The following bug report has been submitted:
Platform: Windows-10-10.0.19043
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:/Users/dharr/Desktop/AK023_NifD Swiss Model/Alignment with
> 3U7Q_NifD.cxs"
Log from Sun Dec 12 16:31:38 2021 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\ui\statusbar.py", line 84, in _expose_event
self.status(self._last_message, self._last_color)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\ui\statusbar.py", line 149, in status
r.update_viewport() # Need this when window resized.
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 1155, in update_viewport
self.set_viewport(*fb.viewport)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 1142, in set_viewport
GL.glViewport(x, y, w, h)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1282,
description = b'invalid operation',
baseOperation = glViewport,
cArguments = (0, 0, 1840, 22)
)
OpenGL.error.GLError: GLError(
err = 1282,
description = b'invalid operation',
baseOperation = glViewport,
cArguments = (0, 0, 1840, 22)
)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
> open https://www.rbvi.ucsf.edu/chimerax/data/conservation-
> coloring/121p-consurf.aln
Summary of feedback from opening
//www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/121p-consurf.aln
fetched from https
---
notes | Fetching 121p-consurf.aln from
https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/121p-consurf.aln
Downloaded 121p-consurf.aln to C:\Users\dharr\Downloads\121p-consurf.aln
Alignment identifier is 121p-consurf.aln
Showing conservation header ("seq_conservation" residue attribute) for
alignment 121p-consurf.aln
Opened 150 sequences from 121p-consurf.aln
> help help:quickstart
> open 3u7q
Summary of feedback from opening 3u7q fetched from pdb
---
notes | Fetching compressed mmCIF 3u7q from
http://files.rcsb.org/download/3u7q.cif
Fetching CCD HCA from http://ligand-expo.rcsb.org/reports/H/HCA/HCA.cif
Fetching CCD ICS from http://ligand-expo.rcsb.org/reports/I/ICS/ICS.cif
Fetching CCD IMD from http://ligand-expo.rcsb.org/reports/I/IMD/IMD.cif
Fetching CCD CA from http://ligand-expo.rcsb.org/reports/C/CA/CA.cif
Fetching CCD 1CL from http://ligand-expo.rcsb.org/reports/1/1CL/1CL.cif
Fetching CCD CLF from http://ligand-expo.rcsb.org/reports/C/CLF/CLF.cif
Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif
3u7q title:
A. vinelandii nitrogenase MoFe protein at atomic resolution [more info...]
Chain information for 3u7q #1
---
Chain | Description | UniProt
A C | Nitrogenase molybdenum-iron protein α chain | NIFD_AZOVI
B D | Nitrogenase molybdenum-iron protein β chain | NIFK_AZOVI
Non-standard residues in 3u7q #1
---
1CL — Fe(8)-S(7) cluster, oxidized
CA — calcium ion
CLF — Fe(8)-S(7) cluster
HCA — 3-hydroxy-3-carboxy-adipic acid
ICS — iron-sulfur-molybdenum cluster with interstitial carbon
IMD — imidazole
MG — magnesium ion
> ui tool show "Show Sequence Viewer"
> select /B/D
9889 atoms, 8672 bonds, 37 pseudobonds, 2513 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> cartoon hide
> cartoon
> open "C:/Users/dharr/Desktop/AK023_NifD Swiss Model/AK023_NifD_SM.pdb"
AK023_NifD_SM.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]
Chain information for AK023_NifD_SM.pdb #2
---
Chain | Description
A | No description available
Non-standard residues in AK023_NifD_SM.pdb #2
---
HCA — (HCA)
Drag select of 9 residues
Drag select of 152 atoms, 477 residues, 1 pseudobonds, 142 bonds
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> ui tool show Matchmaker
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3u7q, chain A (#1) with AK023_NifD_SM.pdb, chain A (#2), sequence
alignment score = 2406.7
RMSD between 477 pruned atom pairs is 0.056 angstroms; (across all 477 pairs:
0.056)
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3u7q, chain A (#1) with AK023_NifD_SM.pdb, chain A (#2), sequence
alignment score = 2406.7
RMSD between 477 pruned atom pairs is 0.056 angstroms; (across all 477 pairs:
0.056)
> ui tool show Matchmaker
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3u7q, chain A (#1) with AK023_NifD_SM.pdb, chain A (#2), sequence
alignment score = 2406.7
RMSD between 477 pruned atom pairs is 0.056 angstroms; (across all 477 pairs:
0.056)
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3u7q, chain A (#1) with AK023_NifD_SM.pdb, chain A (#2), sequence
