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1	<html>
2	<head>
3	<meta charset='utf-8'>
4	<title> ChimeraX Log </title>
5	<script type="text/javascript">
6	window.onload = function() {
7	cxlinks_base="https://www.rbvi.ucsf.edu/chimerax/docs/"
8	if(!window.navigator.userAgent.includes("ChimeraX")){
9	window.onclick = function(e){
10	if(e.target.tagName.toLowerCase()!="a")
11	return true;
12	var url=e.target.getAttribute("href").toLowerCase();
13	if(url.startsWith("help:")){
14	window.location.href = cxlinks_base + url.substring(5);
15	return false;
16	}
17	if(url.startsWith("cxcmd:")){
18	alert("This link only works in a ChimeraX browser and would execute a command.");
19	return false;
20	}
21	return true;
22	}
23	var ls=document.links;
24	for(var i=0;i<ls.length;i++){
25	var link=ls[i];
26	var url=link.getAttribute("href").toLowerCase();
27	if(url.startsWith("cxcmd:"))
28	link.style.color="darkred";
29	}
30	}
31	};
32	</script>
33	<style>
34
35	.cxcmd_as_doc {
36	display: inline;
37	}
38	.cxcmd_as_cmd {
39	display: none;
40	}
41	</style>
42	</head>
43	<body>
44	<h1> ChimeraX Log </h1>
45
46	<table border=1 cellpadding=4 cellspacing=0>
47	<thead>
48	<tr>
49	<th colspan="2">Startup Messages</th>
50	</tr>
51	</thead>
52	<tbody>
53	<tr>
54	<td><i>warning</i></td> <td style="background-color:darkgoldenrod">No presets found in custom preset folder /home/paul/config/chimerax</td> </tr>
55	</tbody>
56	</table><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/alias.html">alias</a> cls close session</div><div class="cxcmd_as_cmd"><a href="cxcmd:alias cls close session">alias cls close session</a></div></div>UCSF ChimeraX version: 1.13.dev202606032116 (2026-06-03)<br>
57	Â© 2016-2026 Regents of the University of California. All rights reserved.<br>
58	<a href="cxcmd:help help:credits.html">How to cite UCSF ChimeraX</a><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> 7wgr format mmcif fromDatabase pdbe_bio</div><div class="cxcmd_as_cmd"><a href="cxcmd:open 7wgr format mmcif fromDatabase pdbe_bio">open 7wgr format mmcif fromDatabase pdbe_bio</a></div></div>
59	<table border=1 cellpadding=4 cellspacing=0>
60	<thead>
61	<tr>
62	<th colspan="2">Summary of feedback from opening 7wgr fetched from pdbe_bio</th>
63	</tr>
64	</thead>
65	<tbody>
66	<tr>
67	<td><i>warning</i></td> <td style="background-color:darkgoldenrod">Missing or incorrect <a='https://mmcif.wwpdb.org/dictionaries/mmcif_std.dic/Categories/entity_poly_seq.html'>sequence information</a>. Inferred polymer connectivity.<br/></td> </tr>
68	</tbody>
69	</table><br/><i>7wgr bioassembly 1</i> title:<br><b>Cryo-electron microscopic structure of the 2-oxoglutarate dehydrogenase (E1) component of the human alpha-ketoglutarate (2-oxoglutarate) dehydrogenase complex</b> <a href="cxcmd:log metadata #1">[more info...]</a><br><br/><table border=1 cellpadding=4 cellspacing=0>
70	<thead>
71	<tr>
72	<th colspan="2">Chain information for 7wgr bioassembly 1 #1</th>
73	</tr>
74	<tr>
75	<th>Chain</th>
76	<th>Description</th>
77
78	</tr>
79	</thead>
80	<tbody>
81	<tr>
82	<td style="text-align:center"><a title="Select chain" href="cxcmd:select /A:129-1023">A</a> <a title="Select chain" href="cxcmd:select /B:129-1023">B</a></td>
83	<td><a title="Show sequence" href="cxcmd:sequence chain #1/A#1/B">2-oxoglutarate dehydrogenase, mitochondrial</a></td>
84
85	</tr>
86	</tbody>
87	</table><br/><table border=1 cellpadding=4 cellspacing=0>
88	<thead>
89	<tr>
90	<th>Non-standard residues in 7wgr bioassembly 1 #1</th>
91	</tr>
92	</thead>
93	<tbody>
94	<tr>
95	<td><a title="select residue" href="cxcmd:sel :CA">CA</a> — <a title="show residue info" href="https://www.rcsb.org/ligand/CA">(CA)</a></td>
96	</tr>
97	<tr>
98	<td><a title="select residue" href="cxcmd:sel :MG">MG</a> — <a title="show residue info" href="https://www.rcsb.org/ligand/MG">(MG)</a></td>
99	</tr>
