FloatOption: name 'singleStep' is not defined

[daniel.palma.i@…]

The following bug report has been submitted:
Platform:        Linux-5.8.18-1-MANJARO-x86_64-with-arch-Manjaro-Linux
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
Input 0 in a FloatOption with min='positive'

Log:
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> chain 2efv A

<class 'chimerax.atomic.structure.AtomicStructure'>  
2efv title:  
Crystal Structure of a Hypothetical Protein(MJ0366) from Methanocaldococcus
jannaschii [more info...]  
  
Chain information for 2efv #1  
---  
Chain | Description  
A | Hypothetical protein MJ0366  
  
Non-standard residues in 2efv #1  
---  
PO4 — phosphate ion  
  
2efv mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> delete #1&~/A

> hide #1 target acs

> ribbon #1

> rainbow #1

> view #1 clip false

> cofr #1

> matrix #1 A alexander closure rays reduceMethod kmt atomName CA tries 20
> chiral false density 7 calcCutoff 0.4 cuda true runParallel true

  
First residue (45): /A ALA 50  
Last residue (72): /A LEU 77  
type| frequency  
---|---  
0_1| 1.0  
  

> select /A:50-77

227 atoms, 227 bonds, 28 residues, 1 model selected  
  
First residue (40): /A ARG 45  
Last residue (77): /A GLU 82  
type| frequency  
---|---  
0_1| 1.0  
  

> select /A:45-82

310 atoms, 310 bonds, 38 residues, 1 model selected  
  
First residue (41): /A ARG 46  
Last residue (75): /A ASN 80  
type| frequency  
---|---  
0_1| 1.0  
  

> select /A:46-80

284 atoms, 284 bonds, 35 residues, 1 model selected  
  
First residue (41): /A ARG 46  
Last residue (73): /A LEU 78  
type| frequency  
---|---  
0_1| 1.0  
  

> select /A:46-78

268 atoms, 268 bonds, 33 residues, 1 model selected  
  
First residue (8): /A ALA 13  
Last residue (81): /A LEU 86  
type| frequency  
---|---  
0_1| 0.55  
3_1| 0.45  
  

> select /A:13-86

615 atoms, 620 bonds, 74 residues, 1 model selected  
  
First residue (6): /A LYS 11  
Last residue (79): /A VAL 84  
type| frequency  
---|---  
3_1| 0.5  
0_1| 0.5  
  

> select /A:11-84

618 atoms, 623 bonds, 74 residues, 1 model selected  
  
First residue (6): /A LYS 11  
Last residue (76): /A CYS 81  
type| frequency  
---|---  
3_1| 0.55  
0_1| 0.45  
  

> select /A:11-81

594 atoms, 599 bonds, 71 residues, 1 model selected  
  
First residue (6): /A LYS 11  
Last residue (75): /A ASN 80  
type| frequency  
---|---  
3_1| 0.55  
0_1| 0.45  
  

> select /A:11-80

588 atoms, 593 bonds, 70 residues, 1 model selected  
  
First residue (16): /A ILE 21  
Last residue (77): /A GLU 82  
type| frequency  
---|---  
0_1| 1.0  
  

> select /A:21-82

511 atoms, 513 bonds, 62 residues, 1 model selected  
  
First residue (8): /A ALA 13  
Last residue (74): /A LEU 79  
type| frequency  
---|---  
0_1| 0.9  
3_1| 0.1  
  

> select /A:13-79

560 atoms, 565 bonds, 67 residues, 1 model selected  
  
First residue (6): /A LYS 11  
Last residue (78): /A LEU 83  
type| frequency  
---|---  
0_1| 0.65  
3_1| 0.35  
  

> select /A:11-83

611 atoms, 616 bonds, 73 residues, 1 model selected  
  
First residue (6): /A LYS 11  
Last residue (78): /A LEU 83  
type| frequency  
---|---  
0_1| 0.65  
3_1| 0.35  
  

> select /A:11-83

611 atoms, 616 bonds, 73 residues, 1 model selected  
  
First residue (6): /A LYS 11  
Last residue (78): /A LEU 83  
type| frequency  
---|---  
0_1| 0.65  
3_1| 0.35  
  

