![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 years ago
Closed 6 years ago
#2523 closed enhancement (fixed)
Better session debugging info
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-10-10)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 0.91 (2019-10-10)
© 2016-2019 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/huihui/Desktop/Crystal structure/alignment_Fn_crRNA_DNA
complex.cxs" format session
opened ChimeraX session
> select clear
> select #1/C
786 atoms, 876 bonds, 1 model selected
> select clear
> select #1/A:662-679
136 atoms, 139 bonds, 1 model selected
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> display -sel
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show ~sel
> show sel atoms
> hide sel atoms
> hide sel atoms
> select #1/A:662-679
136 atoms, 139 bonds, 1 model selected
> show sel cartoons
> hide sel cartoons
> hide sel atoms
> show sel atoms
> hide sel atoms
> hide sel cartoons
> hide sel surfaces
> style sel stick
Changed 136 atom styles
> select #1/A
10607 atoms, 10803 bonds, 9 pseudobonds, 3 models selected
> hide sel atoms
> hide sel cartoons
> style sel sphere
Changed 10607 atom styles
> select #3/C
589 atoms, 661 bonds, 1 model selected
> hide sel atoms
> hide sel cartoons
> close session
> open "/Users/huihui/Desktop/Crystal structure/alignment_Fn_crRNA_DNA
complex.cxs" format session
opened ChimeraX session
> select clear
> color sel byhetero
> select sequence #1/A:662-679
Nothing selected
> select sequence "#1/A: 662-679"
Nothing selected
> select #1/A
10607 atoms, 10803 bonds, 9 pseudobonds, 3 models selected
> show sel cartoons
> select #1/A:1-661
5448 atoms, 5539 bonds, 1 model selected
> hide sel cartoons
> select #1/A:680-1300
4994 atoms, 5108 bonds, 3 pseudobonds, 2 models selected
> hide sel cartoons
> toolshed show "Basic Actions"
> color #1/A #1f508c target c
> color #1/A #f57520 target c
> color #1/A #fd8208 target c
> color #1/A #084fd1 target c
> color #1/A #a5cdff target c
> color #1/A #fc0c44 target c
> color #1/A #cc99cc target c
> select #1/A:667 #2/A:603
18 atoms, 16 bonds, 2 models selected
> select #1/A:667 #2/A:603
18 atoms, 16 bonds, 2 models selected
> select #1/A:667 #2/A:603
18 atoms, 16 bonds, 2 models selected
> select #1/A:667 #2/A:603
18 atoms, 16 bonds, 2 models selected
> select #1/A:667 #2/A:603
18 atoms, 16 bonds, 2 models selected
> select #1/A:667 #2/A:603
18 atoms, 16 bonds, 2 models selected
> style sel stick
Changed 9 atom styles
> style sel stick
Changed 9 atom styles
> show sel atoms
> hide sel atoms
> show sel cartoons
> show sel surfaces
> show sel atoms
> show sel surfaces
> hide sel surfaces
> style sel stick
Changed 9 atom styles
> show sel atoms
> color #1/A #ff9999 target c
> show sel atoms
> interfaces sel & ~solvent
0 buried areas:
> show #1/B target c
> save session "/Users/huihui/Desktop/Crystal structure/alignment_Fn_crRNA_DNA
complex_LKL.cxs"
> close session
> open "/Users/huihui/Desktop/Crystal structure/alignment_As_crRNA_DNA
complex.cxs" format session
opened ChimeraX session
> close session
> open "/Users/huihui/Desktop/Crystal structure/alignment_Fn_crRNA_DNA
complex_LKL.cxs" format session
opened ChimeraX session
> select sel :< 5
10811 atoms, 278 bonds, 3 models selected
> select clear
> select sel :< 5
10811 atoms, 278 bonds, 3 models selected
> select clear
> select sel @< 5
10654 atoms, 85 bonds, 3 models selected
> select clear
> select sel :< 3
10662 atoms, 107 bonds, 3 models selected
> select clear
> select sel @< 3
Nothing selected
> select clear
> select sel @< 3
10596 atoms, 28 bonds, 3 models selected
> style sel ball
Changed 10596 atom styles
> hide sel cartoons
> style sel stick
Changed 10596 atom styles
> close session
> open "/Users/huihui/Desktop/Crystal structure/alignment_Fn_crRNA_DNA
complex_LKL.cxs" format session
opened ChimeraX session
Unknown command: contects sel test others reveal true log true select true
> contacts sel test others reveal true log true select true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
101 contacts
atom1 atom2 overlap distance
6i1k #1/A LYS 677 CG 5xus #3/A LYS 601 CB 3.033 0.727
6i1k #1/A LYS 677 CE 5xus #3/A LYS 601 CD 2.857 0.903
6i1k #1/A LYS 677 C 5xus #3/A LYS 601 CA 2.551 0.939
6i1k #1/A LYS 677 CA 5xus #3/A LYS 601 N 2.333 1.187
6i1k #1/A LYS 677 N 5xus #3/A LYS 600 C 2.293 0.957
6i1k #1/A LYS 677 CA 5xus #3/A LYS 601 CA 2.177 1.583
6i1k #1/A LYS 677 N 5xus #3/A LYS 600 CA 2.142 1.378
6i1k #1/A LYS 677 CG 5xus #3/A LYS 601 CG 2.092 1.668
6i1k #1/A LYS 677 N 5xus #3/A LYS 601 N 1.965 1.315
6i1k #1/A LYS 677 CA 5xus #3/A LYS 600 C 1.915 1.575
6i1k #1/A LYS 677 CG 5xus #3/A LYS 601 CA 1.906 1.854
6i1k #1/A LYS 677 CB 5xus #3/A LYS 601 CB 1.837 1.923
6i1k #1/A LYS 677 CB 5xus #3/A LYS 601 CA 1.823 1.937
6i1k #1/A LYS 677 C 5xus #3/A LYS 601 C 1.821 1.399
6i1k #1/A LYS 677 CE 5xus #3/A LYS 601 CE 1.812 1.948
6i1k #1/A LYS 677 CE 5xus #3/A LYS 601 CG 1.754 2.006
6i1k #1/A LYS 677 CD 5xus #3/A LYS 601 CD 1.711 2.049
6i1k #1/A LYS 677 CD 5xus #3/A LYS 601 CB 1.699 2.061
6i1k #1/A LYS 677 C 5xus #3/A LYS 601 N 1.673 1.577
6i1k #1/A LYS 677 N 5xus #3/A LYS 600 CB 1.647 1.873
6i1k #1/A LYS 677 O 5xus #3/A LYS 601 CA 1.610 1.690
6i1k #1/A LYS 677 CD 5xus #3/A LYS 601 CG 1.586 2.174
6i1k #1/A LYS 677 CB 5xus #3/A LYS 601 N 1.575 1.945
6i1k #1/A LYS 677 O 5xus #3/A LYS 601 O 1.398 1.442
6i1k #1/A LYS 677 O 5xus #3/A LYS 601 C 1.368 1.662
6i1k #1/A LYS 677 NZ 5xus #3/A LYS 601 CD 1.299 2.221
6i1k #1/A LYS 677 CG 5xus #3/A LYS 601 CD 1.250 2.510
6i1k #1/A LYS 677 C 5xus #3/A LYS 600 C 1.242 1.978
6i1k #1/A LYS 677 CA 5xus #3/A LYS 600 O 1.208 2.092
6i1k #1/A LYS 677 CA 5xus #3/A LYS 601 CB 1.117 2.643
6i1k #1/A LYS 677 C 5xus #3/A LYS 600 O 1.099 1.931
6i1k #1/A LYS 677 N 5xus #3/A LYS 600 N 1.066 2.214
6i1k #1/A LYS 677 NZ 5xus #3/A LYS 601 CE 1.062 2.458
6i1k #1/A LYS 677 C 5xus #3/A LYS 601 CB 1.033 2.457
6i1k #1/A LYS 677 CE 5xus #3/A LYS 601 CB 1.028 2.732
6i1k #1/A LYS 677 C 5xus #3/A LYS 601 O 1.020 2.010
6i1k #1/A LYS 677 CB 5xus #3/C DG 5 OP2 1.009 2.291
6i1k #1/A LYS 677 CA 5xus #3/A LYS 600 CA 0.994 2.766
6i1k #1/A LYS 677 CE 5b43 #2/A ASN 630 ND2 0.952 2.568
6i1k #1/A LYS 677 N 5xus #3/A LYS 601 CA 0.891 2.629
6i1k #1/A LYS 677 CG 5xus #3/A LYS 601 N 0.883 2.637
6i1k #1/A LYS 677 CE 5xus #3/A LYS 601 NZ 0.826 2.694
6i1k #1/A LYS 677 C 5xus #3/A TRP 602 N 0.801 2.449
6i1k #1/A LYS 677 NZ 5xus #3/A LYS 601 NZ 0.726 2.554
6i1k #1/A LYS 677 CA 5xus #3/A LYS 600 CB 0.709 3.051
6i1k #1/A LYS 677 CA 5xus #3/A LYS 601 C 0.655 2.835
6i1k #1/A LYS 677 CB 5xus #3/A LYS 601 CG 0.647 3.113
6i1k #1/A LYS 677 N 5xus #3/A LYS 600 O 0.574 2.086
6i1k #1/A LYS 677 CB 5xus #3/A LYS 600 C 0.570 2.920
6i1k #1/A LYS 677 O 5xus #3/A LYS 601 CB 0.436 2.864
6i1k #1/A LYS 677 CG 5xus #3/A LYS 601 C 0.408 3.082
6i1k #1/A LYS 677 CD 5xus #3/A LYS 601 CE 0.382 3.378
