<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">The "--script" option in ChimeraX 1.4 only takes Python scripts, not ChimeraX command scripts. The clue to this is in the error message where is says it is in function "open_python_script". ChimeraX 1.5 accepts either Python or ChimeraX (.cxc) scripts with the --script option.<div class=""><br class=""></div><div class="">For ChimeraX 1.4 just use</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>chimerax --nogui myscript.cxc</div><div class=""><br class=""></div><div class="">The --script option is mostly intended to pass arguments to a script.</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 Nov 28, 2022, at 2:00 PM, Visvaldas K. via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class=""><div class="yahoo-style-wrap" style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;font-size:16px;"><div dir="ltr" data-setdir="false" class="">Dear ChimeraX wizards,<br class=""></div><br class="">I was trying to generate hbond analysis via nogui, by issuing "chimerax --nogui --script "myscript.cxc",<br class=""><br class="">where in the script I put the following commands:<br class=""><br class=""><div class=""><b class="">open /Users/visvaldas/temp0000.pdb</b></div><b class="">select /B<br class="">hbonds sel saveFile /Users/visvaldas/temp00.hbonds restrict cross batch true<br class=""></b><div class=""><b class="">quit</b></div><div class=""><br class=""></div><div class="">However, something is wrong with hbonds line since I am getting this error:</div><div class="">Executing: runscript myscript.cxc<br class="">Traceback (most recent call last):<br class=""> File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/scripting.py", line 83, in open_python_script<br class=""> code = compile(data, stream.name, 'exec')<br class=""> File "myscript.cxc", line 4<br class=""> hbonds sel saveFile /Users/visvaldas/temp00.hbonds restrict cross batch true<br class=""> ^<br class="">SyntaxError: invalid syntax<br class=""><br class=""><div class="">What I am doing wrong? <br class=""></div><div dir="ltr" data-setdir="false" class="">(Also, when using GUI, the hbonds line was much longer, so I deleted those reveal, color, etc entities to make it more relevant to batch. (The "long" line <br class=""></div><div class=""><b class="">hbonds sel saveFile /Users/visvaldas/temp00.hbonds color #fffb00 dashes 5 restrict cross reveal true retainCurrent true</b></div><div class="">from the GUI does not work either)</div><div class=""><br class=""></div><div dir="ltr" data-setdir="false" class="">Best wishes,</div><div dir="ltr" data-setdir="false" class=""><br class=""></div><div dir="ltr" data-setdir="false" class="">Visvaldas<br class=""></div></div></div></div>_______________________________________________<br class="">ChimeraX-users mailing list<br class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="">ChimeraX-users@cgl.ucsf.edu</a><br class="">Manage subscription:<br class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users<br class=""></div></blockquote></div><br class=""></div></body></html>