> select /A:11-83

611 atoms, 616 bonds, 73 residues, 1 model selected  
  
First residue (6): /A LYS 11  
Last residue (78): /A LEU 83  
type| frequency  
---|---  
0_1| 0.65  
3_1| 0.35  
  

> select /A:11-83

611 atoms, 616 bonds, 73 residues, 1 model selected  
  
First residue (6): /A LYS 11  
Last residue (77): /A GLU 82  
type| frequency  
---|---  
3_1| 0.55  
0_1| 0.45  
  

> select /A:11-82

603 atoms, 608 bonds, 72 residues, 1 model selected  
  
First residue (44): /A GLU 49  
Last residue (69): /A SER 74  
type| frequency  
---|---  
0_1| 1.0  
  

> select /A:49-74

215 atoms, 215 bonds, 26 residues, 1 model selected  
  
First residue (47): /A LYS 52  
Last residue (70): /A ALA 75  
type| frequency  
---|---  
0_1| 1.0  
  

> select /A:52-75

197 atoms, 197 bonds, 24 residues, 1 model selected  
  
First residue (47): /A LYS 52  
Last residue (70): /A ALA 75  
type| frequency  
---|---  
0_1| 1.0  
  

> select /A:52-75

197 atoms, 197 bonds, 24 residues, 1 model selected  
  
First residue (47): /A LYS 52  
Last residue (71): /A ASN 76  
type| frequency  
---|---  
0_1| 1.0  
  

> select /A:52-76

205 atoms, 205 bonds, 25 residues, 1 model selected  
  
First residue (47): /A LYS 52  
Last residue (71): /A ASN 76  
type| frequency  
---|---  
0_1| 1.0  
  

> select /A:52-76

205 atoms, 205 bonds, 25 residues, 1 model selected  
  
First residue (34): /A VAL 39  
Last residue (61): /A VAL 66  
type| frequency  
---|---  
0_1| 1.0  
  

> select /A:39-66

233 atoms, 233 bonds, 28 residues, 1 model selected  
  
First residue (34): /A VAL 39  
Last residue (61): /A VAL 66  
type| frequency  
---|---  
0_1| 1.0  
  

> select /A:39-66

233 atoms, 233 bonds, 28 residues, 1 model selected  
  
First residue (34): /A VAL 39  
Last residue (61): /A VAL 66  
type| frequency  
---|---  
0_1| 1.0  
  

> select /A:39-66

233 atoms, 233 bonds, 28 residues, 1 model selected  
  
First residue (37): /A ASP 42  
Last residue (68): /A LYS 73  
type| frequency  
---|---  
0_1| 1.0  
  

> select /A:42-73

267 atoms, 267 bonds, 32 residues, 1 model selected  
  
First residue (25): /A LEU 30  
Last residue (61): /A VAL 66  
type| frequency  
---|---  
0_1| 1.0  
  

> select /A:30-66

309 atoms, 310 bonds, 37 residues, 1 model selected  
  
First residue (25): /A LEU 30  
Last residue (61): /A VAL 66  
type| frequency  
---|---  
0_1| 1.0  
  

> select /A:30-66

309 atoms, 310 bonds, 37 residues, 1 model selected  
  
First residue (51): /A ARG 56  
Last residue (72): /A LEU 77  
type| frequency  
---|---  
0_1| 1.0  
  

> select /A:56-77

174 atoms, 173 bonds, 22 residues, 1 model selected  
  
First residue (6): /A LYS 11  
Last residue (77): /A GLU 82  
type| frequency  
---|---  
3_1| 0.55  
0_1| 0.45  
  

> select /A:11-82

603 atoms, 608 bonds, 72 residues, 1 model selected  
  
First residue (6): /A LYS 11  
Last residue (77): /A GLU 82  
type| frequency  
---|---  
3_1| 0.55  
0_1| 0.45  
  

> select /A:11-82

603 atoms, 608 bonds, 72 residues, 1 model selected  
  
First residue (6): /A LYS 11  
Last residue (77): /A GLU 82  
type| frequency  
---|---  
3_1| 0.55  
0_1| 0.45  
  

