<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="">This appears to be a bug in ChimeraX's “toolshed” startup code for some machines when ChimeraX is started for the first time. I am going to open a ticket in our bug-tracking system for this, with you on the recipient list. You may be able to circumvent the bug by starting ChimeraX with the “—noexit” flag (that’s two dashes, not one long dash), <i class="">i.e.</i><span style="font-style: normal;" class=""> </span>chimera-daily —noexit<div class=""><br class=""></div><div class="">—Eric<br class=""><div class="">
<div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span class="Apple-tab-span" style="white-space: pre;"><br class="Apple-interchange-newline"> </span>Eric Pettersen</div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><br class=""></div></div><div><br class=""><blockquote type="cite" class=""><div class="">On Oct 17, 2019, at 6:13 AM, Brown, Alex <<a href="mailto:Alex.Brown@umassmed.edu" class="">Alex.Brown@umassmed.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; 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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><span class="">Hello and good morning,</span></div><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; 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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><span class=""><br class=""></span></div><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; 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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><span class="">I have always had a great experience using Chimera and so I was hoping to try out ChimeraX for some of our larger cryo-em data sets. However, following download and an install that did not seem to produce an error message, I can not seem to initialize the program. I have copied the output from the command prompt below. Beyond that, I should probably also mention that we are running the centos-release-7-6.1810.2.el7.centos.x86_64 operating system with intel chips and nvidia graphics cards.</span></div><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; 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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><span class=""><br class=""></span></div><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; 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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><span class=""><span class="">[root@gaolab ~]# chimerax-daily<br class=""></span><span class=""></span>NOTE: available bundle cache has not been initialized yet<br class=""></span></div><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; 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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><div class="">WARNING: could not retrieve bundle list from toolshed<br class=""></div><div class="">NOTE: Traceback (most recent call last): <br class=""></div><div class=""> File "/opt/UCSF/ChimeraX-daily/lib/python3.7/runpy.py", line 193, in<br class=""></div><div class="">_run_module_as_main <br class=""></div><div class=""> "__main__", mod_spec) <br class=""></div><div class=""> File "/opt/UCSF/ChimeraX-daily/lib/python3.7/runpy.py", line 85, in<br class=""></div><div class="">_run_code <br class=""></div><div class=""> exec(code, run_globals) <br class=""></div><div class=""> File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-<br class=""></div><div class="">packages/ChimeraX_main.py", line 871, in <module> <br class=""></div><div class=""> exit_code = init(sys.argv) <br class=""></div><div class=""> File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-<br class=""></div><div class="">packages/ChimeraX_main.py", line 580, in init <br class=""></div><div class=""> check_available=opts.get_available_bundles) <br class=""></div><div class=""> File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-<br class=""></div><div class="">packages/chimerax/core/toolshed/__init__.py", line 1681, in init <br class=""></div><div class=""> _toolshed = Toolshed(*args, **kw) <br class=""></div><div class=""> File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-<br class=""></div><div class="">packages/chimerax/core/toolshed/__init__.py", line 359, in __init__ <br class=""></div><div class=""> if not available.has_cache_file(self._cache_dir): <br class=""></div><div class=""> File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-<br class=""></div><div class="">packages/chimerax/core/toolshed/available.py", line 109, in has_cache_file <br class=""></div><div class=""> return os.path.exists(os.path.join(cache_dir, _CACHE_FILE)) <br class=""></div><div class=""> File "/usr/bin/../../opt/UCSF/ChimeraX-daily/lib/python3.7/posixpath.py",<br class=""></div><div class="">line 80, in join <br class=""></div><div class=""> a = os.fspath(a) <br class=""></div><div class="">TypeError: expected str, bytes or os.PathLike object, not NoneType <br class=""></div><div class=""> <span class="Apple-converted-space"> </span><br class=""></div><div class=""><br class=""></div><div class="">BUG: TypeError: expected str, bytes or os.PathLike object, not NoneType <br class=""></div><div class=""> <span class="Apple-converted-space"> </span><br class=""></div><div class="">File "/usr/bin/../../opt/UCSF/ChimeraX-daily/lib/python3.7/posixpath.py", line<br class=""></div><div class="">80, in join <br class=""></div><div class="">a = os.fspath(a) <br class=""></div><div class=""> <span class="Apple-converted-space"> </span><br class=""></div><div class=""> _See log for complete Python traceback._ <br class=""></div><span class=""></span><br class=""></div><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; 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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">Thanks in advance for any support you may be able to provide on this!