6i1k #1/A LYS 677 CD 5xus #3/A LYS 601 CA 0.379 3.381
6i1k #1/A LYS 677 CG 5xus #3/C DG 5 OP2 0.241 3.059
6i1k #1/A LYS 677 CB 5xus #3/C DG 5 P 0.223 3.757
6i1k #1/A LYS 677 O 5xus #3/A LYS 600 O 0.199 2.641
6i1k #1/A LYS 677 N 5xus #3/A SER 599 C 0.196 3.054
6i1k #1/A LYS 677 CD 5b43 #2/A ASN 630 ND2 0.185 3.335
6i1k #1/A LYS 677 NZ 5b43 #2/A ASN 630 ND2 0.171 3.109
6i1k #1/A LYS 677 CB 6i1k #1/C DG 4 OP2 0.168 3.132
6i1k #1/A LYS 677 N 5xus #3/A LYS 600 CG 0.158 3.362
6i1k #1/A LYS 677 C 5xus #3/A LYS 601 CG 0.146 3.344
6i1k #1/A LYS 677 O 5xus #3/A LYS 601 CG 0.111 3.189
6i1k #1/A LYS 677 CA 5xus #3/C DG 5 OP2 0.086 3.214
6i1k #1/A LYS 677 NZ 5xus #3/A LYS 601 CG 0.074 3.446
6i1k #1/A LYS 677 CB 5xus #3/A LYS 601 C 0.027 3.463
6i1k #1/A LYS 677 O 5xus #3/A ALA 604 CB 0.013 3.287
6i1k #1/A LYS 677 C 5xus #3/A LYS 600 CA 0.001 3.489
6i1k #1/A LYS 677 CB 5xus #3/A LYS 600 CB -0.023 3.783
6i1k #1/A LYS 677 CE 5b43 #2/A ASN 630 CB -0.039 3.799
6i1k #1/A LYS 677 N 5b43 #2/A ALA 614 CB -0.045 3.565
6i1k #1/A LYS 677 O 5xus #3/A LYS 600 C -0.045 3.075
6i1k #1/A LYS 677 CD 5xus #3/C DG 5 OP2 -0.050 3.350
6i1k #1/A LYS 677 CB 5xus #3/A LYS 600 CA -0.054 3.814
6i1k #1/A LYS 677 CA 5xus #3/A LYS 600 N -0.057 3.577
6i1k #1/A LYS 677 CA 5xus #3/A LYS 601 CG -0.068 3.828
6i1k #1/A LYS 677 CG 6i1k #1/A SER 678 OG -0.079 3.419
6i1k #1/A LYS 677 N 5xus #3/A LYS 601 CB -0.080 3.600
6i1k #1/A LYS 677 CG 5b43 #2/A ASN 630 CB -0.098 3.858
6i1k #1/A LYS 677 CE 5b43 #2/A ASN 630 CG -0.107 3.597
6i1k #1/A LYS 677 O 5xus #3/A LYS 601 N -0.111 2.771
6i1k #1/A LYS 677 CG 5xus #3/A LYS 601 CE -0.134 3.894
6i1k #1/A LYS 677 CG 5b43 #2/A ASN 630 ND2 -0.144 3.664
6i1k #1/A LYS 677 CA 5xus #3/A TRP 602 N -0.148 3.668
6i1k #1/A LYS 677 N 5xus #3/C DG 5 P -0.178 3.918
6i1k #1/A LYS 677 CA 5xus #3/A LYS 601 O -0.205 3.505
6i1k #1/A LYS 677 CE 5b43 #2/A ASN 631 ND2 -0.211 3.731
6i1k #1/A LYS 677 N 6i1k #1/C DG 4 OP2 -0.217 2.877
6i1k #1/A LYS 677 C 5xus #3/A TRP 602 CA -0.217 3.707
6i1k #1/A LYS 677 O 5b43 #2/A ASN 630 CB -0.227 3.527
6i1k #1/A LYS 677 CD 5xus #3/C DA 4 C2' -0.233 3.993
6i1k #1/A LYS 677 CD 5xus #3/C DA 4 C3' -0.236 3.996
6i1k #1/A LYS 677 CB 5xus #3/A LYS 601 CD -0.240 4.000
6i1k #1/A LYS 677 CG 5xus #3/A TRP 602 N -0.274 3.794
6i1k #1/A LYS 677 CA 6i1k #1/C DG 4 OP2 -0.293 3.593
6i1k #1/A LYS 677 CB 5xus #3/A LYS 600 O -0.315 3.615
6i1k #1/A LYS 677 O 5xus #3/A TRP 602 N -0.328 2.988
6i1k #1/A LYS 677 N 5xus #3/A LYS 601 C -0.351 3.601
6i1k #1/A LYS 677 N 5xus #3/C DG 5 OP2 -0.356 3.016
6i1k #1/A LYS 677 CG 5xus #3/A LYS 600 C -0.368 3.858
6i1k #1/A LYS 677 CG 6i1k #1/A SER 678 CB -0.371 4.131
101 contacts
> select #1/A:13 #2/A:13
15 atoms, 13 bonds, 2 models selected
> contacts sel test others reveal true log true select true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
222 contacts
atom1 atom2 overlap distance
6i1k #1/A LYS 667 CB 5xus #3/A LYS 591 CB 3.271 0.489
6i1k #1/A LYS 667 CG 5xus #3/A LYS 591 CG 3.181 0.579
6i1k #1/A LYS 667 CA 5xus #3/A LYS 591 CA 3.124 0.636
6i1k #1/A LYS 667 CG 5xus #3/A LYS 591 CD 2.667 1.093
6i1k #1/A LYS 667 CD 5xus #3/A LYS 591 CD 2.605 1.155
6i1k #1/A LYS 667 N 5xus #3/A LYS 591 N 2.602 0.678
6i1k #1/A LYS 667 N 5b43 #2/A LYS 603 CA 2.571 0.949
6i1k #1/A LYS 667 CA 5b43 #2/A LYS 603 CA 2.551 1.209
6i1k #1/A LYS 667 CB 5b43 #2/A LYS 603 CB 2.536 1.224
6i1k #1/A LYS 667 CE 5b43 #2/A LYS 603 CD 2.527 1.233
6i1k #1/A LYS 667 C 5xus #3/A LYS 591 C 2.523 0.697
6i1k #1/A LYS 667 C 5b43 #2/A LYS 603 O 2.501 0.529
6i1k #1/A LYS 667 N 5xus #3/A LYS 591 CA 2.437 1.083
6i1k #1/A LYS 667 C 5xus #3/A LYS 591 O 2.262 0.768
6i1k #1/A LYS 667 CG 5xus #3/A LYS 591 CB 2.197 1.563
6i1k #1/A LYS 667 CA 5xus #3/A LYS 591 CB 2.145 1.615
6i1k #1/A LYS 667 CB 5xus #3/A LYS 591 CA 2.128 1.632
6i1k #1/A LYS 667 CB 5xus #3/A LYS 591 CG 2.120 1.640
6i1k #1/A LYS 667 O 5xus #3/A LYS 591 O 2.104 0.736
6i1k #1/A LYS 667 C 5b43 #2/A LYS 603 C 2.101 1.119
6i1k #1/A LYS 667 N 5b43 #2/A LYS 603 N 2.009 1.271
6i1k #1/A LYS 667 CD 5xus #3/A LYS 591 CG 1.974 1.786
6i1k #1/A LYS 667 CB 5b43 #2/A LYS 603 CA 1.954 1.806
6i1k #1/A LYS 667 CG 5b43 #2/A LYS 603 CB 1.951 1.809
6i1k #1/A LYS 667 N 5xus #3/A ASN 590 C 1.873 1.377
6i1k #1/A LYS 667 C 5xus #3/A LYS 591 CA 1.864 1.626
6i1k #1/A LYS 667 CA 5xus #3/A LYS 591 C 1.804 1.686
6i1k #1/A LYS 667 CA 5b43 #2/A LYS 603 C 1.763 1.727
6i1k #1/A LYS 667 NZ 5b43 #2/A LYS 603 CD 1.718 1.802
6i1k #1/A LYS 667 CA 5b43 #2/A LYS 603 CB 1.680 2.080
6i1k #1/A LYS 667 O 5b43 #2/A LYS 603 O 1.678 1.162
6i1k #1/A LYS 667 CE 5b43 #2/A LYS 603 CG 1.639 2.121
6i1k #1/A LYS 667 CA 5xus #3/A LYS 591 N 1.539 1.981
6i1k #1/A LYS 667 N 5b43 #2/A ALA 602 C 1.533 1.717
6i1k #1/A LYS 667 CG 5xus #3/A LYS 591 CE 1.490 2.270
6i1k #1/A LYS 667 CA 5b43 #2/A LYS 603 O 1.434 1.866
6i1k #1/A LYS 667 C 5b43 #2/A LYS 603 CA 1.425 2.065
6i1k #1/A LYS 667 CE 5b43 #2/A LYS 603 CB 1.390 2.370
6i1k #1/A LYS 667 CB 5xus #3/A LYS 591 CD 1.341 2.419
6i1k #1/A LYS 667 CB 5b43 #2/D DA -1 C2' 1.332 2.428
6i1k #1/A LYS 667 N 5b43 #2/A LYS 603 CB 1.287 2.233
6i1k #1/A LYS 667 CE 5xus #3/A LYS 591 CG 1.281 2.479
6i1k #1/A LYS 667 CD 5xus #3/A LYS 591 CB 1.276 2.484
6i1k #1/A LYS 667 N 5xus #3/A LYS 591 CB 1.275 2.245
6i1k #1/A LYS 667 CB 5b43 #2/A LYS 603 CG 1.272 2.488
6i1k #1/A LYS 667 C 5xus #3/A MET 592 N 1.271 1.979
6i1k #1/A LYS 667 CA 5xus #3/A LYS 591 CG 1.262 2.498
6i1k #1/A LYS 667 CD 5b43 #2/A LYS 603 CB 1.253 2.507
6i1k #1/A LYS 667 CD 5xus #3/A LYS 591 CE 1.202 2.558
6i1k #1/A LYS 667 CG 5b43 #2/D DA -1 C2' 1.197 2.563
6i1k #1/A LYS 667 CD 5b43 #2/A LYS 603 CD 1.180 2.580
6i1k #1/A LYS 667 NZ 5b43 #2/A LYS 603 CE 1.172 2.348
6i1k #1/A LYS 667 O 5xus #3/A LYS 591 C 1.167 1.863
6i1k #1/A LYS 667 CE 5b43 #2/A LYS 603 CE 1.151 2.609
6i1k #1/A LYS 667 CE 5xus #3/A LYS 591 CD 1.148 2.612
6i1k #1/A LYS 667 CB 5b43 #2/A LYS 603 C 1.144 2.346
6i1k #1/A LYS 667 CB 5b43 #2/D DA -1 C1' 1.124 2.636
6i1k #1/A LYS 667 NZ 5b43 #2/A LYS 603 NZ 1.120 2.160
6i1k #1/A LYS 667 CA 5xus #3/A LYS 591 O 1.094 2.206
6i1k #1/A LYS 667 CA 5b43 #2/D DA -1 C2' 1.071 2.689
6i1k #1/A LYS 667 N 5b43 #2/A LYS 603 C 1.057 2.193
6i1k #1/A LYS 667 CG 5xus #3/A LYS 591 CA 1.051 2.709
6i1k #1/A LYS 667 CE 5xus #3/A LYS 591 CB 1.047 2.713
6i1k #1/A LYS 667 CB 5xus #3/A LYS 591 C 1.007 2.483
6i1k #1/A LYS 667 CA 5b43 #2/A LYS 603 N 0.996 2.524
6i1k #1/A LYS 667 CG 5b43 #2/A LYS 603 CA 0.986 2.774
6i1k #1/A LYS 667 C 5b43 #2/A MET 604 N 0.982 2.268
6i1k #1/A LYS 667 N 5xus #3/A LYS 591 C 0.925 2.325
6i1k #1/A LYS 667 C 5xus #3/A LYS 591 CB 0.875 2.615
6i1k #1/A LYS 667 N 5b43 #2/A ALA 602 O 0.819 1.841
6i1k #1/A LYS 667 CB 5b43 #2/A LYS 603 O 0.772 2.528
6i1k #1/A LYS 667 N 5xus #3/A LYS 591 CG 0.770 2.750
6i1k #1/A LYS 667 CB 5xus #3/A LYS 591 N 0.762 2.758
6i1k #1/A LYS 667 N 5xus #3/A ASN 590 O 0.754 1.906
6i1k #1/A LYS 667 CA 5xus #3/A ASN 590 C 0.746 2.744