> select /A:11-82

603 atoms, 608 bonds, 72 residues, 1 model selected  
  
First residue (6): /A LYS 11  
Last residue (77): /A GLU 82  
type| frequency  
---|---  
3_1| 0.55  
0_1| 0.45  
  

> select /A:11-82

603 atoms, 608 bonds, 72 residues, 1 model selected  
  
First residue (6): /A LYS 11  
Last residue (77): /A GLU 82  
type| frequency  
---|---  
3_1| 0.55  
0_1| 0.45  
  

> select /A:11-82

603 atoms, 608 bonds, 72 residues, 1 model selected  
  
First residue (5): /A LYS 10  
Last residue (77): /A GLU 82  
type| frequency  
---|---  
3_1| 0.7  
0_1| 0.3  
  

> select /A:10-82

612 atoms, 617 bonds, 73 residues, 1 model selected  
  
First residue (5): /A LYS 10  
Last residue (77): /A GLU 82  
type| frequency  
---|---  
3_1| 0.7  
0_1| 0.3  
  

> select /A:10-82

612 atoms, 617 bonds, 73 residues, 1 model selected  
  
First residue (4): /A GLU 9  
Last residue (77): /A GLU 82  
type| frequency  
---|---  
3_1| 0.6  
0_1| 0.4  
  

> select /A:9-82

621 atoms, 626 bonds, 74 residues, 1 model selected  
  
First residue (6): /A LYS 11  
Last residue (76): /A CYS 81  
type| frequency  
---|---  
3_1| 0.55  
0_1| 0.45  
  

> select /A:11-81

594 atoms, 599 bonds, 71 residues, 1 model selected  
  
First residue (7): /A ARG 12  
Last residue (79): /A VAL 84  
type| frequency  
---|---  
0_1| 0.55  
3_1| 0.45  
  

> select /A:12-84

609 atoms, 614 bonds, 73 residues, 1 model selected  
  
First residue (7): /A ARG 12  
Last residue (80): /A LYS 85  
type| frequency  
---|---  
3_1| 0.6  
0_1| 0.4  
  

> select /A:12-85

618 atoms, 623 bonds, 74 residues, 1 model selected  
  
First residue (7): /A ARG 12  
Last residue (80): /A LYS 85  
type| frequency  
---|---  
3_1| 0.6  
0_1| 0.4  
  

> select /A:12-85

618 atoms, 623 bonds, 74 residues, 1 model selected  
  
First residue (6): /A LYS 11  
Last residue (80): /A LYS 85  
type| frequency  
---|---  
3_1| 0.6  
0_1| 0.4  
  

> select /A:11-85

627 atoms, 632 bonds, 75 residues, 1 model selected  
  
First residue (5): /A LYS 10  
Last residue (76): /A CYS 81  
type| frequency  
---|---  
0_1| 0.6  
3_1| 0.4  
  

> select /A:10-81

603 atoms, 608 bonds, 72 residues, 1 model selected  
  
First residue (6): /A LYS 11  
Last residue (77): /A GLU 82  
type| frequency  
---|---  
3_1| 0.55  
0_1| 0.45  
  

> select /A:11-82

603 atoms, 608 bonds, 72 residues, 1 model selected  
  
First residue (6): /A LYS 11  
Last residue (77): /A GLU 82  
type| frequency  
---|---  
3_1| 0.55  
0_1| 0.45  
  

> select /A:11-82

603 atoms, 608 bonds, 72 residues, 1 model selected  
  
First residue (6): /A LYS 11  
Last residue (75): /A ASN 80  
type| frequency  
---|---  
3_1| 0.55  
0_1| 0.45  
  

> select /A:11-80

588 atoms, 593 bonds, 70 residues, 1 model selected  
  
First residue (3): /A LYS 8  
Last residue (75): /A ASN 80  
type| frequency  
---|---  
3_1| 0.55  
0_1| 0.45  
  

