<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>The problems you are experiencing with your modified structure are indeed fixed in the daily build, so if you get that you will be able to add hydrogens without issue.</div><div class=""><br class=""></div><div class="">--Eric</div><div class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Jul 28, 2021, at 4:12 PM, James Loy <<a href="mailto:jamesmadiganloy@gmail.com" class="">jamesmadiganloy@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Eric, Greg-<div class=""><br class=""></div><div class="">Yes, this is a modified CIF file from the pdb-redo service-- sorry I failed to mention that (that was the end of a long day). I'm attaching the file.</div><div class=""><br class=""></div><div class="">I'm going to hold off on the bug report for now because my colleague has actually been able to run our pipeline successfully for this pdb code. It seems like it might be something with my setup?</div><div class=""><br class=""></div><div class="">I'm sorry to have bothered-- I'll file a bug if we run into this issue again.</div><div class=""><br class=""></div><div class="">Thanks</div><div class="">-James</div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Jul 28, 2021 at 3:27 PM Greg Couch <<a href="mailto:gregc@cgl.ucsf.edu" class="">gregc@cgl.ucsf.edu</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div class=""><p class="">I was unable to reproduce this on a Ubuntu 20.04 system with
ChimeraX 1.2.5. So something weird is going on. Please use the
Help / Report a Bug dialog to provide us with information about
your system. And in your bug report, please include your 5byl.cif
file (~/Downloads/ChimeraX/PDB/5byl.cif file if you didn't modify
it). There is also a chance that this is a hardware error, but
let's start with the bug report.<br class="">
</p><p class=""> -- Greg</p><p class=""><br class="">
</p>
<div class="">On 7/28/2021 12:00 PM, Eric Pettersen
via ChimeraX-users wrote:<br class="">
</div>
<blockquote type="cite" class="">
Hi James,
<div class=""><span style="white-space:pre-wrap" class=""> </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 style="white-space:pre-wrap" class=""> </span>Eric
Pettersen</div>
<div class=""><span style="white-space:pre-wrap" class=""> </span>UCSF
Computer Graphics Lab</div>
</div>
<div class=""><br class="">
<div class=""><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" target="_blank" class="">chimerax-users@cgl.ucsf.edu</a>>
wrote:</div>
<br class="">
<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="">
<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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</blockquote>
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</div>
<br class="">
<fieldset class=""></fieldset>
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</blockquote>
</div>
</blockquote></div><br clear="all" class=""><div class=""><br class=""></div>-- <br class=""><div dir="ltr" class="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>
<span id="cid:f_kro3oze60"><5byl_final.cif></span></div></blockquote></div><br class=""></div></body></html>