6i1k #1/A LYS 667 N 5xus #3/A ASN 590 CA 0.742 2.778
6i1k #1/A LYS 667 O 5b43 #2/A LYS 603 C 0.725 2.305
6i1k #1/A LYS 667 CG 5b43 #2/A LYS 603 CG 0.701 3.059
6i1k #1/A LYS 667 CD 5b43 #2/A LYS 603 CG 0.688 3.072
6i1k #1/A LYS 667 CA 5xus #3/A MET 592 N 0.672 2.848
6i1k #1/A LYS 667 O 5b43 #2/A LYS 607 N 0.643 2.017
6i1k #1/A LYS 667 C 5xus #3/A MET 592 CA 0.636 2.854
6i1k #1/A LYS 667 O 5xus #3/A LYS 591 CA 0.584 2.716
6i1k #1/A LYS 667 CB 5b43 #2/A LYS 603 CD 0.563 3.197
6i1k #1/A LYS 667 CG 5b43 #2/D DA -1 C1' 0.554 3.206
6i1k #1/A LYS 667 CB 5xus #3/D DA -1 C2' 0.542 3.218
6i1k #1/A LYS 667 C 5b43 #2/A MET 604 CA 0.536 2.954
6i1k #1/A LYS 667 CA 5b43 #2/D DA -1 C1' 0.506 3.254
6i1k #1/A LYS 667 CA 5b43 #2/A MET 604 N 0.497 3.023
6i1k #1/A LYS 667 CA 5xus #3/A ASN 590 O 0.496 2.804
6i1k #1/A LYS 667 CA 5xus #3/D DA -1 C2' 0.492 3.268
6i1k #1/A LYS 667 C 5b43 #2/A PRO 606 CD 0.481 3.009
6i1k #1/A LYS 667 C 5xus #3/A LYS 591 N 0.460 2.790
6i1k #1/A LYS 667 CG 5b43 #2/A LYS 603 CD 0.447 3.313
6i1k #1/A LYS 667 O 5b43 #2/A LYS 607 CB 0.437 2.863
6i1k #1/A LYS 667 C 5b43 #2/A LYS 603 CB 0.423 3.067
6i1k #1/A LYS 667 CB 5b43 #2/D DA -1 N9 0.416 3.104
6i1k #1/A LYS 667 O 5b43 #2/A LYS 607 CA 0.415 2.885
6i1k #1/A LYS 667 CD 5b43 #2/D DA -1 C8 0.398 3.242
6i1k #1/A LYS 667 CB 5xus #3/D DA -1 C1' 0.378 3.382
6i1k #1/A LYS 667 CA 5b43 #2/A LYS 603 CG 0.376 3.384
6i1k #1/A LYS 667 CB 5b43 #2/A LYS 603 N 0.363 3.157
6i1k #1/A LYS 667 CD 5b43 #2/D DA -1 N9 0.362 3.158
6i1k #1/A LYS 667 CE 5b43 #2/A LYS 603 NZ 0.339 3.181
6i1k #1/A LYS 667 CA 5b43 #2/A ALA 602 C 0.335 3.155
6i1k #1/A LYS 667 CB 5xus #3/A LYS 591 O 0.315 2.985
6i1k #1/A LYS 667 N 5b43 #2/A ALA 602 CA 0.310 3.210
6i1k #1/A LYS 667 N 5xus #3/A MET 592 N 0.310 2.970
6i1k #1/A LYS 667 CA 5b43 #2/A ALA 602 O 0.287 3.013
6i1k #1/A LYS 667 NZ 5b43 #2/A LYS 603 CG 0.283 3.237
6i1k #1/A LYS 667 CG 5xus #3/D DA -1 C2' 0.261 3.499
6i1k #1/A LYS 667 O 5xus #3/A LYS 595 CB 0.249 3.051
6i1k #1/A LYS 667 CG 5b43 #2/D DA -1 N9 0.233 3.287
6i1k #1/A LYS 667 CD 5b43 #2/D DA -1 C2' 0.218 3.542
6i1k #1/A LYS 667 O 5b43 #2/A PRO 606 CD 0.216 3.084
6i1k #1/A LYS 667 CA 5xus #3/A LYS 591 CD 0.203 3.557
6i1k #1/A LYS 667 N 5b43 #2/A MET 604 N 0.190 3.090
6i1k #1/A LYS 667 O 5xus #3/D DA -1 C1' 0.184 3.116
6i1k #1/A LYS 667 O 6i1k #1/A LYS 671 CB 0.172 3.128
6i1k #1/A LYS 667 CA 5b43 #2/A PRO 606 CD 0.163 3.597
6i1k #1/A LYS 667 CD 5xus #3/A LYS 591 NZ 0.157 3.363
6i1k #1/A LYS 667 N 5b43 #2/A LYS 603 CG 0.154 3.366
6i1k #1/A LYS 667 CD 5b43 #2/D DA -1 C4 0.131 3.359
6i1k #1/A LYS 667 O 5b43 #2/A PRO 606 CB 0.125 3.175
6i1k #1/A LYS 667 C 5b43 #2/D DA -1 C2' 0.118 3.372
6i1k #1/A LYS 667 CB 5xus #3/A LYS 591 CE 0.112 3.648
6i1k #1/A LYS 667 O 5b43 #2/D DA -1 C1' 0.111 3.189
6i1k #1/A LYS 667 O 5b43 #2/A PRO 606 C 0.110 2.920
6i1k #1/A LYS 667 CG 5xus #3/A LYS 591 N 0.108 3.412
6i1k #1/A LYS 667 O 5xus #3/D DA -1 C2' 0.102 3.198
6i1k #1/A LYS 667 CB 5xus #3/A MET 592 N 0.099 3.421
6i1k #1/A LYS 667 O 5b43 #2/A PRO 606 CA 0.093 3.207
6i1k #1/A LYS 667 C 5b43 #2/A LYS 607 N 0.092 3.158
6i1k #1/A LYS 667 C 5b43 #2/D DA -1 C1' 0.079 3.411
6i1k #1/A LYS 667 CB 5b43 #2/A MET 604 N 0.072 3.448
6i1k #1/A LYS 667 O 5b43 #2/A LYS 603 CA 0.071 3.229
6i1k #1/A LYS 667 C 5b43 #2/A LYS 603 N 0.054 3.196
6i1k #1/A LYS 667 CD 5b43 #2/D DA -1 C1' 0.041 3.719
6i1k #1/A LYS 667 CG 5xus #3/A LYS 591 NZ 0.033 3.487
6i1k #1/A LYS 667 CA 5xus #3/D DA -1 C1' 0.024 3.736
6i1k #1/A LYS 667 O 5b43 #2/D DA -1 C2' 0.023 3.277
6i1k #1/A LYS 667 CD 5b43 #2/D DA -1 N7 0.014 3.506
6i1k #1/A LYS 667 C 5b43 #2/A MET 604 C 0.011 3.209
6i1k #1/A LYS 667 C 5xus #3/A PRO 594 CD 0.003 3.487
6i1k #1/A LYS 667 CG 5b43 #2/D DA -1 C8 -0.008 3.648
6i1k #1/A LYS 667 N 5b43 #2/A PRO 606 CD -0.021 3.541
6i1k #1/A LYS 667 O 5b43 #2/A PRO 606 N -0.027 3.087
6i1k #1/A LYS 667 O 5xus #3/A LYS 595 N -0.037 2.697
6i1k #1/A LYS 667 N 5xus #3/A ASN 590 N -0.047 3.327
6i1k #1/A LYS 667 CG 6i1k #1/D DT 1 O4' -0.047 3.387
6i1k #1/A LYS 667 O 5xus #3/A LYS 595 CA -0.051 3.351
6i1k #1/A LYS 667 CB 6i1k #1/D DA 0 N3 -0.051 3.571
6i1k #1/A LYS 667 CD 5b43 #2/D DA -1 C5 -0.052 3.542
6i1k #1/A LYS 667 CA 6i1k #1/D DA 0 C2' -0.059 3.819
6i1k #1/A LYS 667 CB 5b43 #2/D DA -1 C4 -0.059 3.549
6i1k #1/A LYS 667 N 5xus #3/A ASN 590 CB -0.062 3.582
6i1k #1/A LYS 667 O 5xus #3/A MET 592 CA -0.070 3.370
6i1k #1/A LYS 667 CG 6i1k #1/A ASN 666 ND2 -0.080 3.600
6i1k #1/A LYS 667 O 6i1k #1/D DA 0 C1' -0.114 3.414
6i1k #1/A LYS 667 N 6i1k #1/A ASN 666 ND2 -0.117 3.397
6i1k #1/A LYS 667 NZ 5xus #3/A LYS 591 CD -0.120 3.640
6i1k #1/A LYS 667 CA 5b43 #2/A PRO 606 CG -0.135 3.895
6i1k #1/A LYS 667 C 5xus #3/D DA -1 C2' -0.137 3.627
6i1k #1/A LYS 667 CE 5b43 #2/A LYS 603 CA -0.140 3.900
6i1k #1/A LYS 667 CD 5b43 #2/A LYS 603 CA -0.140 3.900
6i1k #1/A LYS 667 O 5xus #3/A PRO 594 CD -0.142 3.442
6i1k #1/A LYS 667 CB 5b43 #2/D DA -1 N3 -0.152 3.672
6i1k #1/A LYS 667 CA 6i1k #1/A GLY 664 O -0.152 3.452
6i1k #1/A LYS 667 C 5xus #3/D DA -1 C1' -0.153 3.643
6i1k #1/A LYS 667 C 5xus #3/A MET 592 C -0.158 3.378
6i1k #1/A LYS 667 CB 5xus #3/D DA -1 N9 -0.160 3.680
6i1k #1/A LYS 667 CG 5b43 #2/D DA -1 C3' -0.163 3.923
6i1k #1/A LYS 667 CG 6i1k #1/D DT 1 C1' -0.172 3.932
6i1k #1/A LYS 667 C 5b43 #2/A LYS 607 CB -0.177 3.667
6i1k #1/A LYS 667 CD 5xus #3/A LYS 591 CA -0.180 3.940
6i1k #1/A LYS 667 CB 5b43 #2/D DA -1 C3' -0.191 3.951
6i1k #1/A LYS 667 O 6i1k #1/D DA 0 C2' -0.203 3.503
6i1k #1/A LYS 667 CB 6i1k #1/D DA 0 C2' -0.204 3.964
6i1k #1/A LYS 667 CB 5xus #3/D DA -1 N3 -0.208 3.728
6i1k #1/A LYS 667 O 5xus #3/A PRO 594 CB -0.210 3.510
6i1k #1/A LYS 667 CE 5xus #3/A LYS 591 CE -0.211 3.971
6i1k #1/A LYS 667 O 5b43 #2/A MET 604 CA -0.214 3.514
6i1k #1/A LYS 667 C 5b43 #2/A PRO 606 N -0.221 3.471
6i1k #1/A LYS 667 O 5xus #3/A LYS 591 CB -0.224 3.524
6i1k #1/A LYS 667 CB 6i1k #1/A GLY 664 O -0.228 3.528
6i1k #1/A LYS 667 CA 5b43 #2/D DA -1 C3' -0.231 3.991
6i1k #1/A LYS 667 C 5b43 #2/A PRO 606 CG -0.232 3.722
6i1k #1/A LYS 667 N 6i1k #1/A GLY 664 O -0.246 2.906
6i1k #1/A LYS 667 O 6i1k #1/A PRO 670 CD -0.246 3.546
6i1k #1/A LYS 667 CD 6i1k #1/D DT 1 O2 -0.248 3.548
6i1k #1/A LYS 667 N 5xus #3/A ASN 590 CG -0.248 3.498
6i1k #1/A LYS 667 N 5b43 #2/A LYS 603 O -0.249 2.909
6i1k #1/A LYS 667 CD 5b43 #2/A LYS 603 CE -0.251 4.011
6i1k #1/A LYS 667 C 5b43 #2/A ILE 605 N -0.251 3.501
6i1k #1/A LYS 667 CG 5xus #3/D DA -1 C1' -0.255 4.015
6i1k #1/A LYS 667 C 6i1k #1/A PRO 670 CD -0.269 3.759
6i1k #1/A LYS 667 CG 5b43 #2/A LYS 603 N -0.270 3.790
6i1k #1/A LYS 667 CG 5b43 #2/A LYS 603 C -0.272 3.762
6i1k #1/A LYS 667 CB 6i1k #1/D DA 0 C1' -0.277 4.037
6i1k #1/A LYS 667 C 5b43 #2/A PRO 606 CB -0.284 3.774
6i1k #1/A LYS 667 O 5xus #3/A MET 592 N -0.289 2.949
6i1k #1/A LYS 667 O 5b43 #2/A PRO 606 CG -0.298 3.598
6i1k #1/A LYS 667 NZ 5b43 #2/A LYS 603 CB -0.301 3.821
6i1k #1/A LYS 667 C 5xus #3/A ASN 590 C -0.318 3.538