100	<tr>
101	<td><a title="select residue" href="cxcmd:sel :TPP">TPP</a> — <a title="show residue info" href="https://www.rcsb.org/ligand/TPP">(TPP)</a></td>
102	</tr>
103	</tbody>
104	</table><br/>Computing secondary structure<br>
105	Opened 1 biological assemblies for 7wgr<br>
106	<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/minimize.html">minimize</a> dockPrep true acMethod gasteiger</div><div class="cxcmd_as_cmd"><a href="cxcmd:minimize dockPrep true acMethod gasteiger">minimize dockPrep true acMethod gasteiger</a></div></div>Starting dock prep<br>
107	Deleting solvent<br>
108	Deleting non-metal-complex ions<br>
109	Deleting non-current alt locs<br>
110	Deleting residues with incomplete backbones<br>
111	Filling out missing side chains<br>
112	/A ASP 170: phi -76.3, psi -19.1 trans<br>
113	/A SER 1023: phi -92.9, psi none trans<br>
114	/B ASP 170: phi -76.3, psi -19.7 trans<br>
115	/B SER 1023: phi -96.4, psi none trans<br>
116	Applying ASP rotamer (chi angles: 60.4 -13.5) to /A ASP 170<br>
117	Applying SER rotamer (chi angles: 65.3) to /A SER 1023<br>
118	Applying ASP rotamer (chi angles: 60.4 -13.5) to /B ASP 170<br>
119	Applying SER rotamer (chi angles: 65.3) to /B SER 1023<br>
120
121	<table border=1 cellpadding=4 cellspacing=0>
122	<thead>
123	<tr>
124	<th colspan="2">Summary of feedback from adding hydrogens to 7wgr bioassembly 1 #1</th>
125	</tr>
126	</thead>
127	<tbody>
128	<tr>
129	<td><i>notes</i></td> <td style="background-color:Canvas">No usable SEQRES records for 7wgr bioassembly 1 (#1) chain A; guessing termini instead<br>No usable SEQRES records for 7wgr bioassembly 1 (#1) chain B; guessing termini instead<br>Chain-initial residues that are actual N termini: /A ALA 129, /B ALA 129<br>Chain-initial residues that are not actual N termini: /A ASN 365, /A MET 602, /B ASN 365, /B MET 602<br>Chain-final residues that are actual C termini: <br>Chain-final residues that are not actual C termini: /A SER 1023, /A ASP 346, /A LYS 574, /B SER 1023, /B ASP 346, /B LYS 574<br>1249 hydrogen bonds<br>Adding 'H' to /A ASN 365<br>Adding 'H' to /A MET 602<br>Adding 'H' to /B ASN 365<br>Adding 'H' to /B MET 602<br>/A SER 1023 is not terminus, removing H atom from 'C'<br>/B SER 1023 is not terminus, removing H atom from 'C'<br>13388 hydrogens added</td> </tr>
130	</tbody>
131	</table><br/>Using Amber 20 recommended default charges and atom types for standard residues<br>
132	Assigning partial charges to residue TPP (net charge -2) with gasteiger method<br>
133	Running ANTECHAMBER command: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/antechamber -i /tmp/tmpnzwl1mel/ante.in.mol2 -fi mol2 -o /tmp/tmpnzwl1mel/ante.out.mol2 -fo mol2 -c gas -nc -2 -j 5 -s 2 -dr n<br>
134	(TPP) <code></code><br/>(TPP) <code>Welcome to antechamber 20.0: molecular input file processor.</code><br/>(TPP) <code></code><br/>(TPP) <code>Info: Finished reading file (/tmp/tmpnzwl1mel/ante.in.mol2); atoms read (42), bonds read (43).</code><br/>(TPP) <code>Info: Determining atomic numbers from atomic symbols which are case sensitive.</code><br/>(TPP) <code>Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac</code><br/>(TPP) <code></code><br/>(TPP) <code></code><br/>(TPP) <code>Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff</code><br/>(TPP) <code>Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/atomtype -i ANTECHAMBER_GAS.AC -o ANTECHAMBER_GAS_AT.AC -d /usr/lib/ucsf-chimerax-daily/bin/amber20/dat/antechamber/ATOMTYPE_GAS.DEF</code><br/>(TPP) <code></code><br/>(TPP) <code>Warning: The net charge of the molecule (-2 ) does not equal the total formal charge (-3.00) according to the Gasteiger atom types.</code><br/>(TPP) <code></code><br/>Charges for residue TPP determined<br>
135	Dock prep finished<br>
136	Traceback (most recent call last):<br>
137	File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 322, in execute<br>
