<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 Noe,<div class=""><br class=""></div><div class=""> There is not a PyPi chimera module so your "pip install chimera" was installing something else, something from 2006 with no description according to the PyPi web page (<a href="https://pypi.org/project/chimera/#description" class="">https://pypi.org/project/chimera/#description</a>).</div><div class=""><br class=""></div><div class=""> Chimera is distributed as an application and you would just open your script file in Chimera 1.16. Chimera includes its own copy of Python compatible with Chimera C++ libraries. But you should instead use our newer program ChimeraX since we no longer developer Chimera. ChimeraX is also an application that includes its own copy of Python. We plan to distribute ChimeraX as a Python library but it is not yet available.</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><br class=""><blockquote type="cite" class=""><div class="">On Dec 6, 2022, at 1:52 AM, Noe Robert via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta charset="UTF-8" class=""><div class="elementToProof" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><span class="elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);">Good morning,<span class="Apple-converted-space"> </span><br class=""></span></div><div class="elementToProof" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><span class="elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);">I'm tr</span><span class="elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);">ying to use a python script for ChimeraX<span class="Apple-converted-space"> </span></span><span class="elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);"><span class="ContentPasted0" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255); display: inline !important;">version 1.5, to automate mutageneses on a specific protein.<span class="Apple-converted-space"> </span></span><br class=""></span></div><div class="elementToProof" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><span class="elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);">As a first try, it looks like this :</span></div><div class="elementToProof" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><span class="elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);"><br class=""></span></div><div class="elementToProof" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><span class="elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);"><div style="color: rgb(212, 212, 212); background-color: rgb(30, 30, 30); font-family: Consolas, "Courier New", monospace; font-weight: normal; font-size: 14px; line-height: 19px;" class=""><span class=""><span class="ContentPasted1" style="color: rgb(197, 134, 192);">from</span><span class="ContentPasted1"> chimera<span class="Apple-converted-space"> </span></span><span class="ContentPasted1" style="color: rgb(197, 134, 192);">import</span><span class="ContentPasted1"> runCommand<span class="Apple-converted-space"> </span></span><span class="ContentPasted1" style="color: rgb(197, 134, 192);">as</span><span class="ContentPasted1"> rc</span></span><div class=""><span class="ContentPasted1">rc(</span><span class="ContentPasted1" style="color: rgb(206, 145, 120);">"open "</span><span class="ContentPasted1"> +<span class="Apple-converted-space"> </span></span><span class="ContentPasted1" style="color: rgb(206, 145, 120);">"hERGts_compiled.pdb"</span><span class="ContentPasted1">)</span></div><div class=""><span class="ContentPasted1">rc(</span><span class="ContentPasted1" style="color: rgb(206, 145, 120);">"color red"</span><span class="ContentPasted1">)</span></div><span class=""><span class="ContentPasted1">rc(</span><span class="ContentPasted1" style="color: rgb(206, 145, 120);">"surf"</span><span class="ContentPasted1">)</span><span class="ContentPasted1" style="color: rgb(244, 71, 71);">;</span></span></div><br class=""></span></div><div class="elementToProof" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><span class="elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);">So it refers to the chimera module for the runCommand. I tried to install it on Python through the command pip but it failed :<span class="Apple-converted-space"> </span><br class=""></span></div><div class="elementToProof" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><span class="elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);"><br class=""></span></div><div class="elementToProof" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><span class="elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);">################################# Example of my shell while trying to install chimera module #######################<br class=""></span></div><div class="elementToProof" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><span class="ContentPasted2 elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);">PS C:> python3 -m pip install chimera<div class="ContentPasted2">Collecting chimera</div><div class="ContentPasted2"> Using cached chimera-0.4.7.tar.gz (355 kB)</div><div class="ContentPasted2"> Preparing metadata (setup.py) ... error</div><div class="ContentPasted2"> error: subprocess-exited-with-error</div><div class="ContentPasted2"> <span class="Apple-converted-space"> </span></div><div class="ContentPasted2"> กม python setup.py egg_info did not run successfully.</div><div class="ContentPasted2"> ฉฆ exit code: 1</div><div class="ContentPasted2"> จtฉค> [9 lines of output]</div><div class="ContentPasted2"> Traceback (most recent call last):</div><div class="ContentPasted2"> File "<string>", line 2, in <module></div><div class="ContentPasted2"> File "<pip-setuptools-caller>", line 34, in <module></div><div class="ContentPasted2"> File "C:\Users\CE PC\AppData\Local\Temp\pip-install-cfq97mii\chimera_bd7187074876462a9782eded8cb3a816\setup.py", line 1, in <module></div><div class="ContentPasted2"> import ez_setup</div><div class="ContentPasted2"> File "C:\Users\CE PC\AppData\Local\Temp\pip-install-cfq97mii\chimera_bd7187074876462a9782eded8cb3a816\ez_setup.py", line 170</div><div class="ContentPasted2"> <span style="background-color: rgb(255, 255, 0);" class=""><span class="Apple-converted-space"> </span>print "Setuptools version",version,"or greater has been installed."</span></div><div class="ContentPasted2"> ^</div><div class="ContentPasted2"> [end of output]</div><div class=""><br class="ContentPasted2"></div><div class="ContentPasted2"> note: This error originates from a subprocess, and is likely not a problem with pip.</div><div class="ContentPasted2">error: metadata-generation-failed</div><div class=""><br class="ContentPasted2"></div><div class="ContentPasted2">กม Encountered error while generating package metadata.</div><div class="ContentPasted2">จtฉค> See above for output.</div><div class=""><br class="ContentPasted2"></div><div class="ContentPasted2">note: This is an issue with the package mentioned above, not pip.</div>hint: See above for details.</span></div><div class="elementToProof" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><span class="ContentPasted2 elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);">######################################################################################################<br class=""></span></div><div class="elementToProof" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><span class="ContentPasted2 elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);"><br class=""></span></div><div class="elementToProof" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><span class="ContentPasted2 elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);">So it looks like the temporary file generated has an error that doesn't allow the installation of the module, and so I cannot use any command from my script as runCommand is not recognized. There seem to be no mention of this issue in the mail archive but one colleague encountered the same problem, which I find strange. Do you have an idea on how to solve this issue ?<span class="Apple-converted-space"> </span><br class=""></span></div><div class="elementToProof" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><span class="ContentPasted2 elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);"><br class=""></span></div><div class="elementToProof" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><span class="ContentPasted2 elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);">Thank you and have a great day,<br class=""></span></div><div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></div><div id="Signature" class=""><div class=""><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">Noจฆ Robert,</div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">Fifth-year student in bioengineering, minor in Bioinformatics and Modelling, at engineering school Polytech Nice Sophia, France</div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">Phone : +33 7 81 00 52 02</div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><i class="">"let's limit the use of our resources and lighten our mails"</i><br class=""></div></div></div></div><div class="elementToProof" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><span class="ContentPasted2 elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);"><br class=""></span></div><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Chimera-users mailing list:<span class="Apple-converted-space"> </span></span><a href="mailto:Chimera-users@cgl.ucsf.edu" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">Chimera-users@cgl.ucsf.edu</a><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Manage subscription:<span class="Apple-converted-space"> </span></span><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users</a></div></blockquote></div><br class=""></div></body></html>