6i1k #1/A LYS 667 CB 5xus #3/A ASN 590 C -0.322 3.812
6i1k #1/A LYS 667 CA 5xus #3/A MET 592 CA -0.324 4.084
6i1k #1/A LYS 667 CA 5xus #3/A PRO 594 CD -0.333 4.093
6i1k #1/A LYS 667 CB 5xus #3/D DA -1 C4 -0.344 3.834
6i1k #1/A LYS 667 CB 5b43 #2/D DA -1 C8 -0.349 3.989
6i1k #1/A LYS 667 CE 5b43 #2/D DA -1 C4 -0.357 3.847
6i1k #1/A LYS 667 CB 6i1k #1/D DA 0 C4 -0.357 3.847
6i1k #1/A LYS 667 CA 5b43 #2/A MET 604 CA -0.364 4.124
6i1k #1/A LYS 667 O 5b43 #2/A MET 604 C -0.368 3.398
6i1k #1/A LYS 667 NZ 5xus #3/A LYS 591 CG -0.371 3.891
6i1k #1/A LYS 667 CE 5xus #3/A LYS 591 CA -0.375 4.135
6i1k #1/A LYS 667 C 5xus #3/A LYS 591 CG -0.386 3.876
6i1k #1/A LYS 667 O 5xus #3/A PRO 594 CG -0.386 3.686
6i1k #1/A LYS 667 CE 6i1k #1/A GLY 664 CA -0.387 4.147
6i1k #1/A LYS 667 N 5b43 #2/A PRO 606 CG -0.388 3.908
6i1k #1/A LYS 667 CA 5b43 #2/A PRO 606 CB -0.391 4.151
6i1k #1/A LYS 667 N 5xus #3/A PRO 589 C -0.392 3.642
6i1k #1/A LYS 667 CG 5b43 #2/D DA -1 C4 -0.398 3.888
222 contacts
> select #1/A:622 #2/A:557
22 atoms, 22 bonds, 2 models selected
> contacts sel test others reveal true log true select true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
226 contacts
atom1 atom2 overlap distance
6i1k #1/A LYS 671 CB 5b43 #2/A LYS 607 CA 3.442 0.318
6i1k #1/A LYS 671 CD 5b43 #2/A LYS 607 CG 3.223 0.537
6i1k #1/A LYS 671 CD 5xus #3/A LYS 595 CG 3.075 0.685
6i1k #1/A LYS 671 CA 5xus #3/A LYS 595 CA 2.943 0.817
6i1k #1/A LYS 671 CB 5xus #3/A LYS 595 CA 2.925 0.835
6i1k #1/A LYS 671 CB 5xus #3/A LYS 595 CB 2.880 0.880
6i1k #1/A LYS 671 NZ 5b43 #2/A LYS 607 CE 2.714 0.806
6i1k #1/A LYS 671 N 5b43 #2/A PRO 606 C 2.704 0.546
6i1k #1/A LYS 671 CD 5xus #3/A LYS 595 CD 2.641 1.119
6i1k #1/A LYS 671 CG 5xus #3/A LYS 595 CG 2.612 1.148
6i1k #1/A LYS 671 N 5xus #3/A PRO 594 C 2.532 0.718
6i1k #1/A LYS 671 NZ 5xus #3/A LYS 595 CE 2.531 0.989
6i1k #1/A LYS 671 N 5xus #3/A LYS 595 N 2.528 0.752
6i1k #1/A LYS 671 C 5xus #3/A LYS 595 C 2.507 0.713
6i1k #1/A LYS 671 CE 5xus #3/A LYS 595 NZ 2.480 1.040
6i1k #1/A LYS 671 NZ 5xus #3/A LYS 595 NZ 2.425 0.855
6i1k #1/A LYS 671 CB 5b43 #2/A LYS 607 CB 2.311 1.449
6i1k #1/A LYS 671 CA 5b43 #2/A LYS 607 CA 2.303 1.457
6i1k #1/A LYS 671 CG 5b43 #2/A LYS 607 CG 2.225 1.535
6i1k #1/A LYS 671 O 5xus #3/A LYS 595 O 2.189 0.651
6i1k #1/A LYS 671 CB 5b43 #2/A LYS 607 C 2.180 1.310
6i1k #1/A LYS 671 CG 5xus #3/A LYS 595 CB 2.137 1.623
6i1k #1/A LYS 671 CE 5xus #3/A LYS 595 CE 2.129 1.631
6i1k #1/A LYS 671 CD 5b43 #2/A LYS 607 CD 2.118 1.642
6i1k #1/A LYS 671 CA 5b43 #2/A LYS 607 C 2.111 1.379
6i1k #1/A LYS 671 CE 5b43 #2/A LYS 607 NZ 2.017 1.503
6i1k #1/A LYS 671 CA 5xus #3/A LYS 595 N 2.012 1.508
6i1k #1/A LYS 671 CE 5b43 #2/A LYS 607 CE 2.004 1.756
6i1k #1/A LYS 671 NZ 5b43 #2/A LYS 607 NZ 2.002 1.278
6i1k #1/A LYS 671 CG 5b43 #2/A LYS 607 CA 1.984 1.776
6i1k #1/A LYS 671 C 5xus #3/A LYS 595 O 1.950 1.080
6i1k #1/A LYS 671 N 5b43 #2/A LYS 607 N 1.909 1.371
6i1k #1/A LYS 671 CA 5xus #3/A LYS 595 C 1.905 1.585
6i1k #1/A LYS 671 CE 5b43 #2/A LYS 607 CG 1.887 1.873
6i1k #1/A LYS 671 CG 5b43 #2/A LYS 607 CB 1.881 1.879
6i1k #1/A LYS 671 CD 5b43 #2/A LYS 607 CB 1.836 1.924
6i1k #1/A LYS 671 C 5b43 #2/A LYS 607 C 1.833 1.387
6i1k #1/A LYS 671 CE 5xus #3/A LYS 595 CD 1.826 1.934
6i1k #1/A LYS 671 CB 5xus #3/A LYS 595 CG 1.808 1.952
6i1k #1/A LYS 671 CB 5b43 #2/A LYS 607 N 1.798 1.722
6i1k #1/A LYS 671 CD 5xus #3/A LYS 595 CB 1.769 1.991
6i1k #1/A LYS 671 CG 5b43 #2/A LYS 607 C 1.743 1.747
6i1k #1/A LYS 671 CA 5b43 #2/A LYS 607 N 1.730 1.790
6i1k #1/A LYS 671 N 5xus #3/A LYS 595 CA 1.727 1.793
6i1k #1/A LYS 671 CE 5xus #3/A LYS 595 CG 1.713 2.047
6i1k #1/A LYS 671 CA 5b43 #2/A PRO 606 O 1.708 1.592
6i1k #1/A LYS 671 CD 5xus #3/A LYS 595 CE 1.704 2.056
6i1k #1/A LYS 671 CG 5xus #3/A LYS 595 CA 1.694 2.066
6i1k #1/A LYS 671 C 5xus #3/A LYS 595 CA 1.681 1.809
6i1k #1/A LYS 671 C 5b43 #2/A CYS 608 N 1.644 1.606
6i1k #1/A LYS 671 CA 5b43 #2/A PRO 606 C 1.642 1.848
6i1k #1/A LYS 671 N 5b43 #2/A PRO 606 CA 1.623 1.897
6i1k #1/A LYS 671 CE 5b43 #2/A LYS 607 CD 1.598 2.162
6i1k #1/A LYS 671 C 5xus #3/A VAL 596 N 1.560 1.690
6i1k #1/A LYS 671 N 5b43 #2/A PRO 606 O 1.551 1.109
6i1k #1/A LYS 671 CB 5xus #3/A LYS 595 N 1.517 2.003
6i1k #1/A LYS 671 CG 5b43 #2/A LYS 607 O 1.513 1.787
6i1k #1/A LYS 671 N 5xus #3/A PRO 594 CA 1.460 2.060
6i1k #1/A LYS 671 CA 5xus #3/A PRO 594 C 1.455 2.035
6i1k #1/A LYS 671 C 5b43 #2/A LYS 607 O 1.446 1.584
6i1k #1/A LYS 671 CD 5b43 #2/A LYS 607 CE 1.441 2.319
6i1k #1/A LYS 671 CA 5xus #3/A LYS 595 CB 1.439 2.321
6i1k #1/A LYS 671 CB 5b43 #2/A LYS 607 CG 1.438 2.322
6i1k #1/A LYS 671 CB 5xus #3/A LYS 595 C 1.400 2.090
6i1k #1/A LYS 671 NZ 5xus #3/A LYS 595 CD 1.388 2.132
6i1k #1/A LYS 671 O 5xus #3/A LYS 595 C 1.355 1.675
6i1k #1/A LYS 671 NZ 5b43 #2/A LYS 607 CD 1.346 2.174
6i1k #1/A LYS 671 CA 5b43 #2/A CYS 608 N 1.340 2.180
6i1k #1/A LYS 671 C 5b43 #2/A CYS 608 CA 1.326 2.164
6i1k #1/A LYS 671 O 5b43 #2/A LYS 607 O 1.313 1.527
6i1k #1/A LYS 671 CA 5b43 #2/A LYS 607 O 1.281 2.019
6i1k #1/A LYS 671 N 5b43 #2/A LYS 607 CA 1.273 2.247
6i1k #1/A LYS 671 CB 5b43 #2/A CYS 608 N 1.245 2.275
6i1k #1/A LYS 671 CG 5xus #3/A LYS 595 CD 1.193 2.567
6i1k #1/A LYS 671 CA 5xus #3/A PRO 594 O 1.175 2.125
6i1k #1/A LYS 671 C 5b43 #2/A SER 609 N 1.175 2.075
6i1k #1/A LYS 671 CB 5b43 #2/A LYS 607 O 1.116 2.184
6i1k #1/A LYS 671 CA 5xus #3/A LYS 595 O 1.101 2.199
6i1k #1/A LYS 671 CD 5xus #3/A LYS 595 NZ 1.086 2.434
6i1k #1/A LYS 671 N 5xus #3/A PRO 594 O 1.069 1.591
6i1k #1/A LYS 671 CD 5b43 #2/A LYS 607 CA 0.996 2.764
6i1k #1/A LYS 671 CG 5xus #3/A LYS 595 C 0.973 2.517
6i1k #1/A LYS 671 C 5xus #3/A VAL 596 CA 0.951 2.539
6i1k #1/A LYS 671 C 5b43 #2/A LYS 607 CA 0.891 2.599
6i1k #1/A LYS 671 C 5b43 #2/A CYS 608 C 0.882 2.338
6i1k #1/A LYS 671 CA 5xus #3/A VAL 596 N 0.875 2.645
6i1k #1/A LYS 671 O 5b43 #2/A LYS 607 C 0.844 2.186
6i1k #1/A LYS 671 CB 5b43 #2/A PRO 606 C 0.813 2.677
6i1k #1/A LYS 671 CA 5b43 #2/A LYS 607 CB 0.802 2.958
6i1k #1/A LYS 671 CD 5b43 #2/A LYS 607 NZ 0.771 2.749
6i1k #1/A LYS 671 N 5xus #3/A PRO 594 CB 0.744 2.776
6i1k #1/A LYS 671 O 5b43 #2/A LEU 612 CD2 0.734 2.566
6i1k #1/A LYS 671 NZ 5b43 #2/A LYS 607 CG 0.733 2.787
6i1k #1/A LYS 671 CD 5b43 #2/A LYS 607 C 0.727 2.763
6i1k #1/A LYS 671 CG 5b43 #2/A LYS 607 CD 0.717 3.043
6i1k #1/A LYS 671 C 5xus #3/A LYS 595 N 0.709 2.541
6i1k #1/A LYS 671 C 5xus #3/A PRO 594 O 0.701 2.329
6i1k #1/A LYS 671 N 5b43 #2/A LYS 607 C 0.674 2.576
6i1k #1/A LYS 671 CE 5b43 #2/C DA 4 O4' 0.656 2.684
6i1k #1/A LYS 671 N 5xus #3/A LYS 595 C 0.651 2.599
6i1k #1/A LYS 671 CG 5b43 #2/A CYS 608 N 0.642 2.878
6i1k #1/A LYS 671 O 5b43 #2/A CYS 608 CA 0.624 2.676
6i1k #1/A LYS 671 CD 5xus #3/A LYS 595 CA 0.617 3.143
6i1k #1/A LYS 671 CA 5xus #3/A LYS 595 CG 0.562 3.198
6i1k #1/A LYS 671 CG 5xus #3/A LYS 595 O 0.561 2.739
6i1k #1/A LYS 671 N 5b43 #2/A PRO 606 N 0.557 2.723
6i1k #1/A LYS 671 CE 5b43 #2/C DA 4 C4' 0.549 3.211