> select /A:8-80

615 atoms, 620 bonds, 73 residues, 1 model selected  
  
First residue (7): /A ARG 12  
Last residue (80): /A LYS 85  
type| frequency  
---|---  
3_1| 0.6  
0_1| 0.4  
  

> select /A:12-85

618 atoms, 623 bonds, 74 residues, 1 model selected  
  
First residue (8): /A ALA 13  
Last residue (77): /A GLU 82  
type| frequency  
---|---  
0_1| 0.85  
3_1| 0.15  
  

> select /A:13-82

583 atoms, 588 bonds, 70 residues, 1 model selected  
  
First residue (6): /A LYS 11  
Last residue (77): /A GLU 82  
type| frequency  
---|---  
3_1| 0.55  
0_1| 0.45  
  

> select /A:11-82

603 atoms, 608 bonds, 72 residues, 1 model selected  

> chain 6nd4 N

<class 'chimerax.atomic.structure.AtomicStructure'>  
6nd4 title:  
Conformational switches control early maturation of the eukaryotic small
ribosomal subunit [more info...]  
  
Chain information for 6nd4 #2  
---  
Chain | Description  
0 | 5'ETS rRNA  
1 | 18S rRNA 5' domain start  
2 | U3 snoRNA  
A | Mpp10  
D | Bud21  
H | Utp17  
I | Utp8  
J | Utp15  
K | Utp9  
L | Utp5  
M | Utp10  
N | Utp4  
O | Utp1  
P | Utp6  
Q | Utp12  
R | Utp13  
S | Utp18  
T | Utp21  
U | Sof1  
W | Utp7  
Z | Imp3  
a | Nop56  
b | Nop58  
c d | Nop1.1  
e f | Snu13  
g | Rrp9  
l | Utp24  
x | Unidentified fragment  
  

> delete #2&~/N

> hide #2 target acs

> ribbon #2

> rainbow #2

> view #2 clip false

> cofr #2

> matrix load #2 N /home/danpal/b.mat atomName CA

  
First residue (506): 6nd4 N #2/N GLY 548  
Last residue (659): 6nd4 N #2/N ARG 757  
type| frequency  
---|---  
0_1| 1.0  
  

> select #2/N:548-757

767 atoms, 765 bonds, 1 pseudobond, 154 residues, 2 models selected  
  
First residue (504): 6nd4 N #2/N GLY 546  
Last residue (655): 6nd4 N #2/N ALA 753  
type| frequency  
---|---  
0_1| 1.0  
  

> select #2/N:546-753

756 atoms, 754 bonds, 1 pseudobond, 152 residues, 2 models selected  
  
First residue (502): 6nd4 N #2/N SER 544  
Last residue (653): 6nd4 N #2/N GLU 751  
type| frequency  
---|---  
0_1| 1.0  
  

> select #2/N:544-751

756 atoms, 754 bonds, 1 pseudobond, 152 residues, 2 models selected  
  
First residue (552): 6nd4 N #2/N PHE 594  
Last residue (653): 6nd4 N #2/N GLU 751  
type| frequency  
---|---  
0_1| 1.0  
  

> select #2/N:594-751

508 atoms, 506 bonds, 1 pseudobond, 102 residues, 2 models selected  
  
First residue (254): 6nd4 N #2/N ASP 282  
Last residue (651): 6nd4 N #2/N SER 749  
type| frequency  
---|---  
0_1| 1.0  
  

> select #2/N:282-749

1976 atoms, 1972 bonds, 3 pseudobonds, 398 residues, 2 models selected  
  
First residue (403): 6nd4 N #2/N GLN 438  
Last residue (653): 6nd4 N #2/N GLU 751  
type| frequency  
---|---  
0_1| 1.0  
  

> select #2/N:438-751

1249 atoms, 1246 bonds, 2 pseudobonds, 251 residues, 2 models selected  
  
First residue (399): 6nd4 N #2/N SER 434  
Last residue (653): 6nd4 N #2/N GLU 751  
type| frequency  
---|---  
0_1| 1.0  
  

