![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 years ago
Closed 4 years ago
#4771 closed defect (fixed)
4v88: acceptor has no neighbors
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Analysis | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-5.4.115-1.el8.elrepo.x86_64-x86_64-with-glibc2.14
ChimeraX Version: 1.2 (2021-04-27 05:33:30 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.2 (2021-04-27)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /yonath_group/disha/Giardia_DH_AR_AB/Final_model_map/chimera/new/Inter_subunit/B5.cxs
> format session
Log from Mon Jun 14 15:26:28 2021UCSF ChimeraX version: 1.2 (2021-04-27)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /yonath_group/disha/Giardia_DH_AR_AB/Final_model_map/chimera/new/Inter_subunit/B4.cxs
> format session
Log from Mon Jun 14 14:22:23 2021UCSF ChimeraX version: 1.2 (2021-04-27)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /yonath_group/disha/Giardia_DH_AR_AB/Final_model_map/chimera/18S_rRNA.cxs
Log from Tue May 18 12:10:33 2021UCSF ChimeraX version: 1.2 (2021-04-27)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /yonath_group/disha/Giardia_DH_AR_AB/Final_model_map/chimera/5SrRNA.cxs
> format session
Log from Tue May 18 11:08:58 2021UCSF ChimeraX version: 1.2 (2021-04-27)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /yonath_group/disha/Giardia_DH_AR_AB/Final_model_map/60s_GL_afterRS12_aligned_new_map_real_space_refined.pdb
> format pdb
Chain information for 60s_GL_afterRS12_aligned_new_map_real_space_refined.pdb
#1
---
Chain | Description
1 | No description available
3 | No description available
4 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
o | No description available
p | No description available
> open /yonath_group/disha/Downloads/4ug0.cif
4ug0.cif title:
Structure of the human 80S ribosome [more info...]
Chain information for 4ug0.cif #2
---
Chain | Description
L5 | 28S ribosomal RNA
L7 | 5S ribosomal RNA
L8 | 5.8S ribosomal RNA
LA | 60S ribosomal protein L8
LB | 60S ribosomal protein L3
LC | 60S ribosomal protein L4
LD | 60S ribosomal protein L5
LE | 60S ribosomal protein L6
LF | 60S ribosomal protein L7
LG | 60S ribosomal protein L7A
LH | 60S ribosomal protein L9
LI | 60S ribosomal protein L10-like
LJ | 60S ribosomal protein L11
LL | 60S ribosomal protein L13
LM | 60S ribosomal protein L14
LN | 60S ribosomal protein L15
LO | 60S ribosomal protein L13A
LP | 60S ribosomal protein L17
LQ | 60S ribosomal protein L18
LR | 60S ribosomal protein L19
LS | 60S ribosomal protein L18A
LT | 60S ribosomal protein L21
LU | 60S ribosomal protein L22
LV | 60S ribosomal protein L23
LW | 60S ribosomal protein L24
LX | 60S ribosomal protein L23A
LY | 60S ribosomal protein L26
LZ | 60S ribosomal protein L27
La | 60S ribosomal protein L27A
Lb | 60S ribosomal protein L29
Lc | 60S ribosomal protein L30
Ld | 60S ribosomal protein L31
Le | 60S ribosomal protein L32
Lf | 60S ribosomal protein L35A
Lg | 60S ribosomal protein L34
Lh | 60S ribosomal protein L35
Li | 60S ribosomal protein L36
Lj | 60S ribosomal protein L37
Lk | 60S ribosomal protein L38
Ll | 60S ribosomal protein L39
Lm | ubiquitin-60S ribosomal protein L40
Ln | 60S ribosomal protein L41
Lo | 60S ribosomal protein L36A
Lp | 60S ribosomal protein L37A
Lr | 60S ribosomal protein L28
Lz | 60S ribosomal protein L10A
S2 | 18S ribosomal RNA
S6 | human initiator met-TRNA-I
SA | 40S ribosomal protein sa
SB | 40S ribosomal protein S3A
SC | 40S ribosomal protein S2
SD | 40S ribosomal protein S3
SE | 40S ribosomal protein S4, X isoform
SF | 40S ribosomal protein S5
SG | 40S ribosomal protein S6
SH | 40S ribosomal protein S7
SI | 40S ribosomal protein S8
