html" class="">http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html</a>, but after entering the code precisely as it is written, am getting back the ModuleNotFoundError: No module named ‘chimera’.<div class=""><br class=""></div><div class="">I’ve tried running the script using both Python2.7 and Python3, and both have resulted in the same error. As a sub-question, is Chimera supported in Python3, or is it best practice to still use Python2?</div><div class=""><div class=""><br class=""></div><div class="">Thank you,</div><div class="">Evan Seitz</div><div class=""><br class=""></div></div><div class="">Chimera version: 1.12.0</div><div class="">OS: macOS High Sierra 10.13.2</div></div>_______________________________________________<br class="">Chimera-dev mailing list<br class=""><a href="mailto:Chimera-dev@cgl.ucsf.edu" class="">Chimera-dev@cgl.ucsf.edu</a><br class=""><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev</a><br class=""></div></blockquote></div><br class=""></div></div></div></blockquote></div><br class=""></div></div></div>_______________________________________________<br class="">Chimera-dev mailing list<br class=""><a href="mailto:Chimera-dev@cgl.ucsf.edu" class="">Chimera-dev@cgl.ucsf.edu</a><br class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev<br class=""></div></blockquote></div><br class=""></div></body></html>