> select #2/N:434-751

1268 atoms, 1265 bonds, 2 pseudobonds, 255 residues, 2 models selected  
  
First residue (399): 6nd4 N #2/N SER 434  
Last residue (651): 6nd4 N #2/N SER 749  
type| frequency  
---|---  
0_1| 1.0  
  

> select #2/N:434-749

1258 atoms, 1255 bonds, 2 pseudobonds, 253 residues, 2 models selected  
  
First residue (453): 6nd4 N #2/N ILE 488  
Last residue (653): 6nd4 N #2/N GLU 751  
type| frequency  
---|---  
0_1| 1.0  
  

> select #2/N:488-751

1001 atoms, 998 bonds, 2 pseudobonds, 201 residues, 2 models selected  
  
First residue (453): 6nd4 N #2/N ILE 488  
Last residue (653): 6nd4 N #2/N GLU 751  
type| frequency  
---|---  
0_1| 1.0  
  

> select #2/N:488-751

1001 atoms, 998 bonds, 2 pseudobonds, 201 residues, 2 models selected  
  
First residue (454): 6nd4 N #2/N CYS 489  
Last residue (654): 6nd4 N #2/N LEU 752  
type| frequency  
---|---  
0_1| 1.0  
  

> select #2/N:489-752

1001 atoms, 998 bonds, 2 pseudobonds, 201 residues, 2 models selected  
  
First residue (451): 6nd4 N #2/N ILE 486  
Last residue (653): 6nd4 N #2/N GLU 751  
type| frequency  
---|---  
0_1| 1.0  
  

> select #2/N:486-751

1011 atoms, 1008 bonds, 2 pseudobonds, 203 residues, 2 models selected  
  
First residue (451): 6nd4 N #2/N ILE 486  
Last residue (651): 6nd4 N #2/N SER 749  
type| frequency  
---|---  
-3_1| 0.8400000000000001  
-5_1| 0.030000000000000027  
  

> select #2/N:486-749

1001 atoms, 998 bonds, 2 pseudobonds, 201 residues, 2 models selected  
  
First residue (567): 6nd4 N #2/N LYS 616  
Last residue (626): 6nd4 N #2/N UNK 683  
type| frequency  
---|---  
0_1| 1.0  
  

> select #2/N:616-683

298 atoms, 297 bonds, 60 residues, 1 model selected  
  
First residue (399): 6nd4 N #2/N SER 434  
Last residue (611): 6nd4 N #2/N ASP 660  
type| frequency  
---|---  
0_1| 1.0  
  

> select #2/N:434-660

1058 atoms, 1055 bonds, 2 pseudobonds, 213 residues, 2 models selected  
  
First residue (403): 6nd4 N #2/N GLN 438  
Last residue (651): 6nd4 N #2/N SER 749  
type| frequency  
---|---  
0_1| 1.0  
  

> select #2/N:438-749

1239 atoms, 1236 bonds, 2 pseudobonds, 249 residues, 2 models selected  
  
First residue (403): 6nd4 N #2/N GLN 438  
Last residue (651): 6nd4 N #2/N SER 749  
type| frequency  
---|---  
0_1| 1.0  
  

> select #2/N:438-749

1239 atoms, 1236 bonds, 2 pseudobonds, 249 residues, 2 models selected  
  
First residue (401): 6nd4 N #2/N ASP 436  
Last residue (651): 6nd4 N #2/N SER 749  
type| frequency  
---|---  
-3_1| 0.9  
-5_1| 0.030000000000000027  
  

> select #2/N:436-749

1248 atoms, 1245 bonds, 2 pseudobonds, 251 residues, 2 models selected  
  
First residue (451): 6nd4 N #2/N ILE 486  
Last residue (651): 6nd4 N #2/N SER 749  
type| frequency  
---|---  
-3_1| 0.8400000000000001  
-5_1| 0.030000000000000027  
  

> select #2/N:486-749

1001 atoms, 998 bonds, 2 pseudobonds, 201 residues, 2 models selected  
  
First residue (552): 6nd4 N #2/N PHE 594  
Last residue (653): 6nd4 N #2/N GLU 751  
type| frequency  
---|---  
0_1| 1.0  
  