SJ | 40S ribosomal protein S9
SK | 40S ribosomal protein S10
SL | 40S ribosomal protein S11
SM | 40S ribosomal protein
SN | 40S ribosomal protein S13
SO | 40S ribosomal protein S14
SP | 40S ribosomal protein S15
SQ | 40S ribosomal protein S16
SR | 40S ribosomal protein S17-like
SS | 40S ribosomal protein S18
ST | 40S ribosomal protein S19
SU | 40S ribosomal protein S20
SV | 40S ribosomal protein S21
SW | 40S ribosomal protein S15A
SX | 40S ribosomal protein S23
SY | 40S ribosomal protein S24
SZ | 40S ribosomal protein S25
Sa | 40S ribosomal protein S26
Sb | 40S ribosomal protein S27
Sc | 40S ribosomal protein S28
Sd | 40S ribosomal protein S29
Se | 40S ribosomal protein S30
Sf | ubiquitin-40S ribosomal protein S27A
Sg | guanine nucleotide-binding protein subunit β-2-like 1
Non-standard residues in 4ug0.cif #2
---
MG — magnesium ion
ZN — zinc ion
> select #1/4, #2/L8
Expected an objects specifier or a keyword
> select #1/4
2958 atoms, 3304 bonds, 2 pseudobonds, 138 residues, 2 models selected
> select add #2/L8
6274 atoms, 7005 bonds, 79 pseudobonds, 296 residues, 4 models selected
> select ~ sel
316610 atoms, 339638 bonds, 4254 pseudobonds, 25972 residues, 6 models
selected
> hide sel atoms
> hide sel cartoons
> select ~ sel
6274 atoms, 7005 bonds, 79 pseudobonds, 296 residues, 4 models selected
> hide sel atoms
> show sel cartoons
> set bgColor white
> mmaker #2/L8 to #1/4 matrix Nucleic showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 60s_GL_afterRS12_aligned_new_map_real_space_refined.pdb, chain 4
(#1) with 4ug0.cif, chain L8 (#2), sequence alignment score = 254.8
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1:
60s_GL_afterRS12_aligned_new_map_real_space_refined.pdb #1/4, 4ug0.cif #2/L8
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 75 pruned atom pairs is 1.063 angstroms; (across all 133 pairs:
6.889)
> select clear
> select #1/4
2958 atoms, 3304 bonds, 2 pseudobonds, 138 residues, 2 models selected
> color (#!1 & sel) red
> select #2/L8
3316 atoms, 3701 bonds, 77 pseudobonds, 158 residues, 2 models selected
> color (#!2 & sel) cornflower blue
> select clear
> save
> /yonath_group/disha/Giardia_DH_AR_AB/Final_model_map/chimera/5_8_rRNA.cxs
> save /yonath_group/disha/Desktop/image1.png supersample 3
> save
> /yonath_group/disha/Giardia_DH_AR_AB/Final_model_map/chimera/5_8S_HS_GL.png
> supersample 3
> select #1/1
52552 atoms, 58724 bonds, 68 pseudobonds, 2446 residues, 2 models selected
> show sel cartoons
> select ~ sel
270332 atoms, 287919 bonds, 4265 pseudobonds, 23822 residues, 6 models
selected
> hide sel cartoons
> select #2/L5
80333 atoms, 89642 bonds, 2751 pseudobonds, 3925 residues, 4 models selected
> show sel cartoons
> style sel sphere
Changed 80333 atom styles
> hide sel atoms
> show sel atoms
> undo
> ui mousemode right "mark surface"
> show sel surfaces
> transparency (#!2 & sel) 40
> transparency (#!2 & sel) 60
> color (#!2 & sel) cornflower blue
> select #1/1
52552 atoms, 58724 bonds, 68 pseudobonds, 2446 residues, 2 models selected
> show sel surfaces
> color (#!1 & sel) red
> select clear
> transparency 30
> transparency 60
> select clear
> transparency 30
> hide surfaces
> show surfaces
> undo
> hide surfaces
> select #1/1
52552 atoms, 58724 bonds, 68 pseudobonds, 2446 residues, 2 models selected
> select add #2/L5
132885 atoms, 148366 bonds, 2819 pseudobonds, 6371 residues, 7 models selected
> show sel surfaces
> surface style #1.2#2.4 dot
> surface style #1.2#2.4 mesh
> hide sel surfaces
> select clear
> open /yonath_group/disha/Downloads/7k00.cif
7k00.cif title:
Structure of the Bacterial Ribosome at 2 Angstrom Resolution [more info...]