6i1k #1/A LYS 671 CB 5xus #3/A LYS 595 CD 0.548 3.212
6i1k #1/A LYS 671 CB 5xus #3/A VAL 596 N 0.542 2.978
6i1k #1/A LYS 671 C 5b43 #2/A PRO 606 O 0.529 2.501
6i1k #1/A LYS 671 O 5xus #3/A LYS 595 CA 0.527 2.773
6i1k #1/A LYS 671 NZ 6i1k #1/C DA 2 N3 0.499 2.381
6i1k #1/A LYS 671 N 5b43 #2/A CYS 608 N 0.495 2.785
6i1k #1/A LYS 671 O 5b43 #2/A LEU 612 CG 0.488 2.812
6i1k #1/A LYS 671 NZ 5xus #3/A LYS 595 CG 0.479 3.041
6i1k #1/A LYS 671 C 5xus #3/A PRO 594 C 0.477 2.743
6i1k #1/A LYS 671 N 5xus #3/A LYS 595 CB 0.469 3.051
6i1k #1/A LYS 671 N 5b43 #2/A PRO 606 CB 0.467 3.053
6i1k #1/A LYS 671 O 5b43 #2/A CYS 608 C 0.461 2.569
6i1k #1/A LYS 671 CB 5xus #3/A LYS 595 O 0.458 2.842
6i1k #1/A LYS 671 C 5xus #3/A LYS 595 CB 0.438 3.052
6i1k #1/A LYS 671 O 5xus #3/A VAL 596 CA 0.432 2.868
6i1k #1/A LYS 671 CA 5b43 #2/A PRO 606 CA 0.421 3.339
6i1k #1/A LYS 671 CE 5xus #3/D DT -2 O2 0.421 2.879
6i1k #1/A LYS 671 N 5xus #3/A PRO 594 N 0.414 2.866
6i1k #1/A LYS 671 CA 5b43 #2/A CYS 608 CA 0.401 3.359
6i1k #1/A LYS 671 CE 5b43 #2/A LYS 607 CB 0.381 3.379
6i1k #1/A LYS 671 O 5xus #3/A SER 599 CB 0.364 2.936
6i1k #1/A LYS 671 CB 5b43 #2/A PRO 606 O 0.360 2.940
6i1k #1/A LYS 671 CB 5xus #3/A PRO 594 C 0.343 3.147
6i1k #1/A LYS 671 CG 5xus #3/A LYS 595 CE 0.327 3.433
6i1k #1/A LYS 671 CD 5b43 #2/A LYS 607 O 0.321 2.979
6i1k #1/A LYS 671 CG 5b43 #2/A LYS 607 N 0.290 3.230
6i1k #1/A LYS 671 CE 5xus #3/A LYS 595 CB 0.286 3.474
6i1k #1/A LYS 671 C 5xus #3/A VAL 596 C 0.267 2.953
6i1k #1/A LYS 671 CA 5b43 #2/A SER 609 N 0.267 3.253
6i1k #1/A LYS 671 CA 5xus #3/A PRO 594 CA 0.258 3.502
6i1k #1/A LYS 671 NZ 6i1k #1/C DA 2 C1' 0.258 3.262
6i1k #1/A LYS 671 CB 5xus #3/D DA -1 C4' 0.248 3.512
6i1k #1/A LYS 671 N 5b43 #2/A ILE 605 C 0.237 3.013
6i1k #1/A LYS 671 C 5b43 #2/A PRO 606 C 0.233 2.987
6i1k #1/A LYS 671 O 5b43 #2/A SER 609 N 0.210 2.450
6i1k #1/A LYS 671 C 5b43 #2/A LYS 607 N 0.202 3.048
6i1k #1/A LYS 671 CE 6i1k #1/C DA 3 O4' 0.183 3.157
6i1k #1/A LYS 671 CB 6i1k #1/A LYS 667 O 0.172 3.128
6i1k #1/A LYS 671 O 6i1k #1/A SER 675 CB 0.153 3.147
6i1k #1/A LYS 671 N 5xus #3/A VAL 596 N 0.148 3.132
6i1k #1/A LYS 671 CB 5b43 #2/A CYS 608 CA 0.147 3.613
6i1k #1/A LYS 671 NZ 6i1k #1/C DA 2 C2 0.142 3.258
6i1k #1/A LYS 671 NZ 5xus #3/C DA 3 N3 0.137 2.743
6i1k #1/A LYS 671 C 5b43 #2/A SER 609 CA 0.119 3.371
6i1k #1/A LYS 671 CD 5b43 #2/A CYS 608 N 0.096 3.424
6i1k #1/A LYS 671 CB 5xus #3/D DA -1 O4' 0.085 3.255
6i1k #1/A LYS 671 CB 5b43 #2/A LYS 607 CD 0.080 3.680
6i1k #1/A LYS 671 NZ 5xus #3/C DA 3 C2 0.078 3.322
6i1k #1/A LYS 671 CE 6i1k #1/D DT -1 O2 0.075 3.225
6i1k #1/A LYS 671 O 5xus #3/A VAL 596 N 0.075 2.585
6i1k #1/A LYS 671 C 5xus #3/A LYS 595 CG 0.070 3.420
6i1k #1/A LYS 671 CG 5xus #3/A LYS 595 N 0.057 3.463
6i1k #1/A LYS 671 O 5b43 #2/A CYS 608 N 0.036 2.624
6i1k #1/A LYS 671 CD 5xus #3/A LYS 595 C 0.027 3.463
6i1k #1/A LYS 671 CG 5xus #3/A VAL 596 N 0.018 3.502
6i1k #1/A LYS 671 CE 5b43 #2/C DA 4 C1' 0.018 3.742
6i1k #1/A LYS 671 CA 5b43 #2/A LYS 607 CG 0.014 3.746
6i1k #1/A LYS 671 CG 5xus #3/A LYS 595 NZ 0.001 3.519
6i1k #1/A LYS 671 C 5xus #3/A PHE 597 N -0.006 3.256
6i1k #1/A LYS 671 CG 5b43 #2/A LYS 607 CE -0.014 3.774
6i1k #1/A LYS 671 NZ 5b43 #2/C DA 3 C1' -0.015 3.535
6i1k #1/A LYS 671 CE 6i1k #1/C DA 2 N3 -0.026 3.546
6i1k #1/A LYS 671 NZ 6i1k #1/C DA 2 C4 -0.029 3.279
6i1k #1/A LYS 671 O 5xus #3/A VAL 596 C -0.041 3.071
6i1k #1/A LYS 671 CA 5xus #3/D DA -1 C4' -0.044 3.804
6i1k #1/A LYS 671 CA 5b43 #2/A GLN 611 CB -0.051 3.811
6i1k #1/A LYS 671 O 5xus #3/A SER 599 CA -0.053 3.353
6i1k #1/A LYS 671 CG 5b43 #2/A CYS 608 CA -0.054 3.814
6i1k #1/A LYS 671 N 5xus #3/A LEU 593 C -0.062 3.312
6i1k #1/A LYS 671 CB 6i1k #1/A MET 668 O -0.068 3.368
6i1k #1/A LYS 671 CG 5xus #3/D DA -1 O4' -0.072 3.412
6i1k #1/A LYS 671 N 5b43 #2/A LYS 607 CB -0.080 3.600
6i1k #1/A LYS 671 N 5b43 #2/A ILE 605 O -0.098 2.758
6i1k #1/A LYS 671 N 5b43 #2/A SER 609 N -0.104 3.384
6i1k #1/A LYS 671 NZ 6i1k #1/C DA 1 C2 -0.106 3.506
6i1k #1/A LYS 671 CA 5xus #3/A VAL 596 CA -0.115 3.875
6i1k #1/A LYS 671 C 5b43 #2/A CYS 608 CB -0.119 3.609
6i1k #1/A LYS 671 CB 5xus #3/D DA -1 C1' -0.132 3.892
6i1k #1/A LYS 671 CE 5xus #3/C DA 4 O4' -0.132 3.472
6i1k #1/A LYS 671 CB 6i1k #1/D DA 0 C1' -0.135 3.895
6i1k #1/A LYS 671 O 5b43 #2/A LYS 607 CA -0.141 3.441
6i1k #1/A LYS 671 NZ 5b43 #2/C DA 4 O4' -0.151 2.851
6i1k #1/A LYS 671 NZ 5xus #3/D DT -2 O2 -0.154 2.814
6i1k #1/A LYS 671 CB 5xus #3/A LYS 591 O -0.154 3.454
6i1k #1/A LYS 671 O 5b43 #2/A SER 609 CA -0.161 3.461
6i1k #1/A LYS 671 CE 5b43 #2/C DA 4 C5' -0.173 3.933
6i1k #1/A LYS 671 O 5xus #3/A PRO 594 O -0.182 3.022
6i1k #1/A LYS 671 CG 5xus #3/D DA -1 C4' -0.202 3.962
6i1k #1/A LYS 671 NZ 5xus #3/C DA 2 C2 -0.230 3.630
6i1k #1/A LYS 671 CE 6i1k #1/C DA 3 C4' -0.261 4.021
6i1k #1/A LYS 671 C 5b43 #2/A LEU 612 CD2 -0.263 3.753
6i1k #1/A LYS 671 CA 5b43 #2/A CYS 608 C -0.264 3.754
6i1k #1/A LYS 671 NZ 5b43 #2/C DA 3 N3 -0.269 3.149
6i1k #1/A LYS 671 CE 5xus #3/C DA 4 C4' -0.269 4.029
6i1k #1/A LYS 671 CA 6i1k #1/A MET 668 O -0.275 3.575
6i1k #1/A LYS 671 CE 6i1k #1/C DA 3 C1' -0.277 4.037
6i1k #1/A LYS 671 CB 5xus #3/A PRO 594 O -0.283 3.583
6i1k #1/A LYS 671 NZ 5b43 #2/C DA 4 C4' -0.295 3.815
6i1k #1/A LYS 671 CB 5b43 #2/A PRO 606 CA -0.307 4.067
6i1k #1/A LYS 671 N 5xus #3/A PRO 594 CD -0.307 3.827
6i1k #1/A LYS 671 NZ 5b43 #2/C DA 4 C1' -0.307 3.827
6i1k #1/A LYS 671 CA 5b43 #2/A GLN 611 N -0.326 3.846
6i1k #1/A LYS 671 CD 5xus #3/D DT -2 O2 -0.328 3.628
6i1k #1/A LYS 671 CG 5b43 #2/A LYS 607 NZ -0.329 3.849
6i1k #1/A LYS 671 CA 5xus #3/A PRO 594 CB -0.332 4.092
6i1k #1/A LYS 671 O 6i1k #1/A SER 675 CA -0.333 3.633
6i1k #1/A LYS 671 NZ 6i1k #1/C DA 2 N9 -0.339 3.619
6i1k #1/A LYS 671 CB 5b43 #2/A MET 604 O -0.342 3.642
6i1k #1/A LYS 671 C 5b43 #2/A LYS 607 CB -0.342 3.832
6i1k #1/A LYS 671 CD 5b43 #2/C DA 4 C4' -0.344 4.104
6i1k #1/A LYS 671 CB 6i1k #1/D DA 0 C4' -0.350 4.110
6i1k #1/A LYS 671 CE 5b43 #2/A LYS 607 CA -0.357 4.117
6i1k #1/A LYS 671 CB 6i1k #1/A MET 668 CA -0.362 4.122
6i1k #1/A LYS 671 CE 5b43 #2/A LYS 607 O -0.371 3.671
6i1k #1/A LYS 671 N 5xus #3/A PRO 594 CG -0.376 3.896
6i1k #1/A LYS 671 CB 6i1k #1/D DA 0 O4' -0.376 3.716
6i1k #1/A LYS 671 CA 6i1k #1/D DA 0 C4' -0.377 4.137
6i1k #1/A LYS 671 O 5b43 #2/A PRO 606 O -0.380 3.220
6i1k #1/A LYS 671 N 5b43 #2/A PRO 606 CD -0.395 3.915
226 contacts
Alignment identifier is 1.A
Alignment identifier is 1.C
Alignment identifier is 1.D
Alignment identifier is 2.A
Alignment identifier is 2.C
Alignment identifier is 3.A
Alignment identifier is 3.C
Alignment identifier is 3.D
> save session "/Users/huihui/Desktop/Crystal structure/alignment_Fn_crRNA_DNA
complex_LKL.cxs"
> close session
> open 6I1K format mmCIF fromDatabase pdb
6i1k title:
Crystal structure of catalytically inactive FnCas12a in complex with a crRNA
guide and a dsDNA target [more info...]