alignment score = 2406.7
RMSD between 477 pruned atom pairs is 0.056 angstroms; (across all 477 pairs:
0.056)
> save "C:/Users/dharr/Desktop/AK023_NifD Swiss Model/Alignment with
> 3U7Q_NifD.cxs"
Drag select of 202 atoms, 954 residues, 1 pseudobonds, 184 bonds
> hide sel atoms
> select ::name="HCA"
28 atoms, 26 bonds, 2 residues, 2 models selected
> show sel target ab
> select ::name="ICS"
18 atoms, 30 bonds, 1 residue, 1 model selected
> show sel target ab
> select clear
> open https://www.rbvi.ucsf.edu/chimerax/data/conservation-
> coloring/121p-consurf.aln
Summary of feedback from opening
//www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/121p-consurf.aln
fetched from https
---
notes | Fetching 121p-consurf(1).aln from
https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/121p-consurf.aln
Downloaded 121p-consurf.aln to C:\Users\dharr\Downloads\121p-consurf(1).aln
Alignment identifier is 121p-consurf(1).aln
Showing conservation header ("seq_conservation" residue attribute) for
alignment 121p-consurf(1).aln
Opened 150 sequences from 121p-consurf(1).aln
> color red
> undo
> select clear
[Repeated 1 time(s)]
> ui tool show "Modeller Comparative"
> help morph
> ui tool show "Model Loops"
> ui tool show "Modeller Comparative"
No alignments chosen for modeling
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> sequence chain #2/A
Alignment identifier is 2/A
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
> sequence chain #2/A
Destroying pre-existing alignment with identifier 2/A
Alignment identifier is 2/A
> ui tool show Matchmaker
> matchmaker #2 to #1 showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3u7q, chain A (#1) with AK023_NifD_SM.pdb, chain A (#2), sequence
alignment score = 2406.7
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 3u7q #1/A, AK023_NifD_SM.pdb
#2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 477 pruned atom pairs is 0.056 angstroms; (across all 477 pairs:
0.056)
> help align
> select #1/A:461-480 #2/A:471-490
343 atoms, 353 bonds, 40 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [461-492]
RMSD: 0.067
> select clear
[Repeated 2 time(s)]
> select #1/A:7
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:7 #2/A:17
17 atoms, 15 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [7] RMSD:
0.106
> select #1/A:7
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:7
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:7
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:7 #2/A:17
17 atoms, 15 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [7] RMSD:
0.106
> show sel target ab
> select clear
> select #1/A:11
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:11 #2/A:21
11 atoms, 9 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [11] RMSD:
0.055
> select #1/A:25
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:25 #2/A:35
20 atoms, 18 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [25] RMSD:
0.049
> select #1/A:29
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:29 #2/A:39
13 atoms, 11 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [29] RMSD:
0.050
> select #1/A:37
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:37-38 #2/A:47-48
27 atoms, 26 bonds, 4 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [37-38] RMSD:
0.105
> select #1/A:40
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:40 #2/A:50
16 atoms, 14 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [40] RMSD:
0.131
> select #1/A:47
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:47 #2/A:57
15 atoms, 13 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [47] RMSD:
0.079
> select #1/A:53
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:53 #2/A:63
17 atoms, 15 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [53] RMSD:
0.065
> select #1/A:56
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:56 #2/A:66
15 atoms, 13 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [56] RMSD:
0.097
> select #1/A:138
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:138 #2/A:148
15 atoms, 13 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [138] RMSD:
0.043
> select #1/A:165
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:165 #2/A:175
11 atoms, 9 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [165] RMSD:
0.052
> select #1/A:167
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:167 #2/A:177