Chain information for 7k00.cif #3
---
Chain | Description
0 | 50S ribosomal protein L33
1 | 50S ribosomal protein L34
2 | 50S ribosomal protein L35
3 | 50S ribosomal protein L36
4 | 50S ribosomal protein L31
5 | E-site tRNA
A | 16S rRNA
B | 30S ribosomal protein S2
C | 30S ribosomal protein S3
D | 30S ribosomal protein S4
E | 30S ribosomal protein S5
F | 30S ribosomal protein S6
G | 30S ribosomal protein S7
H | 30S ribosomal protein S8
I | 30S ribosomal protein S9
J | 30S ribosomal protein S10
K | 30S ribosomal protein S11
L | 30S ribosomal protein S12
M | 30S ribosomal protein S13
N | 30S ribosomal protein S14
O | 30S ribosomal protein S15
P | 30S ribosomal protein S16
Q | 30S ribosomal protein S17
R | 30S ribosomal protein S18
S | 30S ribosomal protein S19
T | 30S ribosomal protein S20
U | 30S ribosomal protein S21
X | mRNA
Y | A-site tRNA-val
Z | P-site tRNA-fMet
a | 23S rRNA
b | 5S rRNA
c | 50S ribosomal protein L2
d | 50S ribosomal protein L3
e | 50S ribosomal protein L4
f | 50S ribosomal protein L5
g | 50S ribosomal protein L6
h | 50S ribosomal protein L9
i | 50S ribosomal protein L13
j | 50S ribosomal protein L14
k | 50S ribosomal protein L15
l | 50S ribosomal protein L16
m | 50S ribosomal protein L17
n | 50S ribosomal protein L18
o | 50S ribosomal protein L19
p | 50S ribosomal protein L20
q | 50S ribosomal protein L21
r | 50S ribosomal protein L22
s | 50S ribosomal protein L23
t | 50S ribosomal protein L24
u | 50S ribosomal protein L25
v | 50S ribosomal protein L27
w | 50S ribosomal protein L28
x | 50S ribosomal protein L29
y | 50S ribosomal protein L30
z | 50S ribosomal protein L32
Non-standard residues in 7k00.cif #3
---
MG — magnesium ion
MS6 — (2S)-2-amino-4-(methylsulfanyl)butane-1-thiol
PAR — paromomycin (paromomycin I; amminosidin; catenulin; crestomycin;
monomycin A; neomycin E)
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))
SPM — spermine
ZN — zinc ion
> select #3
149338 atoms, 154090 bonds, 6235 pseudobonds, 17719 residues, 4 models
selected
> hide sel atoms
> show sel cartoons
> hide sel cartoons
> select #3/a
63520 atoms, 66364 bonds, 3884 pseudobonds, 7004 residues, 4 models selected
> show sel cartoons
> color (#!3 & sel) forest green
> mmaker #3/a to #1/1 matrix Nucleic showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 60s_GL_afterRS12_aligned_new_map_real_space_refined.pdb, chain 1
(#1) with 7k00.cif, chain a (#3), sequence alignment score = 3722
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2:
60s_GL_afterRS12_aligned_new_map_real_space_refined.pdb #1/1, 7k00.cif #3/a
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 727 pruned atom pairs is 1.346 angstroms; (across all 2280 pairs:
22.997)
> select clear
> hide #!3 models
> save /yonath_group/disha/Desktop/image2.png supersample 3
> save
> /yonath_group/disha/Giardia_DH_AR_AB/Final_model_map/chimera/28S_HS_GL.png
> supersample 3
> show #!3 models
> hide #!2 models
> save
> /yonath_group/disha/Giardia_DH_AR_AB/Final_model_map/chimera/28S_EC_GL.png
> supersample 3
> save
> /yonath_group/disha/Giardia_DH_AR_AB/Final_model_map/chimera/23S_rRNA.cxs
> select #3/a
63520 atoms, 66364 bonds, 3884 pseudobonds, 7004 residues, 4 models selected
> hide sel cartoons
> select #1/3
2501 atoms, 2797 bonds, 117 residues, 1 model selected
> select add #2/L7
5064 atoms, 5655 bonds, 109 pseudobonds, 242 residues, 5 models selected
> select ~ sel
467158 atoms, 495078 bonds, 10459 pseudobonds, 43745 residues, 10 models
selected
> hide sel & #!1,3 cartoons
> select ~ sel
5064 atoms, 5655 bonds, 109 pseudobonds, 242 residues, 4 models selected
> show sel & #!1 cartoons
> show #!2 models