</div><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; 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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">-Alex<br class=""></div><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; 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; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></div><div id="Signature" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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 class=""></div><div style="font-family: Tahoma; font-size: 13px;" class=""><div style="font-size: 13.3333px;" class=""><b style="color: rgb(32, 31, 30); font-family: Calibri, sans-serif; font-size: 11pt; font-style: inherit; font-variant-ligatures: inherit; font-variant-caps: inherit;" class=""><span style="font-size: 10pt; font-family: Arial, sans-serif;" class="">Alexander Brown IV, PhD</span></b><br class=""></div><div style="font-size: 13.3333px;" class=""><div style="margin: 0px; color: rgb(32, 31, 30); text-align: start; background-color: rgb(255, 255, 255); font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="margin: 0px; font-size: 10pt; font-family: Arial, sans-serif;" class="">Postdoctoral Researcher</span></div><div style="margin: 0px; color: rgb(32, 31, 30); text-align: start; background-color: rgb(255, 255, 255); font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="margin: 0px; font-size: 10pt; font-family: Arial, sans-serif;" class="">Horae Gene Therapy Center</span></div><div style="margin: 0px; color: rgb(32, 31, 30); text-align: start; background-color: rgb(255, 255, 255); font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="margin: 0px; font-size: 10pt; font-family: Arial, sans-serif;" class="">Li Weibo Institute for Rare Diseases Research</span></div><div style="margin: 0px; color: rgb(32, 31, 30); text-align: start; background-color: rgb(255, 255, 255); font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="margin: 0px; font-size: 10pt; font-family: Arial, sans-serif;" class="">University of Massachusetts Medical School</span></div><div style="margin: 0px; color: rgb(32, 31, 30); text-align: start; background-color: rgb(255, 255, 255); font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="margin: 0px; font-size: 10pt; font-family: Arial, sans-serif;" class="">368 Plantation Street, AS6-2011</span></div><div style="margin: 0px; color: rgb(32, 31, 30); text-align: start; background-color: rgb(255, 255, 255); font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="margin: 0px; font-size: 10pt; font-family: Arial, sans-serif;" class="">Worcester, MA 01605</span></div><div style="margin: 0px; color: rgb(32, 31, 30); text-align: start; background-color: rgb(255, 255, 255); font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="margin: 0px; font-size: 10pt; font-family: Arial, sans-serif;" class="">Phone: (508) 856-3316</span></div><div style="margin: 0px; color: rgb(32, 31, 30); text-align: start; background-color: rgb(255, 255, 255); font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="margin: 0px; font-size: 10pt; font-family: Arial, sans-serif;" class="">Email:<span class=""> </span><a href="mailto:alex.brown@umassmed.edu" target="_blank" rel="noopener noreferrer" style="margin: 0px;" class="">alex.brown@umassmed.edu</a></span><u class=""><span style="margin: 0px; color: rgb(5, 99, 193);" class=""></span></u></div><p style="margin: 0px; color: rgb(32, 31, 30); text-align: start; background-color: rgb(255, 255, 255); font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="margin: 0px;" class=""> </span></p><div style="margin: 0px; color: rgb(32, 31, 30); text-align: start; background-color: rgb(255, 255, 255); font-size: 11pt; font-family: Calibri, sans-serif;" class=""><i class=""><span style="margin: 0px; font-size: 10pt; font-family: Arial, sans-serif;" class="">Confidentiality Notice:</span></i></div><div style="margin: 0px; color: rgb(32, 31, 30); text-align: start; background-color: rgb(255, 255, 255); font-size: 11pt; font-family: Calibri, sans-serif;" class=""><i class=""><span style="margin: 0px; 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If you are not the intended recipient, please contact the sender immediately and destroy or permanently delete all copies of the original message.</span></i></div><br class=""></div></div></div><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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: normal; 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: normal; 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="">ChimeraX-users mailing list</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" style="font-family: Helvetica; font-size: 12px; 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-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">ChimeraX-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: normal; 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: normal; 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><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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=""><a href="http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" style="font-family: Helvetica; font-size: 12px; 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-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a></div></blockquote></div><br class=""></div></body></html>