138	cmd.run(cmd_text)<br>
139	File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3245, in run<br>
140	result = ci.function(session, **kw_args)<br>
141	^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
142	File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/minimize/cmd.py", line 57, in cmd_minimize<br>
143	dock_prep_caller(session, [structure], memorize_name="minimization", nogui=True,<br>
144	File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/dock_prep/cmd.py", line 146, in dock_prep_caller<br>
145	run_steps(session, state, structures)<br>
146	File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/dock_prep/cmd.py", line 161, in run_steps<br>
147	step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'], state['memorize_name'],<br>
148	File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/dock_prep/prep.py", line 150, in prep<br>
149	callback(session, state, structures)<br>
150	File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/dock_prep/cmd.py", line 161, in run_steps<br>
151	step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'], state['memorize_name'],<br>
152	File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/addh/dock_prep.py", line 56, in run_for_dock_prep<br>
153	callback(session, state, structures)<br>
154	File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/dock_prep/cmd.py", line 161, in run_steps<br>
155	step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'], state['memorize_name'],<br>
156	File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/add_charge/dock_prep.py", line 58, in run_for_dock_prep<br>
157	callback(session, state, structures)<br>
158	File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/dock_prep/cmd.py", line 156, in run_steps<br>
159	callback()<br>
160	File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/dock_prep/prep.py", line 149, in <lambda><br>
161	state['callback'] = lambda cb=cb, ps=postscript: (ps(), cb())<br>
162	^^^^<br>
163	File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/minimize/cmd.py", line 59, in <lambda><br>
164	steps=max_steps: _minimize(ses, struct, fixed, updates, log, steps), **kw)<br>
165	^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
166	File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/minimize/cmd.py", line 262, in _minimize<br>
167	system = forcefield.createSystem(top, nonbondedCutoff=1*nanometer, constraints=HBonds)<br>
168	^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
169	File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/openmm/app/forcefield.py", line 1279, in createSystem<br>
170	data.setAtomClasses(self)<br>
171	File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/openmm/app/forcefield.py", line 683, in setAtomClasses<br>
172	self.atomClasses = [classNameForType[self.atomType[atom]] for atom in self.atoms]<br>
173	^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
174	File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/openmm/app/forcefield.py", line 683, in <listcomp><br>
175	self.atomClasses = [classNameForType[self.atomType[atom]] for atom in self.atoms]<br>
176	~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^<br>
177	KeyError: 'N'<br>
178	<br/>KeyError: 'N'<br><br> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/openmm/app/forcefield.py", line 683, in <listcomp><br> self.atomClasses = [classNameForType[self.atomType[atom]] for atom in self.atoms]<br> ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^<br><br><i>See log for complete Python traceback.</i><br><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/log.html#save">log save</a> log_minimize_7wgr.html</div><div class="cxcmd_as_cmd"><a href="cxcmd:log save log_minimize_7wgr.html">log save log_minimize_7wgr.html</a></div></div></body>
179	</html>

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