11 atoms, 9 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [167] RMSD:
0.052
> select #1/A:169
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:169 #2/A:179
16 atoms, 14 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [169] RMSD:
0.058
> select #1/A:171
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/A:171 #2/A:181
10 atoms, 8 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [171] RMSD:
0.051
> select #1/A:175
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:175 #2/A:185
10 atoms, 8 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [175] RMSD:
0.065
> select #1/A:178
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:178 #2/A:188
15 atoms, 13 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [178] RMSD:
0.068
> select #1/A:208
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/A:208 #2/A:218
10 atoms, 8 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [208] RMSD:
0.067
> select #1/A:212
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:212 #2/A:222
17 atoms, 15 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [212] RMSD:
0.046
> select #1/A:214
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:214-215 #2/A:224-225
28 atoms, 26 bonds, 4 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [214-215]
RMSD: 0.057
> select #1/A:217
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:217 #2/A:227
14 atoms, 12 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [217] RMSD:
0.062
> select #1/A:249
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:249 #2/A:259
13 atoms, 11 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [249] RMSD:
0.083
> select #1/A:258
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:258 #2/A:268
13 atoms, 11 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [258] RMSD:
0.078
> select #1/A:262
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:262 #2/A:272
16 atoms, 14 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [262] RMSD:
0.061
> select #1/A:304
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:304 #2/A:314
18 atoms, 16 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [304] RMSD:
0.032
> select #1/A:311
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:311 #2/A:321
14 atoms, 12 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [311] RMSD:
0.027
> select #1/A:315
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:315 #2/A:325
18 atoms, 16 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [315] RMSD:
0.073
> select #1/A:322
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:322 #2/A:332
14 atoms, 12 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [322] RMSD:
0.070
> select #1/A:339
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:339 #2/A:349
15 atoms, 13 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [339] RMSD:
0.062
> select #1/A:355
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:355 #2/A:365
15 atoms, 13 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [355] RMSD:
0.045
> select #1/A:391
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:391 #2/A:401
16 atoms, 14 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [391] RMSD:
0.072
> select #1/A:396
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:396-397 #2/A:406-407
27 atoms, 25 bonds, 4 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [396-397]
RMSD: 0.057
> select #1/A:416
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:416 #2/A:426
15 atoms, 13 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [416] RMSD:
0.069
> select #1/A:429
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/A:429 #2/A:439
23 atoms, 23 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [429] RMSD:
0.064
> select #1/A:440
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:440 #2/A:450
18 atoms, 16 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [440] RMSD:
0.047
> select #1/A:480
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:480 #2/A:490
19 atoms, 17 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [480] RMSD:
0.070
> show sel target ab
> select clear
> select #1/A:11
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:11 #2/A:21
11 atoms, 9 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [11] RMSD:
0.055
> show sel target ab
> select #1/A:25
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:25 #2/A:35
