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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> 6i4q fromDatabase pdbe_bio format mmcif</div><div class="cxcmd_as_cmd"><a href="cxcmd:open 6i4q fromDatabase pdbe_bio format mmcif">open 6i4q fromDatabase pdbe_bio format mmcif</a></div></div>
59	<table border=1 cellpadding=4 cellspacing=0>
60	<thead>
61	<tr>
62	<th colspan="2">Summary of feedback from opening 6i4q fetched from pdbe_bio</th>
63	</tr>
64	</thead>
65	<tbody>
66	<tr>
67	<td><i>warnings</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/>Atom H is not in the residue template for VAL /B:-6</td> </tr>
68	</tbody>
69	</table><br/><i>6i4q bioassembly 1</i> title:<br><b>Crystal structure of the human dihydrolipoamide dehydrogenase at 1.75 Angstrom resolution</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 6i4q 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:3-474">A</a></td>
83	<td><a title="Show sequence" href="cxcmd:sequence chain #1/A">Dihydrolipoyl dehydrogenase, mitochondrial</a></td>
84
85	</tr>
86	<tr>
87	<td style="text-align:center"><a title="Select chain" href="cxcmd:select /B:-6-474">B</a></td>
88	<td><a title="Show sequence" href="cxcmd:sequence chain #1/B">Dihydrolipoyl dehydrogenase, mitochondrial</a></td>
89
90	</tr>
91	</tbody>
92	</table><br/><table border=1 cellpadding=4 cellspacing=0>
93	<thead>
94	<tr>
95	<th>Non-standard residues in 6i4q bioassembly 1 #1</th>
96	</tr>
97	</thead>
98	<tbody>
99	<tr>
100	<td><a title="select residue" href="cxcmd:sel :BTB">BTB</a> — <a title="show residue info" href="https://www.rcsb.org/ligand/BTB">(BTB)</a></td>
101	</tr>
102	<tr>
103	<td><a title="select residue" href="cxcmd:sel :FAD">FAD</a> — <a title="show residue info" href="https://www.rcsb.org/ligand/FAD">(FAD)</a></td>
104	</tr>
105	<tr>
106	<td><a title="select residue" href="cxcmd:sel :SO4">SO4</a> — <a title="show residue info" href="https://www.rcsb.org/ligand/SO4">(SO4)</a></td>
107	</tr>
108	</tbody>
109	</table><br/>249 atoms have alternate locations. Control/examine alternate locations with <b><a href="cxcmd:help help:user/tools/altlocexplorer.html">Altloc Explorer</a></b> [<a href="cxcmd:ui tool show 'Altloc Explorer'">start tool...</a>] or the <b><a href="cxcmd:help altlocs">altlocs</a></b> command.<br/>Computing secondary structure<br>
110	Opened 1 biological assemblies for 6i4q<br>
111	<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/delete.html">delete</a> :btb :so4 :hoh</div><div class="cxcmd_as_cmd"><a href="cxcmd:delete :btb :so4 :hoh">delete :btb :so4 :hoh</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/minimize.html">minimize</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:minimize">minimize</a></div></div>Starting dock prep<br>
112	Deleting solvent<br>
113	Deleting non-metal-complex ions<br>
114	Deleting non-current alt locs<br>
115	Deleting residues with incomplete backbones<br>
116
117	<table border=1 cellpadding=4 cellspacing=0>
118	<thead>
119	<tr>
120	<th colspan="2">Summary of feedback from adding hydrogens to 6i4q bioassembly 1 #1</th>
121	</tr>
122	</thead>
123	<tbody>
124	<tr>
125	<td><i>notes</i></td> <td style="background-color:Canvas">No usable SEQRES records for 6i4q bioassembly 1 (#1) chain A; guessing termini instead<br>No usable SEQRES records for 6i4q bioassembly 1 (#1) chain B; guessing termini instead<br>Chain-initial residues that are actual N termini: /A GLN 3<br>Chain-initial residues that are not actual N termini: /B VAL -6<br>Chain-final residues that are actual C termini: /A PHE 474, /B PHE 474<br>Chain-final residues that are not actual C termini: <br>905 hydrogen bonds<br>5 hydrogens added</td> </tr>
126	</tbody>
127	</table><br/>Using Amber 20 recommended default charges and atom types for standard residues<br>
128	Assigning partial charges to residue FAD (net charge -1) with am1-bcc method<br>
129	Running ANTECHAMBER command: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /tmp/tmpk4pcolip/ante.in.mol2 -fi mol2 -o /tmp/tmpk4pcolip/ante.out.mol2 -fo mol2 -c bcc -nc -1 -j 5 -s 2 -dr n<br>