> select #2/N:594-751

508 atoms, 506 bonds, 1 pseudobond, 102 residues, 2 models selected  

> matrix load #2 N /home/danpal/knotmap_6nd4_N.txt atomName CA

Traceback (most recent call last):  
File "/home/danpal/chimerax_start/xtest/topogui.py", line 276, in load_matrix  
run(self.session, command)  
File "/home/danpal/lib/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/home/danpal/lib/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "/home/danpal/chimerax_start/xtest/topo.py", line 308, in load_matrix  
matrix = read_matrix(path)  
File "/home/danpal/chimerax_start/xtest/topo.py", line 293, in read_matrix  
return topoly.translate_matrix(path, topoly.OutputFormat.Dictionary)  
File "/home/danpal/.local/share/ChimeraX/1.1/site-
packages/topoly/__init__.py", line 1463, in translate_matrix  
return data2dictionary(data, knot=knot, beg=beg)  
File "/home/danpal/.local/share/ChimeraX/1.1/site-
packages/topoly/manipulation.py", line 118, in data2dictionary  
return strdict2dictionary(data)  
File "/home/danpal/.local/share/ChimeraX/1.1/site-
packages/topoly/manipulation.py", line 92, in strdict2dictionary  
ident, knot_data = line.strip().split()  
ValueError: too many values to unpack (expected 2)  
  
ValueError: too many values to unpack (expected 2)  
  
File "/home/danpal/.local/share/ChimeraX/1.1/site-
packages/topoly/manipulation.py", line 92, in strdict2dictionary  
ident, knot_data = line.strip().split()  
  
See log for complete Python traceback.  
  

> matrix load #2 N /home/danpal/knotmap_6nd4_N.txt atomName CA

the length of the matrix is (748) different than the number of selected atoms
(678)  

> ui tool show "Show Sequence Viewer"

> sequence chain #2/N

Alignment identifier is 2/N  

> matrix load #1 A /home/danpal/2efv.mat atomName CA

> matrix save #1 A /home/danpal/r.mat

> chain 2efv A

<class 'chimerax.atomic.structure.AtomicStructure'>  
2efv title:  
Crystal Structure of a Hypothetical Protein(MJ0366) from Methanocaldococcus
jannaschii [more info...]  
  
Chain information for 2efv #3  
---  
Chain | Description  
A | Hypothetical protein MJ0366  
  
Non-standard residues in 2efv #3  
---  
PO4 — phosphate ion  
  
2efv mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> delete #3&~/A

> hide #3 target acs

> ribbon #3

> rainbow #3

> view #3 clip false

> cofr #3

Traceback (most recent call last):  
File "/home/danpal/lib/chimerax-1.1/lib/python3.7/site-
packages/chimerax/ui/options/containers.py", line 287, in _save  
setattr(opt.settings, opt.attr_name, opt.value)  
AttributeError: 'NoneType' object has no attribute 'rc_new_model_name'  
  
AttributeError: 'NoneType' object has no attribute 'rc_new_model_name'  
  
File "/home/danpal/lib/chimerax-1.1/lib/python3.7/site-
packages/chimerax/ui/options/containers.py", line 287, in _save  
setattr(opt.settings, opt.attr_name, opt.value)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/danpal/lib/chimerax-1.1/lib/python3.7/site-
packages/chimerax/ui/options/containers.py", line 287, in _save  
setattr(opt.settings, opt.attr_name, opt.value)  
AttributeError: 'NoneType' object has no attribute 'rc_new_model_name'  
  
AttributeError: 'NoneType' object has no attribute 'rc_new_model_name'  
  
File "/home/danpal/lib/chimerax-1.1/lib/python3.7/site-
packages/chimerax/ui/options/containers.py", line 287, in _save  
setattr(opt.settings, opt.attr_name, opt.value)  
  
See log for complete Python traceback.  
  