Chain information for 6i1k #1
---
Chain | Description
A | CRISPR-associated endonuclease Cas12a
B | crRNA (40-MER)
C | DNA target strand (38-MER)
D | DNA non-target strand (33-MER)
Non-standard residues in 6i1k #1
---
EDO — 1,2-ethanediol (ethylene glycol)
MG — magnesium ion
> delete solvent
> select /A
10607 atoms, 10803 bonds, 9 pseudobonds, 3 models selected
> hide sel cartoons
> hide sel atoms
> select /B
853 atoms, 942 bonds, 17 pseudobonds, 2 models selected
> hide sel cartoons
> hide sel atoms
> hide sel atoms
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 827 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 827 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 827 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 827 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 827 atom styles
> nucleotides sel tube/slab shape box
> color sel bynucleotide
> toolshed show "Basic Actions"
> color /B #999999 target abp
> hide /B target c
> show /B target c
> hide /B target c
> hide /B target abp
> show /B target abp
> select clear
> close session
> open 6I1K format mmCIF fromDatabase pdb
6i1k title:
Crystal structure of catalytically inactive FnCas12a in complex with a crRNA
guide and a dsDNA target [more info...]
Chain information for 6i1k #1
---
Chain | Description
A | CRISPR-associated endonuclease Cas12a
B | crRNA (40-MER)
C | DNA target strand (38-MER)
D | DNA non-target strand (33-MER)
Non-standard residues in 6i1k #1
---
EDO — 1,2-ethanediol (ethylene glycol)
MG — magnesium ion
> select /A
10653 atoms, 10803 bonds, 29 pseudobonds, 3 models selected
> hide sel atoms
> hide sel cartoons
> select /B
869 atoms, 942 bonds, 24 pseudobonds, 3 models selected
> nucleotides sel tube/slab shape box
> hide sel cartoons
> delete solvent
Alignment identifier is 1.B
> select clear
Alignment identifier is 1.A
Destroying pre-existing alignment with identifier 1.B
Alignment identifier is 1.B
Alignment identifier is 1.C
Alignment identifier is 1.D
> select /A
10607 atoms, 10803 bonds, 9 pseudobonds, 3 models selected
Expected an objects specifier or a keyword
Expected an objects specifier or a keyword
> show sel atoms
> show sel cartoons
> show sel atoms
> hide sel atoms
> show sel atoms
Expected a keyword
> contacts sel test others reveal true log true select true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
19 contacts
atom1 atom2 overlap distance
/A LYS 667 O /A LYS 671 CB 0.172 3.128
/A LYS 667 CG /D DT 1 O4' -0.047 3.387
/A LYS 667 CB /D DA 0 N3 -0.051 3.571
/A LYS 667 CA /D DA 0 C2' -0.059 3.819
/A LYS 667 CG /A ASN 666 ND2 -0.080 3.600
/A LYS 667 O /D DA 0 C1' -0.114 3.414
/A LYS 667 N /A ASN 666 ND2 -0.117 3.397
/A LYS 667 CA /A GLY 664 O -0.152 3.452
/A LYS 667 CG /D DT 1 C1' -0.172 3.932
/A LYS 667 O /D DA 0 C2' -0.203 3.503
/A LYS 667 CB /D DA 0 C2' -0.204 3.964
/A LYS 667 CB /A GLY 664 O -0.228 3.528
/A LYS 667 N /A GLY 664 O -0.246 2.906
/A LYS 667 O /A PRO 670 CD -0.246 3.546
/A LYS 667 CD /D DT 1 O2 -0.248 3.548
/A LYS 667 C /A PRO 670 CD -0.269 3.759
/A LYS 667 CB /D DA 0 C1' -0.277 4.037
/A LYS 667 CB /D DA 0 C4 -0.357 3.847
/A LYS 667 CE /A GLY 664 CA -0.387 4.147
19 contacts
> show sel atoms
> contacts sel test others reveal true log true select true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
21 contacts
atom1 atom2 overlap distance
/A LYS 671 NZ /C DA 2 N3 0.499 2.381
/A LYS 671 NZ /C DA 2 C1' 0.258 3.262
/A LYS 671 CE /C DA 3 O4' 0.182 3.158
/A LYS 671 CB /A LYS 667 O 0.172 3.128
/A LYS 671 O /A SER 675 CB 0.153 3.147
/A LYS 671 NZ /C DA 2 C2 0.142 3.258
/A LYS 671 CE /D DT -1 O2 0.075 3.225
/A LYS 671 CE /C DA 2 N3 -0.026 3.546
/A LYS 671 NZ /C DA 2 C4 -0.029 3.279
/A LYS 671 CB /A MET 668 O -0.068 3.368
/A LYS 671 NZ /C DA 1 C2 -0.106 3.506
/A LYS 671 CB /D DA 0 C1' -0.135 3.895
/A LYS 671 CE /C DA 3 C4' -0.261 4.021
/A LYS 671 CA /A MET 668 O -0.275 3.575
/A LYS 671 CE /C DA 3 C1' -0.277 4.037
/A LYS 671 O /A SER 675 CA -0.333 3.633
/A LYS 671 NZ /C DA 2 N9 -0.339 3.619
/A LYS 671 CB /D DA 0 C4' -0.350 4.110
/A LYS 671 CB /A MET 668 CA -0.362 4.122
/A LYS 671 CB /D DA 0 O4' -0.376 3.716
/A LYS 671 CA /D DA 0 C4' -0.377 4.137
21 contacts
> show sel atoms
> contacts sel test others reveal true log true select true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
5 contacts
atom1 atom2 overlap distance
/A LYS 677 CB /C DG 4 OP2 0.168 3.132
/A LYS 677 CG /A SER 678 OG -0.079 3.419
/A LYS 677 N /C DG 4 OP2 -0.217 2.877
/A LYS 677 CA /C DG 4 OP2 -0.293 3.593
/A LYS 677 CG /A SER 678 CB -0.371 4.131
5 contacts
> save session "/Users/huihui/Desktop/Crystal structure/FnCpf1_6I1K.cxs"
> close session
> open 5B43 format mmCIF fromDatabase pdb
5b43 title:
Crystal structure of Acidaminococcus sp. Cpf1 in complex with crRNA and target
DNA [more info...]
Chain information for 5b43 #1
---
Chain | Description
A | CRISPR-associated endonuclease Cpf1
B | RNA (43-mer)
C | DNA (34-mer)
D | DNA (5'-D(*CP*ap*GP*TP*CP*CP*TP*TP*TP*A)-3')
Non-standard residues in 5b43 #1
---
EDO — 1,2-ethanediol (ethylene glycol)
NA — sodium ion
> select /A
10194 atoms, 10398 bonds, 5 pseudobonds, 3 models selected
> hide sel cartoons
> hide sel atoms
> select /B
848 atoms, 946 bonds, 16 pseudobonds, 2 models selected
> nucleotides sel tube/slab shape box
> show sel cartoons
> hide sel cartoons
> select clear
Alignment identifier is 1.A
Alignment identifier is 1.B
Alignment identifier is 1.C
Alignment identifier is 1.D
> show sel atoms
> show sel atoms
> hide sel atoms
> show sel cartoons
> show sel atoms
> contacts sel test others reveal true log true select true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
19 contacts
atom1 atom2 overlap distance
/A LYS 603 CB /D DA -1 C2' 0.174 3.586
/A LYS 603 O /D DA -1 C1' 0.111 3.189
/A LYS 603 O /A LYS 607 CB 0.088 3.212
/A LYS 603 CA /D DA -1 C2' 0.029 3.731
/A LYS 603 CG /A ASP 600 O -0.033 3.333
/A LYS 603 C /A PRO 606 CD -0.037 3.527
/A LYS 603 CB /D DA -1 C1' -0.059 3.819
/A LYS 603 O /D DA -1 C2' -0.088 3.388
/A LYS 603 O /A PRO 606 CD -0.108 3.408
/A LYS 603 CA /A PRO 606 CD -0.161 3.921
/A LYS 603 CG /A ASP 600 CB -0.176 3.936
/A LYS 603 CD /D DA -1 N3 -0.190 3.710
/A LYS 603 CD /D DA -1 C2 -0.202 3.842
/A LYS 603 CE /D DA -1 C2 -0.265 3.905
/A LYS 603 CE /A ASP 600 CB -0.347 4.107
/A LYS 603 O /A LYS 607 N -0.349 3.009
/A LYS 603 CA /D DA -1 C1' -0.387 4.147
/A LYS 603 O /A LYS 607 CA -0.390 3.690
/A LYS 603 CD /D DA -1 C4 -0.395 3.885
19 contacts
> show sel atoms
> contacts sel test others reveal true log true select true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
27 contacts
atom1 atom2 overlap distance
/A LYS 607 CE /C DA 3 N3 0.173 3.347
/A LYS 607 CB /A LYS 603 O 0.088 3.212
/A LYS 607 CB /D DA -1 C1' 0.073 3.687
/A LYS 607 CB /D DA -1 O4' 0.055 3.285
/A LYS 607 CE /D DT -2 O2 0.020 3.280
/A LYS 607 CE /C DA 2 C2 0.003 3.637
/A LYS 607 O /A LEU 612 CD2 -0.050 3.350
/A LYS 607 CD /D DT -2 O2 -0.100 3.400
/A LYS 607 CD /D DA -1 N3 -0.101 3.621
/A LYS 607 CE /C DA 3 C1' -0.115 3.875
/A LYS 607 NZ /C DA 4 C1' -0.117 3.637
/A LYS 607 CD /A MET 604 CE -0.206 3.966
/A LYS 607 CB /A MET 604 O -0.209 3.509
/A LYS 607 CA /D DA -1 C4' -0.217 3.977
/A LYS 607 NZ /D DT -2 O2 -0.229 2.889
/A LYS 607 CD /A MET 604 SD -0.231 3.881
/A LYS 607 NZ /C DA 3 N3 -0.281 3.161
/A LYS 607 NZ /C DA 3 C2 -0.284 3.684
/A LYS 607 CE /C DA 4 O4' -0.292 3.632
/A LYS 607 NZ /C DA 4 O4' -0.302 3.002
/A LYS 607 CA /D DA -1 O4' -0.325 3.665
/A LYS 607 CB /A MET 604 CA -0.333 4.093
/A LYS 607 N /A LYS 603 O -0.349 3.009
/A LYS 607 CB /D DA -1 C4' -0.366 4.126
/A LYS 607 CA /A MET 604 O -0.370 3.670
/A LYS 607 CD /D DA -1 C2 -0.389 4.029
/A LYS 607 CA /A LYS 603 O -0.390 3.690
27 contacts
> show sel atoms
> contacts sel test others reveal true log true select true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
10 contacts
atom1 atom2 overlap distance
/A LYS 613 CG /C DG 5 OP1 0.044 3.256
/A LYS 613 O /A ALA 617 CB 0.037 3.263
/A LYS 613 N /C DG 5 OP1 -0.019 2.679
/A LYS 613 CG /C DG 5 C5' -0.143 3.903
/A LYS 613 CG /C DG 5 P -0.199 4.179
/A LYS 613 CB /C DG 5 OP1 -0.237 3.537
/A LYS 613 CA /A THR 616 OG1 -0.261 3.601
/A LYS 613 N /C DG 5 P -0.261 4.001
/A LYS 613 O /A ALA 617 N -0.321 2.981
/A LYS 613 CA /C DG 5 OP1 -0.378 3.678
10 contacts
> select /C
612 atoms, 686 bonds, 1 model selected
> style sel stick
Changed 612 atom styles
> nucleotides sel ladder
> select /D
198 atoms, 220 bonds, 1 model selected
> nucleotides sel ladder
> nucleotides sel ladder
> nucleotides sel ladder
> save session "/Users/huihui/Desktop/Crystal structure/AsCpf1_5B43.cxs"
> select clear
> close session
> open 5xus format mmCIF fromDatabase pdb
5xus title:
Crystal structure of Lachnospiraceae bacterium ND2006 Cpf1 in complex with
crRNA and target DNA (TTTA PAM) [more info...]