130	(FAD) <code></code><br/>(FAD) <code>Welcome to antechamber 20.0: molecular input file processor.</code><br/>(FAD) <code></code><br/>(FAD) <code>Info: Finished reading file (/tmp/tmpk4pcolip/ante.in.mol2); atoms read (85), bonds read (90).</code><br/>(FAD) <code>Info: Determining atomic numbers from atomic symbols which are case sensitive.</code><br/>(FAD) <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/>(FAD) <code></code><br/>(FAD) <code></code><br/>(FAD) <code>Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff</code><br/>(FAD) <code>Info: Total number of electrons: 408; net charge: -1</code><br/>(FAD) <code></code><br/>(FAD) <code>Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out</code><br/>(FAD) <code></code><br/>(FAD) <code>Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /usr/lib/ucsf-chimerax-daily/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1</code><br/>(FAD) <code></code><br/>(FAD) <code>Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC</code><br/>(FAD) <code></code><br/>Charges for residue FAD determined<br>
131	Dock prep finished<br>
132	Traceback (most recent call last):<br>
133	File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 322, in execute<br>
134	cmd.run(cmd_text)<br>
135	File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3245, in run<br>
136	result = ci.function(session, **kw_args)<br>
137	^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
138	File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/minimize/cmd.py", line 57, in cmd_minimize<br>
139	dock_prep_caller(session, [structure], memorize_name="minimization", nogui=True,<br>
140	File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/dock_prep/cmd.py", line 146, in dock_prep_caller<br>
141	run_steps(session, state, structures)<br>
142	File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/dock_prep/cmd.py", line 161, in run_steps<br>
143	step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'], state['memorize_name'],<br>
144	File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/dock_prep/prep.py", line 150, in prep<br>
145	callback(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/addh/dock_prep.py", line 56, in run_for_dock_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/add_charge/dock_prep.py", line 58, 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 156, in run_steps<br>
155	callback()<br>
156	File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/dock_prep/prep.py", line 149, in <lambda><br>
157	state['callback'] = lambda cb=cb, ps=postscript: (ps(), cb())<br>
158	^^^^<br>
159	File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/minimize/cmd.py", line 59, in <lambda><br>
160	steps=max_steps: _minimize(ses, struct, fixed, updates, log, steps), **kw)<br>
161	^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
162	File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/minimize/cmd.py", line 262, in _minimize<br>
163	system = forcefield.createSystem(top, nonbondedCutoff=1*nanometer, constraints=HBonds)<br>
164	^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
165	File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/openmm/app/forcefield.py", line 1279, in createSystem<br>
166	data.setAtomClasses(self)<br>
167	File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/openmm/app/forcefield.py", line 683, in setAtomClasses<br>
168	self.atomClasses = [classNameForType[self.atomType[atom]] for atom in self.atoms]<br>
169	^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
170	File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/openmm/app/forcefield.py", line 683, in <listcomp><br>
171	self.atomClasses = [classNameForType[self.atomType[atom]] for atom in self.atoms]<br>
172	~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^<br>
173	KeyError: 'N'<br>
174	<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_6i4q.html</div><div class="cxcmd_as_cmd"><a href="cxcmd:log save log_minimize_6i4q.html">log save log_minimize_6i4q.html</a></div></div></body>
175	</html>

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