Illegal TopolyStructureTool 'rc_parent' attribute value
(<chimerax.atomic.structure.AtomicStructure object at 0x7f888b4f8210>),
leaving attribute unchanged  
Traceback (most recent call last):  
File "/home/danpal/lib/chimerax-1.1/lib/python3.7/site-
packages/chimerax/ui/options/containers.py", line 292, in _save  
settings.save(settings=save_settings)  
File "/home/danpal/lib/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/settings.py", line 218, in save  
ConfigFile.__setattr__(self, name, self._cur_settings[name], call_save=False)  
File "/home/danpal/lib/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 359, in __setattr__  
self._session, value)  
File "/home/danpal/lib/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 490, in convert_to_string  
new_value = self.convert_from_string(session, str_value)  
File "/home/danpal/lib/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 481, in convert_from_string  
return self.from_str(str_value)  
File "/home/danpal/lib/chimerax-1.1/lib/python3.7/ast.py", line 46, in
literal_eval  
node_or_string = parse(node_or_string, mode='eval')  
File "/home/danpal/lib/chimerax-1.1/lib/python3.7/ast.py", line 35, in parse  
return compile(source, filename, mode, PyCF_ONLY_AST)  
File "<unknown>", line 1  
<chimerax.atomic.structure.AtomicStructure object at 0x7f888b4f8210>  
^  
SyntaxError: invalid syntax  
  
File "", line 1  
  
^  
SyntaxError: invalid syntax  
  
File "/home/danpal/lib/chimerax-1.1/lib/python3.7/ast.py", line 35, in parse  
return compile(source, filename, mode, PyCF_ONLY_AST)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/danpal/lib/chimerax-1.1/lib/python3.7/site-
packages/chimerax/ui/options/containers.py", line 292, in _save  
settings.save(settings=save_settings)  
File "/home/danpal/lib/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/settings.py", line 218, in save  
ConfigFile.__setattr__(self, name, self._cur_settings[name], call_save=False)  
File "/home/danpal/lib/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 359, in __setattr__  
self._session, value)  
File "/home/danpal/lib/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 490, in convert_to_string  
new_value = self.convert_from_string(session, str_value)  
File "/home/danpal/lib/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 481, in convert_from_string  
return self.from_str(str_value)  
File "/home/danpal/lib/chimerax-1.1/lib/python3.7/ast.py", line 46, in
literal_eval  
node_or_string = parse(node_or_string, mode='eval')  
File "/home/danpal/lib/chimerax-1.1/lib/python3.7/ast.py", line 35, in parse  
return compile(source, filename, mode, PyCF_ONLY_AST)  
File "<unknown>", line 1  
#1  
^  
SyntaxError: unexpected EOF while parsing  
  
File "", line 1  
#1  
^  
SyntaxError: unexpected EOF while parsing  
  
File "/home/danpal/lib/chimerax-1.1/lib/python3.7/ast.py", line 35, in parse  
return compile(source, filename, mode, PyCF_ONLY_AST)  
  
See log for complete Python traceback.  
  
Illegal TopolyStructureTool 'rc_parent' attribute value
(<chimerax.atomic.structure.AtomicStructure object at 0x7f888b4f8210>),
leaving attribute unchanged  
Illegal TopolyStructureTool 'rc_parent' attribute value
(<chimerax.atomic.structure.AtomicStructure object at 0x7f888b4f8210>),
leaving attribute unchanged  
Illegal TopolyStructureTool 'rc_parent' attribute value
(<chimerax.atomic.structure.AtomicStructure object at 0x7f888b4f8210>),
leaving attribute unchanged  

> usage closure

closure model chainId [method]  
— Closes the structure using the specified method  
chainId: a text string  
method: one of closed, direction, mass_center, one_point, rays, or two_points  

> usage reduce

reduce model chainId [newModelName a text string] [parent a model specifier]
[inheritColors true or false] [renumber true or false]  
— Reduces the structure using the KMT algorithm  
chainId: a text string  

> usage generate

generate chainType lengths [bondLength bondLength] [close true or false]
[newModelName a text string] [parent a model specifier]  
— Randomly generates the specified polygon  
chainType: one of loop or walk  
lengths: some an integer ≥ 1  
bondLength: a number > 0  
No model or chain selected  
No model or chain selected  