> select ~ sel
467158 atoms, 495078 bonds, 10459 pseudobonds, 43745 residues, 10 models
selected
> hide sel cartoons
> select #2/L7
2563 atoms, 2858 bonds, 109 pseudobonds, 125 residues, 3 models selected
> show sel cartoons
> select clear
> select #1/3
2501 atoms, 2797 bonds, 117 residues, 1 model selected
> select #1/3
2501 atoms, 2797 bonds, 117 residues, 1 model selected
> color (#!1 & sel) red
> select #2/L7
2563 atoms, 2858 bonds, 109 pseudobonds, 125 residues, 3 models selected
> color (#!2 & sel) forest green
> select clear
> save
> /yonath_group/disha/Giardia_DH_AR_AB/Final_model_map/chimera/5S_EC_GL.png
> supersample 3
> save
> /yonath_group/disha/Giardia_DH_AR_AB/Final_model_map/chimera/5S_HS_GL.png
> supersample 3
> save /yonath_group/disha/Giardia_DH_AR_AB/Final_model_map/chimera/5SrRNA.cxs
——— End of log from Tue May 18 11:08:58 2021 ———
opened ChimeraX session
> open
> /yonath_group/disha/Giardia_DH_AR_AB/Phenix/50S_realspacerefinement_GL_TV/50S_GL_FR_initial_real_space_refined.pdb
Chain information for 50S_GL_FR_initial_real_space_refined.pdb #4
---
Chain | Description
1 | No description available
3 | No description available
4 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
o | No description available
p | No description available
> select #4
106616 atoms, 114610 bonds, 76 pseudobonds, 8687 residues, 2 models selected
> hide sel atoms
> select #4/3
2501 atoms, 2797 bonds, 117 residues, 1 model selected
> show sel cartoons
> mmaker #4/3 to #1/3 matrix Nucleic showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 60s_GL_afterRS12_aligned_new_map_real_space_refined.pdb, chain 3
(#1) with 50S_GL_FR_initial_real_space_refined.pdb, chain 3 (#4), sequence
alignment score = 464
Alignment identifier is 3
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3
Hiding conservation header for alignment 3
Chains used in RMSD evaluation for alignment 3:
60s_GL_afterRS12_aligned_new_map_real_space_refined.pdb #1/3,
50S_GL_FR_initial_real_space_refined.pdb #4/3
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3
RMSD between 10 pruned atom pairs is 1.331 angstroms; (across all 116 pairs:
9.938)
> color sel dim gray
> select clear
> hide #!2 models
> mmaker #4/3 to #1/3 matrix Nucleic showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 60s_GL_afterRS12_aligned_new_map_real_space_refined.pdb, chain 3
(#1) with 50S_GL_FR_initial_real_space_refined.pdb, chain 3 (#4), sequence
alignment score = 464
Alignment identifier is 4
Showing conservation header ("seq_conservation" residue attribute) for
alignment 4
Hiding conservation header for alignment 4
Chains used in RMSD evaluation for alignment 4:
60s_GL_afterRS12_aligned_new_map_real_space_refined.pdb #1/3,
50S_GL_FR_initial_real_space_refined.pdb #4/3
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 4
RMSD between 10 pruned atom pairs is 1.331 angstroms; (across all 116 pairs:
9.938)
> open /yonath_group/disha/Downloads/4v88.cif
Summary of feedback from opening /yonath_group/disha/Downloads/4v88.cif
---
warnings | Ignoring microheterogeneity for label_seq_id 3 in chain
Ignoring microheterogeneity for label_seq_id 4 in chain DO
Ignoring microheterogeneity for label_seq_id 11 in chain DO
Ignoring microheterogeneity for label_seq_id 13 in chain DO
Ignoring microheterogeneity for label_seq_id 16 in chain DO
35 messages similar to the above omitted
Atom OP1 has no neighbors to form bonds with according to residue template for
G /A5:420
Atom OP2 has no neighbors to form bonds with according to residue template for
G /A5:420
4v88.cif title:
The structure of the eukaryotic ribosome at 3.0 A resolution. [more info...]