Chain information for 5xus #1
---
Chain | Description
A | LbCpf1
B | crRNA
C | DNA (29-mer)
D | DNA (5'-D(*CP*GP*TP*CP*CP*TP*TP*TP*A)-3')
Non-standard residues in 5xus #1
---
EDO — 1,2-ethanediol (ethylene glycol)
MG — magnesium ion
NA — sodium ion
> select /A
9843 atoms, 9979 bonds, 5 pseudobonds, 3 models selected
> hide sel cartoons
> hide sel atoms
> delete solvent
Alignment identifier is 1.A
> select ~sel
1622 atoms, 1810 bonds, 92 pseudobonds, 3 models selected
> select clear
Destroying pre-existing alignment with identifier 1.A
Alignment identifier is 1.A
Alignment identifier is 1.B
Alignment identifier is 1.C
Alignment identifier is 1.D
> select /B
856 atoms, 953 bonds, 18 pseudobonds, 3 models selected
> show sel atoms
> show sel atoms
> hide sel atoms
> show sel atoms
> show sel cartoons
> hide sel cartoons
> select /C
589 atoms, 661 bonds, 1 model selected
> nucleotides sel ladder
> hide sel cartoons
> show sel cartoons
> show sel atoms
> nucleotides sel ladder
> select /D
177 atoms, 196 bonds, 1 model selected
> show sel cartoons
> nucleotides sel ladder
> hide sel atoms
> show sel atoms
> nucleotides sel ladder
> nucleotides sel ladder
> nucleotides sel ladder
> show sel cartoons
> show sel atoms
> show sel atoms
> hide sel atoms
> show sel atoms
> contacts sel test others reveal true log true select true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
17 contacts
atom1 atom2 overlap distance
/A LYS 591 CD /D DA -1 C2' 0.138 3.622
/A LYS 591 O /A LYS 595 CB 0.106 3.194
/A LYS 591 CB /D DA -1 C2' 0.069 3.691
/A LYS 591 CB /D DA -1 C1' -0.101 3.861
/A LYS 591 O /D DA -1 C1' -0.106 3.406
/A LYS 591 CA /D DA -1 C2' -0.114 3.874
/A LYS 591 CE /D DA -1 C2' -0.128 3.888
/A LYS 591 CG /D DA -1 C2' -0.163 3.923
/A LYS 591 C /A PRO 594 CD -0.235 3.725
/A LYS 591 CD /D DA -1 N9 -0.289 3.809
/A LYS 591 O /A PRO 594 CD -0.289 3.589
/A LYS 591 O /D DA -1 C2' -0.312 3.612
/A LYS 591 CD /D DA -1 C8 -0.316 3.956
/A LYS 591 CD /D DA -1 C1' -0.357 4.117
/A LYS 591 CG /A ASN 590 ND2 -0.369 3.889
/A LYS 591 CA /A GLY 588 O -0.391 3.691
/A LYS 591 CA /A PRO 594 CD -0.396 4.156
17 contacts
> show sel atoms
> contacts sel test others reveal true log true select true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
23 contacts
atom1 atom2 overlap distance
/A LYS 595 CB /A LYS 591 O 0.106 3.194
/A LYS 595 CE /C DA 3 N3 0.076 3.444
/A LYS 595 O /A SER 599 CB 0.022 3.278
/A LYS 595 CD /A MET 592 SD -0.081 3.731
/A LYS 595 NZ /C DA 3 C2 -0.093 3.493
/A LYS 595 CA /D DA -1 C4' -0.096 3.856
/A LYS 595 CB /D DA -1 C1' -0.125 3.885
/A LYS 595 CB /D DA -1 O4' -0.131 3.471
/A LYS 595 NZ /C DA 3 N3 -0.148 3.028
/A LYS 595 NZ /D DT -2 O2 -0.168 2.828
/A LYS 595 CE /C DA 3 C1' -0.200 3.960
/A LYS 595 CB /D DA -1 C4' -0.254 4.014
/A LYS 595 CE /D DT -2 O2 -0.276 3.576
/A LYS 595 NZ /C DA 4 O4' -0.283 2.983
/A LYS 595 CE /C DA 4 O4' -0.288 3.628
/A LYS 595 CB /A MET 592 O -0.292 3.592
/A LYS 595 CE /C DA 3 O4' -0.311 3.651
/A LYS 595 CD /D DT -2 O2 -0.347 3.647
/A LYS 595 NZ /C DA 4 C4' -0.354 3.874
/A LYS 595 CB /A MET 592 CA -0.384 4.144
/A LYS 595 NZ /C DA 4 C1' -0.393 3.913
/A LYS 595 O /A PRO 594 O -0.398 3.238
/A LYS 595 CE /C DA 2 C2 -0.399 4.039
23 contacts
> show sel atoms
> contacts sel test others reveal true log true select true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
8 contacts
atom1 atom2 overlap distance
/A LYS 601 NZ /C DA 4 P 0.113 3.627
/A LYS 601 O /A ALA 604 CB 0.058 3.241
/A LYS 601 CB /C DG 5 OP2 -0.012 3.312
/A LYS 601 NZ /C DA 4 OP2 -0.251 2.911
/A LYS 601 N /C DG 5 OP2 -0.290 2.950
/A LYS 601 CD /C DA 4 P -0.307 4.287
/A LYS 601 N /C DG 5 P -0.351 4.091
/A LYS 601 CA /C DG 5 OP2 -0.390 3.690
8 contacts
> contacts sel test others reveal true log true select true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
21 contacts
atom1 atom2 overlap distance
/C DC 0 O4' /C DC -1 C2' 0.144 3.196
/C DC 0 C5' /C DC -1 C2' 0.119 3.641
/C DC 0 N4 /C DC -1 N4 0.114 3.166
/C DC 0 C6 /C DC -1 C2' 0.086 3.554
/C DC 0 N4 /C DC -1 C4 -0.019 3.269
/C DC 0 N3 /B G 0 N1 -0.044 2.924
/C DC 0 O2 /B G 0 N2 -0.079 2.739
/C DC 0 N4 /C DC -1 C5 -0.108 3.508
/C DC 0 C2' /A SER 739 CB -0.127 3.887
/C DC 0 C2' /A GLY 740 O -0.134 3.434
/C DC 0 C5 /C DC -1 C5 -0.179 3.699
/C DC 0 C5 /C DC -1 C6 -0.187 3.707
/C DC 0 C4 /C DC -1 C4 -0.224 3.444
/C DC 0 C4' /C DC -1 C2' -0.287 4.047
/C DC 0 C2 /B G 0 N2 -0.295 3.545
/C DC 0 C4 /C DC -1 C5 -0.310 3.680
/C DC 0 C5' /C DT 1 C7 -0.319 4.079
/C DC 0 C5' /C DT 1 C5' -0.350 4.110
/C DC 0 N4 /B G 0 O6 -0.367 3.027
/C DC 0 C4' /C DT 1 C5' -0.393 4.153
/C DC 0 O2 /A PRO 799 CB -0.397 3.697
21 contacts
> show sel atoms
> show sel atoms
> save session "/Users/huihui/Desktop/Crystal structure/LbCpf1_5XUS.cxs"
> close session
> open "/Users/huihui/Desktop/Crystal structure/AsCpf1_5B43.cxs" format
session
opened ChimeraX session
> contacts sel test others reveal true log true select true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
40 contacts
atom1 atom2 overlap distance
/C DC 0 N3 /B G 0 N1 0.231 2.649
/C DC 0 O4' /C DC -1 C2' 0.172 3.168
/C DC 0 O2 /B G 0 N2 0.155 2.505
/C DC 0 C1' /A GLN 784 NE2 0.134 3.386
/C DC 0 C6 /C DC -1 C2' 0.104 3.536
/C DC 0 C2' /A ASN 782 CB 0.084 3.676
/C DC 0 N4 /C DC -1 N4 0.059 3.221
/C DC 0 C5' /C DC -1 C2' 0.019 3.741
/C DC 0 C2' /A GLY 783 O -0.022 3.322
/C DC 0 C2 /B G 0 N2 -0.027 3.277
/C DC 0 C4' /A GLN 784 CB -0.045 3.805
/C DC 0 C5 /C DC -1 C5 -0.061 3.581
/C DC 0 N4 /C DC -1 C5 -0.070 3.470
/C DC 0 C5 /C DC -1 C6 -0.072 3.592
/C DC 0 N4 /C DC -1 C4 -0.106 3.356
/C DC 0 C2' /A PRO 874 CG -0.171 3.931
/C DC 0 C5' /C DT 1 C5' -0.217 3.977
/C DC 0 O2 /A PRO 874 CB -0.219 3.519
/C DC 0 C2 /B G 0 N1 -0.220 3.470
/C DC 0 C4 /C DC -1 C5 -0.223 3.593
/C DC 0 N3 /B G 0 C2 -0.224 3.474
/C DC 0 N4 /B G 0 O6 -0.225 2.885
/C DC 0 C4 /C DC -1 C4 -0.231 3.451
/C DC 0 N3 /B G 0 C6 -0.286 3.536
/C DC 0 N4 /B G 0 N1 -0.293 3.573
/C DC 0 C4' /C DC -1 C2' -0.303 4.063
/C DC 0 C4 /B G 0 N1 -0.313 3.563
/C DC 0 O3' /A GLY 783 CA -0.321 3.661
/C DC 0 C1' /A GLN 784 CB -0.332 4.092
/C DC 0 C5' /C DT 1 C6 -0.333 3.973
/C DC 0 C5' /C DT 1 O5' -0.338 3.678
/C DC 0 C4' /C DT 1 C5' -0.353 4.113
/C DC 0 C5' /C DT 1 C7 -0.359 4.119
/C DC 0 O4' /A GLN 784 NE2 -0.361 3.061
/C DC 0 N4 /B G 0 C6 -0.363 3.613
/C DC 0 O4' /A GLN 784 CB -0.368 3.708
/C DC 0 O3' /A GLY 783 N -0.377 3.077
/C DC 0 O2 /B G 0 C2 -0.389 3.419
/C DC 0 O3' /A ASN 782 CB -0.395 3.735
/C DC 0 C6 /C DC -1 C3' -0.400 4.040
40 contacts
> show sel atoms
> show sel atoms
> save session "/Users/huihui/Desktop/Crystal structure/AsCpf1_5B43.cxs"
> close session
> open "/Users/huihui/Desktop/Crystal structure/FnCpf1_6I1K.cxs" format
session
opened ChimeraX session
> contacts sel test others reveal true log true select true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
21 contacts
atom1 atom2 overlap distance
/C DT -1 C5' /C DC -2 C2' 0.201 3.559
/C DT -1 O4' /C DC -2 C2' 0.173 3.167
/C DT -1 O3' /A GLY 826 CA 0.127 3.213
/C DT -1 C4' /A GLU 827 CG 0.107 3.653
/C DT -1 N3 /B A 1 N1 0.092 2.788
/C DT -1 C6 /C DC -2 C2' 0.083 3.557
/C DT -1 N3 /B A 1 C2 -0.001 3.401
/C DT -1 C2' /A ASN 825 CB -0.036 3.796
/C DT -1 O3' /A GLY 826 N -0.087 2.787
/C DT -1 C7 /C DC -2 C6 -0.108 3.748
/C DT -1 C7 /C DC -2 C5 -0.125 3.765
/C DT -1 O2 /A PRO 883 CB -0.146 3.446
/C DT -1 C2' /A GLY 826 N -0.206 3.726
/C DT -1 C4' /C DC -2 C2' -0.213 3.973
/C DT -1 C4 /B A 1 N1 -0.218 3.468
/C DT -1 O4 /B A 1 N1 -0.251 3.311
/C DT -1 C5' /C DT 0 C5' -0.262 4.022
/C DT -1 C3' /A GLY 826 N -0.281 3.801
/C DT -1 P /C EDO 101 O1 -0.339 3.899
/C DT -1 C4 /C DC -2 N3 -0.382 3.632
/C DT -1 C4' /C DT 0 C5' -0.396 4.156
21 contacts
> show sel atoms
> hide sel atoms
> show sel atoms
> save session "/Users/huihui/Desktop/Crystal structure/FnCpf1_6I1K.cxs"
> close session
> open 5MGA
Summary of feedback from opening 5MGA fetched from pdb
---
note | Fetching compressed mmCIF 5mga from
http://files.rcsb.org/download/5mga.cif
5mga title:
Structure of the Cpf1 endonuclease R-loop complex after DNA cleavage [more
info...]
