<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 Matt,<div class=""><br class=""></div><div class=""> We don’t have a guide to porting Chimera 1 extensions to ChimeraX yet. We have not yet even made an alpha release of ChimeraX, and have just one outside developer who is writing a new extension rather than porting an old one.</div><div class=""><br class=""></div><div class=""> We will be providing info on porting extensions in the future. A major ChimeraX goal is to improve support for extension developers. Here are some basics about porting.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>1) Chimera 1 uses the Tk window tookit for dialogs, menus, buttons, … while ChimeraX uses the Qt toolkit.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>2) All attributes of molecules and maps are accessible from Python in both Chimera 1 and ChimeraX.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>3) Methods for density maps are mostly identical in Chimera 1 and ChimeraX.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>4) Methods for molecules, atoms, residues are mostly the same but with some changes (e.g. alt locs are different, chain ids can be longer than 1 character …)</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>5) To get better performance operating on large numbers of atoms there are new numpy array based methods to change atom attributes.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>6) The packaging of an extension is different. Chimera 1 uses a ChimeraExtension.py file. ChimeraX uses Python wheels and a online distribution site called Tool Shed, <a href="https://cxtoolshed.rbvi.ucsf.edu" class="">https://cxtoolshed.rbvi.ucsf.edu</a>, and ChimeraX menu Tools / General / Toolshed allows one click installs of any tools.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>7) Chimera 1 did not provide programming API documentation, while ChimeraX has API documentation <a href="http://www.rbvi.ucsf.edu/chimerax/docs/devel/index.html" class="">http://www.rbvi.ucsf.edu/chimerax/docs/devel/index.html</a></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>8) Chimera 1 used Python 2, ChimeraX uses Python 3. Python 3 import statements and print statements are different and integer divide produces a float, but mostly it is the same.</div><div class=""><br class=""></div><div class="">Most Chimera 1 extensions have a graphical user interface in Python / Tk that is often a lot of the code. Now we use Python / Qt because support for Tk is poor. Qt is totally different so all graphical user interface will have to be rewritten.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Jan 12, 2017, at 11:51 AM, Dougherty, Matthew T wrote:</div><br class="Apple-interchange-newline"><div class=""><div id="divtagdefaultwrapper" dir="ltr" style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-size: 12pt; font-family: Calibri, Arial, Helvetica, sans-serif;" class=""><div style="margin-top: 0px; margin-bottom: 0px;" class="">Hi Tom,</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Are there any guidelines, docs or examples as to converting extensions into chimeraX?</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div id="Signature" class=""><div id="divtagdefaultwrapper" style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;" class=""><div class="BodyFragment"><font size="2" class=""><div class="PlainText">Matthew Dougherty<br class="">National Center for Macromolecular Imaging<br class="">Baylor College of Medicine<br class=""><span style="font-size: 13pt; font-family: Calibri;" class="">=================================================</span><br class=""></div><div class="PlainText"><span style="font-size: 13pt; font-family: Calibri;" class="">=================================================</span></div></font></div></div></div></div></div></blockquote></div><br class=""></div></body></html>