Chain information for 4v88.cif #5
---
Chain | Description
A1 A5 | 25S rRNA
A2 | 18S ribosomal RNA
A3 A7 | 5S rRNA
A4 A8 | 5.8S rRNA
A6 | 18S rRNA
AA CA | 40S ribosomal protein S0-A
AB CB | 40S ribosomal protein S1-A
AC CC | 40S ribosomal protein S2
AD CD | 40S ribosomal protein S3
AE CE | 40S ribosomal protein S4-A
AF CF | 40S ribosomal protein S5
AG CG | 40S ribosomal protein S6-A
AH CH | 40S ribosomal protein S7-A
AI CI | 40S ribosomal protein S8-A
AJ CJ | 40S ribosomal protein S9-A
AK CK | 40S ribosomal protein S10-A
AL CL | 40S ribosomal protein S11-A
AM CM | 40S ribosomal protein S12
AN CN | 40S ribosomal protein S13
AO CO | 40S ribosomal protein S14-A
AP CP | 40S ribosomal protein S15
AQ CQ | 40S ribosomal protein S16-A
AR CR | 40S ribosomal protein S17-A
AS CS | 40S ribosomal protein S18-A
AT CT | 40S ribosomal protein S19-A
AU CU | 40S ribosomal protein S20
AV CV | 40S ribosomal protein S21-A
AW CW | 40S ribosomal protein S22-A
AX CX | 40S ribosomal protein S23-A
AY CY | 40S ribosomal protein S24-A
AZ CZ | 40S ribosomal protein S25-A
Aa Ca | 40S ribosomal protein S26-A
Ab Cb | 40S ribosomal protein S27-A
Ac Cc | 40S ribosomal protein S28-A
Ad Cd | 40S ribosomal protein S29-A
Ae Ce | 40S ribosomal protein S30-A
Af Cf | 40S ribosomal protein S31
Ag Cg | Guanine nucleotide-binding protein subunit beta-like protein (ASC1,
RACK1)
Ah | Suppressor protein STM1
BA DA | 60S ribosomal protein L2-A
BB DB | 60S ribosomal protein L3
BC DC | 60S ribosomal protein L4-A
BD DD | 60S ribosomal protein L5
BE DE | 60S ribosomal protein L6-A
BF DF | 60S ribosomal protein L7-A
BG DG | 60S ribosomal protein L8-A
BH DH | 60S ribosomal protein L9-A
BI DI | 60S ribosomal protein L10
BJ DJ | 60S ribosomal protein L11-A
BL DL | 60S ribosomal protein L13-A
BM DM | 60S ribosomal protein L14-A
BN DN | 60S ribosomal protein L15-A
BO DO | 60S ribosomal protein L16-A, 60S ribosomal protein L16-B
BP DP | 60S ribosomal protein L17-A
BQ DQ | 60S ribosomal protein L18-A
BR DR | 60S ribosomal protein L19-A
BS DS | 60S ribosomal protein L20-A
BT DT | 60S ribosomal protein L21-A
BU DU | 60S ribosomal protein L22-A
BV DV | 60S ribosomal protein L23-A
BW DW | 60S ribosomal protein L24-A
BX DX | 60S ribosomal protein L25
BY DY | 60S ribosomal protein L26-A
BZ DZ | 60S ribosomal protein L27-A
Ba Da | 60S ribosomal protein L28
Bb Db | 60S ribosomal protein L29
Bc Dc | 60S ribosomal protein L30
Bd Dd | 60S ribosomal protein L31-A
Be De | 60S ribosomal protein L32
Bf Df | 60S ribosomal protein L33-A
Bg Dg | 60S ribosomal protein L34-A
Bh Dh | 60S ribosomal protein L35-A
Bi Di | 60S ribosomal protein L36-A
Bj Dj | 60S ribosomal protein L37-A
Bk Dk | 60S ribosomal protein L38
Bl Dl | 60S ribosomal protein L39
Bm Dm | 60S ribosomal protein L40
Bn Dn | 60S ribosomal protein L41-A
Bo Do | 60S ribosomal protein L42-A
Bp Dp | 60S ribosomal protein L43-A
Ch | Suppressor protein STM1
DK | Ribosomal protein L12
Dq | 60S acidic ribosomal protein P0
Dr | Ribosomal protein P1 α
Ds | Ribosomal protein P2 β
Non-standard residues in 4v88.cif #5
---
MG — magnesium ion
OHX — osmium (III) hexammine (osmium(6+) hexaazanide)
ZN — zinc ion
4v88.cif mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