20 atoms, 18 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [25] RMSD:
0.049
> show sel target ab
> select #1/A:29
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:29 #2/A:39
13 atoms, 11 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [29] RMSD:
0.050
> show sel target ab
> select #1/A:37
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:37-38 #2/A:47-48
27 atoms, 26 bonds, 4 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [37-38] RMSD:
0.105
> show sel target ab
> select #1/A:40
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:40 #2/A:50
16 atoms, 14 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [40] RMSD:
0.131
> show sel target ab
> select #1/A:47
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:47 #2/A:57
15 atoms, 13 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [47] RMSD:
0.079
> show sel target ab
> select #1/A:53
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:53 #2/A:63
17 atoms, 15 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [53] RMSD:
0.065
> show sel target ab
> select #1/A:56
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:56 #2/A:66
15 atoms, 13 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [56] RMSD:
0.097
> show sel target ab
> select #1/A:138
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:138 #2/A:148
15 atoms, 13 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [138] RMSD:
0.043
> show sel target ab
> select #1/A:165
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:165 #2/A:175
11 atoms, 9 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [165] RMSD:
0.052
> show sel target ab
> select #1/A:167
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:167 #2/A:177
11 atoms, 9 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [167] RMSD:
0.052
> show sel target ab
> select #1/A:169
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:169 #2/A:179
16 atoms, 14 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [169] RMSD:
0.058
> show sel target ab
> select #1/A:171
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/A:171 #2/A:181
10 atoms, 8 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [171] RMSD:
0.051
> show sel target ab
> select #1/A:175
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:175 #2/A:185
10 atoms, 8 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [175] RMSD:
0.065
> show sel target ab
> select #1/A:178
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:178 #2/A:188
15 atoms, 13 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [178] RMSD:
0.068
> show sel target ab
> select #1/A:208
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/A:208 #2/A:218
10 atoms, 8 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [208] RMSD:
0.067
> show sel target ab
> select #1/A:212
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:212 #2/A:222
17 atoms, 15 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [212] RMSD:
0.046
> show sel target ab
> select #1/A:214
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:214-215 #2/A:224-225
28 atoms, 26 bonds, 4 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [214-215]
RMSD: 0.057
> show sel target ab
> select #1/A:217
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:217 #2/A:227
14 atoms, 12 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [217] RMSD:
0.062
> show sel target ab
> select #1/A:249
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:249 #2/A:259
13 atoms, 11 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [249] RMSD:
0.083
> show sel target ab
> select #1/A:258
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:258 #2/A:268
13 atoms, 11 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [258] RMSD:
0.078
> show sel target ab
> select #1/A:262
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:262 #2/A:272
16 atoms, 14 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [262] RMSD:
0.061
> show sel target ab
> select #1/A:304
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:304 #2/A:314
18 atoms, 16 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [304] RMSD:
0.032
> show sel target ab
> select #1/A:311
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:311 #2/A:321
14 atoms, 12 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [311] RMSD:
0.027
> show sel target ab
> select #1/A:315