Chain information for 5mga #1
---
Chain | Description
A | CRISPR-associated endonuclease Cpf1
B | RNA (40-mer)
C | DNA (26-mer)
D | DNA (5'-D(P*CP*GP*TP*TP*ap*GP*ap*GP*ap*ap*GP*T)-3')
Non-standard residues in 5mga #1
---
MG — magnesium ion
> select /A
9709 atoms, 9769 bonds, 18 pseudobonds, 2 models selected
> hide sel atoms
> hide sel cartoons
> select /B
858 atoms, 947 bonds, 17 pseudobonds, 2 models selected
> hide sel cartoons
> select /C
532 atoms, 591 bonds, 1 model selected
> nucleotides sel ladder
> select /D
252 atoms, 279 bonds, 1 model selected
> nucleotides sel ladder
> select clear
Alignment identifier is 1.A
Alignment identifier is 1.B
Alignment identifier is 1.C
Alignment identifier is 1.D
> show sel cartoons
> save session "/Users/huihui/Desktop/Crystal structure/FnCpf1_5MGA.cxs"
Traceback (most recent call last):
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 276, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molobject.py", line 631, in take_snapshot
data = {'structure': self.structure,
File "cymol.pyx", line 1378, in
chimerax.atomic.cymol.CyResidue.structure.__get__
RuntimeError: Residue already deleted
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 794, in save
session.save(output, version=version, include_maps=include_maps)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 556, in save
mgr.discovery(self._state_containers)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in discovery
self.processed[key] = self.process(obj, parents)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 278, in process
msg = 'Error while saving session data for %s: %s' % (_obj_chain(parents,
obj), e)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 199, in _obj_chain
if hasattr(o, 'name'):
File "cymol.pyx", line 1082, in chimerax.atomic.cymol.CyResidue.name.__get__
RuntimeError: Residue already deleted
RuntimeError: Residue already deleted
File "cymol.pyx", line 1082, in chimerax.atomic.cymol.CyResidue.name.__get__
See log for complete Python traceback.
Traceback (most recent call last):
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 276, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molobject.py", line 631, in take_snapshot
data = {'structure': self.structure,
File "cymol.pyx", line 1378, in
chimerax.atomic.cymol.CyResidue.structure.__get__
RuntimeError: Residue already deleted
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 882, in <lambda>
save_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_save_cb(sess))
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 612, in file_save_cb
self.save_dialog.display(self, session)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/save_dialog.py", line 139, in display
fmt.save(session, filename)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 1089, in save
run(session, cmd)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2837, in run
result = ci.function(session, **kw_args)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 981, in save_session
save(session, filename, **kw)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/save.py", line 61, in save
fmt.export(session, filename, fmt.nicknames[0], **kw)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/io.py", line 220, in export
result = self.export_func(session, path, **kw)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 794, in save
session.save(output, version=version, include_maps=include_maps)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 556, in save
mgr.discovery(self._state_containers)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in discovery
self.processed[key] = self.process(obj, parents)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 278, in process
msg = 'Error while saving session data for %s: %s' % (_obj_chain(parents,
obj), e)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 199, in _obj_chain
if hasattr(o, 'name'):
File "cymol.pyx", line 1082, in chimerax.atomic.cymol.CyResidue.name.__get__
RuntimeError: Residue already deleted
RuntimeError: Residue already deleted
File "cymol.pyx", line 1082, in chimerax.atomic.cymol.CyResidue.name.__get__
See log for complete Python traceback.
> save session "/Users/huihui/Desktop/Crystal structure/FnCpf1_5MGA.cxs"
Traceback (most recent call last):
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 276, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molobject.py", line 631, in take_snapshot
data = {'structure': self.structure,
File "cymol.pyx", line 1378, in
chimerax.atomic.cymol.CyResidue.structure.__get__
RuntimeError: Residue already deleted
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 794, in save
session.save(output, version=version, include_maps=include_maps)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 556, in save
mgr.discovery(self._state_containers)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in discovery
self.processed[key] = self.process(obj, parents)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 278, in process
msg = 'Error while saving session data for %s: %s' % (_obj_chain(parents,
obj), e)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 199, in _obj_chain
if hasattr(o, 'name'):
File "cymol.pyx", line 1082, in chimerax.atomic.cymol.CyResidue.name.__get__
RuntimeError: Residue already deleted
RuntimeError: Residue already deleted
File "cymol.pyx", line 1082, in chimerax.atomic.cymol.CyResidue.name.__get__
See log for complete Python traceback.
Traceback (most recent call last):
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 276, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molobject.py", line 631, in take_snapshot
data = {'structure': self.structure,
File "cymol.pyx", line 1378, in
chimerax.atomic.cymol.CyResidue.structure.__get__
RuntimeError: Residue already deleted
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 882, in <lambda>
save_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_save_cb(sess))
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 612, in file_save_cb
self.save_dialog.display(self, session)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/save_dialog.py", line 139, in display
fmt.save(session, filename)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 1089, in save
run(session, cmd)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2837, in run
result = ci.function(session, **kw_args)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 981, in save_session
save(session, filename, **kw)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/save.py", line 61, in save
fmt.export(session, filename, fmt.nicknames[0], **kw)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/io.py", line 220, in export
result = self.export_func(session, path, **kw)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 794, in save
session.save(output, version=version, include_maps=include_maps)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 556, in save
mgr.discovery(self._state_containers)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in discovery
self.processed[key] = self.process(obj, parents)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 278, in process
msg = 'Error while saving session data for %s: %s' % (_obj_chain(parents,
obj), e)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 199, in _obj_chain
if hasattr(o, 'name'):
File "cymol.pyx", line 1082, in chimerax.atomic.cymol.CyResidue.name.__get__
RuntimeError: Residue already deleted
RuntimeError: Residue already deleted
File "cymol.pyx", line 1082, in chimerax.atomic.cymol.CyResidue.name.__get__
See log for complete Python traceback.
> save session "/Users/huihui/Desktop/Crystal structure/FnCpf1_cut.cxs"
Traceback (most recent call last):
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 276, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molobject.py", line 631, in take_snapshot
data = {'structure': self.structure,
File "cymol.pyx", line 1378, in
chimerax.atomic.cymol.CyResidue.structure.__get__
RuntimeError: Residue already deleted
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 794, in save
session.save(output, version=version, include_maps=include_maps)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 556, in save
mgr.discovery(self._state_containers)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in discovery
self.processed[key] = self.process(obj, parents)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 278, in process
msg = 'Error while saving session data for %s: %s' % (_obj_chain(parents,
obj), e)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 199, in _obj_chain
if hasattr(o, 'name'):
File "cymol.pyx", line 1082, in chimerax.atomic.cymol.CyResidue.name.__get__
RuntimeError: Residue already deleted
RuntimeError: Residue already deleted
File "cymol.pyx", line 1082, in chimerax.atomic.cymol.CyResidue.name.__get__
See log for complete Python traceback.
Traceback (most recent call last):
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 276, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molobject.py", line 631, in take_snapshot
data = {'structure': self.structure,
File "cymol.pyx", line 1378, in
chimerax.atomic.cymol.CyResidue.structure.__get__
RuntimeError: Residue already deleted
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 882, in <lambda>
save_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_save_cb(sess))
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 612, in file_save_cb
self.save_dialog.display(self, session)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/save_dialog.py", line 139, in display
fmt.save(session, filename)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 1089, in save
run(session, cmd)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2837, in run
result = ci.function(session, **kw_args)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 981, in save_session
save(session, filename, **kw)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/save.py", line 61, in save
fmt.export(session, filename, fmt.nicknames[0], **kw)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/io.py", line 220, in export
result = self.export_func(session, path, **kw)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 794, in save
session.save(output, version=version, include_maps=include_maps)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 556, in save
mgr.discovery(self._state_containers)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in discovery
self.processed[key] = self.process(obj, parents)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 278, in process
msg = 'Error while saving session data for %s: %s' % (_obj_chain(parents,
obj), e)
File
"/private/var/folders/1w/65vj632534j7dt1dkmzq_hvh0000gp/T/AppTranslocation/C92CF23C-C834-44BE-8FC0-B2BDDD650D86/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 199, in _obj_chain
if hasattr(o, 'name'):
File "cymol.pyx", line 1082, in chimerax.atomic.cymol.CyResidue.name.__get__
RuntimeError: Residue already deleted
RuntimeError: Residue already deleted
File "cymol.pyx", line 1082, in chimerax.atomic.cymol.CyResidue.name.__get__
See log for complete Python traceback.
OpenGL version: 4.1 INTEL-12.10.12
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.
Change History (3)
comment:1 by , 6 years ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Better session debugging info |
| Type: | defect → enhancement |
comment:2 by , 6 years ago
Yes, that code was invoked, but got an error when trying to print the object stack. Will repr(o) where o is a deleted Residue work?
comment:3 by , 6 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
I think it must, or else the "RuntimeError: Residue already deleted" wouldn't work.
Note:
See TracTickets
for help on using tickets.
Hi Greg,
--Eric