Associated 4v88.cif chain DK to 4ug0.cif, chain L8 with 0 mismatches
Associated 4v88.cif chain Dr to
60s_GL_afterRS12_aligned_new_map_real_space_refined.pdb, chain 4 with 0
mismatches
Associated 4v88.cif chain Ds to
60s_GL_afterRS12_aligned_new_map_real_space_refined.pdb, chain 4 with 0
mismatches
Chains used in RMSD evaluation for alignment 1:
60s_GL_afterRS12_aligned_new_map_real_space_refined.pdb #1/4, 4ug0.cif #2/L8,
4v88.cif #5/DK
Associated 4v88.cif chain DK to
60s_GL_afterRS12_aligned_new_map_real_space_refined.pdb, chain 1 with 0
mismatches
Associated 4v88.cif chain Dr to
60s_GL_afterRS12_aligned_new_map_real_space_refined.pdb, chain 1 with 0
mismatches
Associated 4v88.cif chain Ds to
60s_GL_afterRS12_aligned_new_map_real_space_refined.pdb, chain 1 with 0
mismatches
Chains used in RMSD evaluation for alignment 2:
60s_GL_afterRS12_aligned_new_map_real_space_refined.pdb #1/1, 7k00.cif #3/a,
4v88.cif #5/DK
> select #5
413613 atoms, 431464 bonds, 19219 pseudobonds, 36905 residues, 4 models
selected
> hide sel atoms
> select #5/A7
2696 atoms, 2883 bonds, 215 pseudobonds, 160 residues, 3 models selected
> show sel cartoons
> undo
> show sel cartoons
> ui tool show "Color Actions"
> color sel rebecca purple
> select clear
> mmaker #5/A7 to #1/3 matrix Nucleic showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 60s_GL_afterRS12_aligned_new_map_real_space_refined.pdb, chain 3
(#1) with 4v88.cif, chain A7 (#5), sequence alignment score = 188.8
Alignment identifier is 3
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3
Hiding conservation header for alignment 3
Chains used in RMSD evaluation for alignment 3:
60s_GL_afterRS12_aligned_new_map_real_space_refined.pdb #1/3, 4v88.cif #5/A7
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3
RMSD between 67 pruned atom pairs is 1.107 angstroms; (across all 112 pairs:
3.983)
> hide #!4 models
> save /yonath_group/disha/Giardia_DH_AR_AB/Final_model_map/chimera/5SrRNA.cxs
> save
> /yonath_group/disha/Giardia_DH_AR_AB/Final_model_map/chimera/5S_SC_GL.png
> width 1194 height 813 supersample 3
> show #!2 models
> save
> /yonath_group/disha/Giardia_DH_AR_AB/Final_model_map/chimera/5_8S_HS_SC_GL.png
> width 1194 height 813 supersample 3
> open
> /yonath_group/disha/Giardia_DH_AR_AB/Final_model_map/Giardia_SSU_real_space_refined.pdb
Chain information for Giardia_SSU_real_space_refined.pdb #6
---
Chain | Description
2 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
n | No description available
> select all
1050704 atoms, 1108891 bonds, 29961 pseudobonds, 94695 residues, 18 models
selected
> hide sel & #!1-3,5-6 cartoons
> hide sel & #!1-3,5-6 atoms
> select 6/2
Expected an objects specifier or a keyword
> select #6/2
28472 atoms, 31812 bonds, 48 pseudobonds, 1325 residues, 2 models selected
> show sel cartoons
> color (#!6 & sel) red
> select clear
> select #2/S2
36966 atoms, 41243 bonds, 1121 pseudobonds, 1808 residues, 4 models selected
> show sel cartoons
> color (#!2 & sel) cornflower blue
> select clear
> select #3/A
34830 atoms, 36578 bonds, 1974 pseudobonds, 3678 residues, 4 models selected
> show sel cartoons
> color (#!3 & sel) forest green
> select clear
> select #4/2
Nothing selected
> show #!1-3,5-6 cartoons
> select clear
> select clear
> select clear
> select #4/2
Nothing selected
> select #5/A6
39637 atoms, 42488 bonds, 2925 pseudobonds, 2234 residues, 4 models selected
> show sel cartoons
> ui tool show "Color Actions"
> color sel rebecca purple
> select clear
> hide #!2 models
> show #!2 models
> hide #!3 models
> hide #!5 models
> save
> /yonath_group/disha/Giardia_DH_AR_AB/Final_model_map/chimera/18S_HS_GL.png
> width 1194 height 813 supersample 3
> save
> /yonath_group/disha/Giardia_DH_AR_AB/Final_model_map/chimera/18S_rRNA.cxs
——— End of log from Tue May 18 12:10:33 2021 ———
opened ChimeraX session
> select #1/1
52552 atoms, 58724 bonds, 68 pseudobonds, 2446 residues, 2 models selected
> show sel cartoons
> color (#!1 & sel) dark gray
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> select #6
58253 atoms, 62084 bonds, 98 pseudobonds, 5116 residues, 2 models selected
> color (#!6 & sel) dark gray
> select clear
> select #2
218776 atoms, 234864 bonds, 4237 pseudobonds, 17789 residues, 4 models
selected
> color (#!2 & sel) light sea green
> color (#!2 & sel) gray
> ui tool show "Color Actions"
> color sel dark khaki
> select #2/L5
80333 atoms, 89642 bonds, 2751 pseudobonds, 3925 residues, 4 models selected
> show sel cartoons
> select clear
> select #2/L5:3765-3768
85 atoms, 94 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 85 atom styles
> color (#!2 & sel) red
> select #2/L5:3759-3760
44 atoms, 49 bonds, 2 residues, 1 model selected
> show sel atoms
> color (#!2 & sel) red
> style sel stick
Changed 44 atom styles
> select #2/L5:3762
20 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 20 atom styles
> color (#!2 & sel) red
> select #2/L5:3759-3760, 3762
64 atoms, 70 bonds, 3 residues, 1 model selected
> select #2/L5:3759-3760, 3762, 3765-3768
149 atoms, 164 bonds, 7 residues, 1 model selected
> select ~sel
1050555 atoms, 1108727 bonds, 29961 pseudobonds, 94688 residues, 18 models
selected
> hide sel & #!1-2,6 cartoons
> select #2/S2:1707-1709, 1826-1829, 1849-1850, 1059-1058
194 atoms, 214 bonds, 3 pseudobonds, 9 residues, 2 models selected
> show sel atoms
> show sel cartoons
> style sel stick
Changed 194 atom styles
> color (#!2 & sel) red
> color (#!2 & sel) lime
Drag select of 247 atoms, 16 residues, 3 pseudobonds, 272 bonds
> ui tool show H-Bonds
> hbonds reveal true
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.8/site-packages/chimerax/hbonds/tool.py",
line 52, in run_hbonds
run(self.session, " ".join(self.gui.get_command()))
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/opt/UCSF/ChimeraX/lib/python3.8/site-packages/chimerax/hbonds/cmd.py",
line 83, in cmd_hbonds
result = hb_func(session, struct_info, dist_slop=dist_slop,
angle_slop=angle_slop, **base_kw)
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/hbonds/hbond.py", line 494, in find_hbonds
acc_atoms, acc_data = _find_acceptors(structure, a_params,
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/hbonds/hbond.py", line 812, in _find_acceptors
bonded_geom = type_info[atom.neighbors[0].idatm_type].geometry
IndexError: list index out of range
IndexError: list index out of range
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/hbonds/hbond.py", line 812, in _find_acceptors