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:315 #2/A:325
18 atoms, 16 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [315] RMSD:
0.073
> show sel target ab
> select #1/A:322
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:322 #2/A:332
14 atoms, 12 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [322] RMSD:
0.070
> show sel target ab
> select #1/A:339
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:339 #2/A:349
15 atoms, 13 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [339] RMSD:
0.062
> show sel target ab
> select #1/A:355
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:355 #2/A:365
15 atoms, 13 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [355] RMSD:
0.045
> show sel target ab
> select #1/A:391
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:391 #2/A:401
16 atoms, 14 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [391] RMSD:
0.072
> show sel target ab
> select #1/A:396
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:396-397 #2/A:406-407
27 atoms, 25 bonds, 4 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [396-397]
RMSD: 0.057
> show sel target ab
> select #1/A:416
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:416 #2/A:426
15 atoms, 13 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [416] RMSD:
0.069
> show sel target ab
> select #1/A:429
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/A:429 #2/A:439
23 atoms, 23 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [429] RMSD:
0.064
> show sel target ab
> select #1/A:440
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:440 #2/A:450
18 atoms, 16 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [440] RMSD:
0.047
> show sel target ab
> save "C:/Users/dharr/Desktop/AK023_NifD Swiss Model/Alignment with
> 3U7Q_NifD.cxs"
——— End of log from Sun Dec 12 16:31:38 2021 ———
opened ChimeraX session
> select clear
> select #1/A:11
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:11 #2/A:21
11 atoms, 9 bonds, 2 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [11] RMSD:
0.055
> select #1/A:11,25 #2/A:21,35
31 atoms, 27 bonds, 4 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [11] + 1
other block RMSD: 0.052
> select #1/A:11,25,29 #2/A:21,35,39
44 atoms, 38 bonds, 6 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [11] + 2
other blocks RMSD: 0.051
> select #1/A:11,25,29,37-38 #2/A:21,35,39,47-48
71 atoms, 64 bonds, 10 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [11] + 3
other blocks RMSD: 0.077
> select #1/A:11,25,29,37-38,40 #2/A:21,35,39,47-48,50
87 atoms, 78 bonds, 12 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [11] + 4
other blocks RMSD: 0.089
> select #1/A:11,25,29,37-38,40,47 #2/A:21,35,39,47-48,50,57
102 atoms, 91 bonds, 14 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [11] + 5
other blocks RMSD: 0.087
> select #1/A:11,25,29,37-38,40,47,53 #2/A:21,35,39,47-48,50,57,63
119 atoms, 106 bonds, 16 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [11] + 6
other blocks RMSD: 0.085
> select #1/A:11,25,29,37-38,40,47,53,56 #2/A:21,35,39,47-48,50,57,63,66
134 atoms, 119 bonds, 18 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [11] + 7
other blocks RMSD: 0.086
> select #1/A:11,25,29,37-38,40,47,53,56,138
> #2/A:21,35,39,47-48,50,57,63,66,148
149 atoms, 132 bonds, 20 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [11] + 8
other blocks RMSD: 0.083
> select #1/A:11,25,29,37-38,40,47,53,56,138,165
> #2/A:21,35,39,47-48,50,57,63,66,148,175
160 atoms, 141 bonds, 22 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [11] + 9
other blocks RMSD: 0.081
> select #1/A:11,25,29,37-38,40,47,53,56,138,165,167
> #2/A:21,35,39,47-48,50,57,63,66,148,175,177
171 atoms, 150 bonds, 24 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [11] + 10
other blocks RMSD: 0.079
> select #1/A:11,25,29,37-38,40,47,53,56,138,165,167,169
> #2/A:21,35,39,47-48,50,57,63,66,148,175,177,179
187 atoms, 164 bonds, 26 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [11] + 11
other blocks RMSD: 0.077
> select #1/A:11,25,29,37-38,40,47,53,56,138,165,167,169,175
> #2/A:21,35,39,47-48,50,57,63,66,148,175,177,179,185
197 atoms, 172 bonds, 28 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [11] + 12
other blocks RMSD: 0.077
> select #1/A:11,25,29,37-38,40,47,53,56,138,165,167,169,175,178
> #2/A:21,35,39,47-48,50,57,63,66,148,175,177,179,185,188
212 atoms, 185 bonds, 30 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [11] + 13
other blocks RMSD: 0.076
> select #1/A:11,25,29,37-38,40,47,53,56,138,165,167,169,171,175,178
> #2/A:21,35,39,47-48,50,57,63,66,148,175,177,179,181,185,188
222 atoms, 193 bonds, 32 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [11] + 14
other blocks RMSD: 0.075
> select #1/A:11,25,29,37-38,40,47,53,56,138,165,167,169,171,175,178,208
> #2/A:21,35,39,47-48,50,57,63,66,148,175,177,179,181,185,188,218
232 atoms, 201 bonds, 34 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [11] + 15
other blocks RMSD: 0.074
> select #1/A:11,25,29,37-38,40,47,53,56,138,165,167,169,171,175,178,208,212
> #2/A:21,35,39,47-48,50,57,63,66,148,175,177,179,181,185,188,218,222
249 atoms, 216 bonds, 36 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [11] + 16
other blocks RMSD: 0.073
> select
> #1/A:11,25,29,37-38,40,47,53,56,138,165,167,169,171,175,178,208,212,214-215
> #2/A:21,35,39,47-48,50,57,63,66,148,175,177,179,181,185,188,218,222,224-225
277 atoms, 242 bonds, 40 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [11] + 17
other blocks RMSD: 0.072
> select
> #1/A:11,25,29,37-38,40,47,53,56,138,165,167,169,171,175,178,208,212,214-215,217
> #2/A:21,35,39,47-48,50,57,63,66,148,175,177,179,181,185,188,218,222,224-225,227
291 atoms, 254 bonds, 42 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [11] + 18
other blocks RMSD: 0.071
> select
> #1/A:11,25,29,37-38,40,47,53,56,138,165,167,169,171,175,178,208,212,214-215,217,249
> #2/A:21,35,39,47-48,50,57,63,66,148,175,177,179,181,185,188,218,222,224-225,227,259
304 atoms, 265 bonds, 44 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [11] + 19
other blocks RMSD: 0.072
> select
> #1/A:11,25,29,37-38,40,47,53,56,138,165,167,169,171,175,178,208,212,214-215,217,249,258
> #2/A:21,35,39,47-48,50,57,63,66,148,175,177,179,181,185,188,218,222,224-225,227,259,268
317 atoms, 276 bonds, 46 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [11] + 20
other blocks RMSD: 0.072
> select
> #1/A:11,25,29,37-38,40,47,53,56,138,165,167,169,171,175,178,208,212,214-215,217,249,258,262
> #2/A:21,35,39,47-48,50,57,63,66,148,175,177,179,181,185,188,218,222,224-225,227,259,268,272
333 atoms, 290 bonds, 48 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [11] + 21
other blocks RMSD: 0.072
> select
> #1/A:11,25,29,37-38,40,47,53,56,138,165,167,169,171,175,178,208,212,214-215,217,249,258,262,304
> #2/A:21,35,39,47-48,50,57,63,66,148,175,177,179,181,185,188,218,222,224-225,227,259,268,272,314
351 atoms, 306 bonds, 50 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [11] + 22
other blocks RMSD: 0.070
> select
> #1/A:11,25,29,37-38,40,47,53,56,138,165,167,169,171,175,178,208,212,214-215,217,249,258,262,304,311
> #2/A:21,35,39,47-48,50,57,63,66,148,175,177,179,181,185,188,218,222,224-225,227,259,268,272,314,321
365 atoms, 318 bonds, 52 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [11] + 23
other blocks RMSD: 0.069
> select
> #1/A:11,25,29,37-38,40,47,53,56,138,165,167,169,171,175,178,208,212,214-215,217,249,258,262,304,311,315
> #2/A:21,35,39,47-48,50,57,63,66,148,175,177,179,181,185,188,218,222,224-225,227,259,268,272,314,321,325
383 atoms, 334 bonds, 54 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [11] + 24
other blocks RMSD: 0.069
> select
> #1/A:11,25,29,37-38,40,47,53,56,138,165,167,169,171,175,178,208,212,214-215,217,249,258,262,304,311,315,322
> #2/A:21,35,39,47-48,50,57,63,66,148,175,177,179,181,185,188,218,222,224-225,227,259,268,272,314,321,325,332
397 atoms, 346 bonds, 56 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [11] + 25
other blocks RMSD: 0.069
> select
> #1/A:11,25,29,37-38,40,47,53,56,138,165,167,169,171,175,178,208,212,214-215,217,249,258,262,304,311,315,322,339
> #2/A:21,35,39,47-48,50,57,63,66,148,175,177,179,181,185,188,218,222,224-225,227,259,268,272,314,321,325,332,349
412 atoms, 359 bonds, 58 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [11] + 26
other blocks RMSD: 0.069
> select
> #1/A:11,25,29,37-38,40,47,53,56,138,165,167,169,171,175,178,208,212,214-215,217,249,258,262,304,311,315,322,339,355
> #2/A:21,35,39,47-48,50,57,63,66,148,175,177,179,181,185,188,218,222,224-225,227,259,268,272,314,321,325,332,349,365
427 atoms, 372 bonds, 60 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [11] + 27