> generate walk 10 bondLength 3.8 close false

> generate loop 10 bondLength 3.8 close false

Traceback (most recent call last):  
File "/home/danpal/lib/chimerax-1.1/lib/python3.7/site-
packages/chimerax/ui/options/options.py", line 389, in <lambda>  
self._float_widget.valueChanged.connect(lambda val, s=self: s.make_callback())  
File "/home/danpal/lib/chimerax-1.1/lib/python3.7/site-
packages/chimerax/ui/options/options.py", line 168, in make_callback  
self.set_attribute()  
File "/home/danpal/lib/chimerax-1.1/lib/python3.7/site-
packages/chimerax/ui/options/options.py", line 141, in set_attribute  
setattr(self.settings, self.attr_name, self.value)  
File "/home/danpal/lib/chimerax-1.1/lib/python3.7/site-
packages/chimerax/ui/options/options.py", line 371, in get_value  
val = self._float_widget.value()  
File "/home/danpal/lib/chimerax-1.1/lib/python3.7/site-
packages/chimerax/ui/options/options.py", line 886, in value  
step = singleStep()  
NameError: name 'singleStep' is not defined  
  
NameError: name 'singleStep' is not defined  
  
File "/home/danpal/lib/chimerax-1.1/lib/python3.7/site-
packages/chimerax/ui/options/options.py", line 886, in value  
step = singleStep()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/danpal/lib/chimerax-1.1/lib/python3.7/site-
packages/chimerax/ui/options/options.py", line 389, in <lambda>  
self._float_widget.valueChanged.connect(lambda val, s=self: s.make_callback())  
File "/home/danpal/lib/chimerax-1.1/lib/python3.7/site-
packages/chimerax/ui/options/options.py", line 168, in make_callback  
self.set_attribute()  
File "/home/danpal/lib/chimerax-1.1/lib/python3.7/site-
packages/chimerax/ui/options/options.py", line 141, in set_attribute  
setattr(self.settings, self.attr_name, self.value)  
File "/home/danpal/lib/chimerax-1.1/lib/python3.7/site-
packages/chimerax/ui/options/options.py", line 371, in get_value  
val = self._float_widget.value()  
File "/home/danpal/lib/chimerax-1.1/lib/python3.7/site-
packages/chimerax/ui/options/options.py", line 886, in value  
step = singleStep()  
NameError: name 'singleStep' is not defined  
  
NameError: name 'singleStep' is not defined  
  
File "/home/danpal/lib/chimerax-1.1/lib/python3.7/site-
packages/chimerax/ui/options/options.py", line 886, in value  
step = singleStep()  
  
See log for complete Python traceback.  
  




OpenGL version: 4.6 (Core Profile) Mesa 20.2.2
OpenGL renderer: AMD Radeon(TM) Vega 8 Graphics (RAVEN, DRM 3.38.0, 5.8.18-1-MANJARO, LLVM 11.0.0)
OpenGL vendor: X.Org
Manufacturer: Acer
Model: Aspire A315-41
OS: Manjaro Linux 20.2 Nibia
Architecture: 64bit ELF
CPU: 8 AMD Ryzen 5 2500U with Radeon Vega Mobile Gfx
Cache Size: 512 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           10Gi       5.2Gi       193Mi       192Mi       5.3Gi       4.9Gi
	Swap:          22Gi        49Mi        22Gi

Graphics:
	03:00.0 VGA compatible controller [0300]: Advanced Micro Devices, Inc. [AMD/ATI] Raven Ridge [Radeon Vega Series / Radeon Vega Mobile Series] [1002:15dd] (rev c4)	
	Subsystem: Acer Incorporated [ALI] Device [1025:1259]	
	Kernel driver in use: amdgpu
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    argparse: 1.4.0
    Babel: 2.8.0
    backcall: 0.2.0
    biopython: 1.78
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    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: 1.0
    ChimeraX-Hbonds: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 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-XKnot: 0.1
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    topoly: 0.9.8
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

[Eric Pettersen]

Hi Daniel,

Thanks for reporting this bug. I will investigate as soon as I can.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab