<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="">Hi James,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Is this somehow a modified version of 5byl? I don't get this error with 5byl in the 1.2.5 release, though I am using Mac and not Linux (shouldn't matter AFAIK). At any rate, try getting the daily build and trying that. It has some fixes related to adding hydrogens to structures with alt locs.</div><div class=""><br class=""></div><div class=""><div class="">--Eric</div><div class=""><br class=""></div><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><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Jul 27, 2021, at 9:54 PM, James Loy 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 dir="ltr" class="">Hi folks-<div class=""><br class=""></div><div class="">I'm trying to add hydrogens to an mmCIF file (5byl) using the <font face="monospace" class="">addh</font> command. However, every time I try, I encounter the following error:</div><div class=""><br class=""></div><div class=""><font face="monospace" class="">Traceback (most recent call last):<br class=""> File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/ChimeraX_main.py", line 712, in init<br class=""> run(sess, cmd)<br class=""> File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/core/commands/run.py", line 36, in run<br class=""> results = command.run(text, log=log, return_json=return_json)<br class=""> File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/core/commands/cli.py", line 2852, in run<br class=""> result = ci.function(session, **kw_args)<br class=""> File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/addh/cmd.py", line 63, in cmd_addh<br class=""> add_h_func(session, structures, template=template, in_isolation=in_isolation, **prot_schemes)<br class=""> File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/addh/cmd.py", line 170, in hbond_add_hydrogens<br class=""> add_hydrogens(session, atoms, type_info_for_atom, naming_schemas, hydrogen_totals,<br class=""> File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/addh/hbond.py", line 214, in add_hydrogens<br class=""> _attach_hydrogens(atom, altloc_hpos_info, bonding_info)<br class=""> File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/addh/hbond.py", line 895, in _attach_hydrogens<br class=""> add_altloc_hyds(atom, altloc_hpos_info, invert, bonding_info, total_hydrogens, naming_schema)<br class=""> File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/addh/cmd.py", line 862, in add_altloc_hyds<br class=""> h = new_hydrogen(atom, i+1, total_hydrogens, naming_schema,<br class=""> File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/addh/cmd.py", line 882, in new_hydrogen<br class=""> metal_pos = metal.get_alt_loc_coord(alt_loc)<br class=""> File "atomic_cpp/cymol.pyx", line 587, in chimerax.atomic.cymol.CyAtom.get_alt_loc_coord<br class="">ValueError: Atom /A MG 702 MG has no alt loc B</font><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">I'm using ucsf-chimerax_1.2.5-1_amd64.deb installed on Ubuntu 20.04. I've done some digging, and I cannot figure out what is going on. Any help would be appreciated.</div><div class=""><br class=""></div><div class="">Thanks in advance!</div><div class="">-James</div><div class="">-- <br class=""><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class="">James Loy, Ph. D.</div><div class="">614.915.9792<br class=""></div><div class=""><a href="https://www.linkedin.com/in/james-m-loy-ph-d-ba2256a/" target="_blank" class="">LinkedIn</a><br class=""></div></div></div></div></div></div></div>
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