other blocks RMSD: 0.069
> select
> #1/A:11,25,29,37-38,40,47,53,56,138,165,167,169,171,175,178,208,212,214-215,217,249,258,262,304,311,315,322,339,355,391
> #2/A:21,35,39,47-48,50,57,63,66,148,175,177,179,181,185,188,218,222,224-225,227,259,268,272,314,321,325,332,349,365,401
443 atoms, 386 bonds, 62 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [11] + 28
other blocks RMSD: 0.069
> select
> #1/A:11,25,29,37-38,40,47,53,56,138,165,167,169,171,175,178,208,212,214-215,217,249,258,262,304,311,315,322,339,355,391,396-397
> #2/A:21,35,39,47-48,50,57,63,66,148,175,177,179,181,185,188,218,222,224-225,227,259,268,272,314,321,325,332,349,365,401,406-407
470 atoms, 411 bonds, 66 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [11] + 29
other blocks RMSD: 0.068
> select
> #1/A:11,25,29,37-38,40,47,53,56,138,165,167,169,171,175,178,208,212,214-215,217,249,258,262,304,311,315,322,339,355,391,396-397,416
> #2/A:21,35,39,47-48,50,57,63,66,148,175,177,179,181,185,188,218,222,224-225,227,259,268,272,314,321,325,332,349,365,401,406-407,426
485 atoms, 424 bonds, 68 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [11] + 30
other blocks RMSD: 0.068
> select
> #1/A:11,25,29,37-38,40,47,53,56,138,165,167,169,171,175,178,208,212,214-215,217,249,258,262,304,311,315,322,339,355,391,396-397,416,429
> #2/A:21,35,39,47-48,50,57,63,66,148,175,177,179,181,185,188,218,222,224-225,227,259,268,272,314,321,325,332,349,365,401,406-407,426,439
508 atoms, 447 bonds, 70 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [11] + 31
other blocks RMSD: 0.068
> select
> #1/A:11,25,29,37-38,40,47,53,56,138,165,167,169,171,175,178,208,212,214-215,217,249,258,262,304,311,315,322,339,355,391,396-397,416,429,440
> #2/A:21,35,39,47-48,50,57,63,66,148,175,177,179,181,185,188,218,222,224-225,227,259,268,272,314,321,325,332,349,365,401,406-407,426,439,450
526 atoms, 463 bonds, 72 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [11] + 32
other blocks RMSD: 0.067
> name frozen "Varying residues" sel
registering illegal selector name "Varying residues"
> name frozen "Varying residues" sel
registering illegal selector name "Varying residues"
> select clear
> select Varying residues
Expected an objects specifier or a keyword
> select
> #1/A:11,25,29,37-38,40,47,53,56,138,165,167,169,171,175,178,208,212,214-215,217,249,258,262,304,311,315,322,339,355,391,396-397,416,429,440
> #2/A:21,35,39,47-48,50,57,63,66,148,175,177,179,181,185,188,218,222,224-225,227,259,268,272,314,321,325,332,349,365,401,406-407,426,439,450
526 atoms, 463 bonds, 72 residues, 2 models selected
Seqview [ID: 1] region 3u7q, chain A..AK023_NifD_SM.pdb, chain A [11] + 33
other blocks RMSD: 0.067
> name frozen var_res sel
registering illegal selector name "var_res"
> name frozen var_res sel
registering illegal selector name "var_res"
> help selector
No help found for 'selector'
> help selection
No help found for 'selection'
> help select
> help define selector
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 297, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\help_viewer\cmd.py", line 70, in help
url = cli.command_url(cmd_name)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2986, in command_url
return _get_help_url(cmd.command_name.split())
AttributeError: 'NoneType' object has no attribute 'split'
AttributeError: 'NoneType' object has no attribute 'split'
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2986, in command_url
return _get_help_url(cmd.command_name.split())
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 497.09
OpenGL renderer: NVIDIA GeForce RTX 3060/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Gigabyte Technology Co., Ltd.
Model: B550 UD AC
OS: Microsoft Windows 10 Home (Build 19043)
Memory: 17,063,206,912
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 5700G with Radeon Graphics
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.10.8
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
comtypes: 1.1.10
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.3
ParmEd: 3.2.0
parso: 0.8.3
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pywin32: 228
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
WMI: 1.5.1
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
The command_url function should have raised an error when it didn't find a command for the whole text.