bonded_geom = type_info[atom.neighbors[0].idatm_type].geometry
See log for complete Python traceback.
> ui tool show H-Bonds
> hbonds color #000000 reveal true
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.8/site-packages/chimerax/hbonds/tool.py",
line 52, in run_hbonds
run(self.session, " ".join(self.gui.get_command()))
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/opt/UCSF/ChimeraX/lib/python3.8/site-packages/chimerax/hbonds/cmd.py",
line 83, in cmd_hbonds
result = hb_func(session, struct_info, dist_slop=dist_slop,
angle_slop=angle_slop, **base_kw)
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/hbonds/hbond.py", line 494, in find_hbonds
acc_atoms, acc_data = _find_acceptors(structure, a_params,
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/hbonds/hbond.py", line 812, in _find_acceptors
bonded_geom = type_info[atom.neighbors[0].idatm_type].geometry
IndexError: list index out of range
IndexError: list index out of range
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/hbonds/hbond.py", line 812, in _find_acceptors
bonded_geom = type_info[atom.neighbors[0].idatm_type].geometry
See log for complete Python traceback.
> hbonds color #000000 reveal true
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.8/site-packages/chimerax/hbonds/tool.py",
line 52, in run_hbonds
run(self.session, " ".join(self.gui.get_command()))
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/opt/UCSF/ChimeraX/lib/python3.8/site-packages/chimerax/hbonds/cmd.py",
line 83, in cmd_hbonds
result = hb_func(session, struct_info, dist_slop=dist_slop,
angle_slop=angle_slop, **base_kw)
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/hbonds/hbond.py", line 494, in find_hbonds
acc_atoms, acc_data = _find_acceptors(structure, a_params,
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/hbonds/hbond.py", line 812, in _find_acceptors
bonded_geom = type_info[atom.neighbors[0].idatm_type].geometry
IndexError: list index out of range
IndexError: list index out of range
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/hbonds/hbond.py", line 812, in _find_acceptors
bonded_geom = type_info[atom.neighbors[0].idatm_type].geometry
See log for complete Python traceback.
> select clear
> select #1/1
52552 atoms, 58724 bonds, 68 pseudobonds, 2446 residues, 2 models selected
> show sel cartoons
> select #6/2
28472 atoms, 31812 bonds, 48 pseudobonds, 1325 residues, 2 models selected
> show sel cartoons
> select clear
> select #6/2:1409
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #6/2:1410
20 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select #6/2:1411
20 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select #6/2:1410@C4'
1 atom, 1 residue, 1 model selected
> style sel stick
Changed 1 atom style
> style sel stick
Changed 1 atom style
> select #6/2:1411
20 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 20 atom styles
> select #6/2:1410@C3'
1 atom, 1 residue, 1 model selected
> style sel stick
Changed 1 atom style
> select #6/2:1410
20 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 20 atom styles
> color sel purple
> color sel cornflower blue
> select #6/2:1411
20 atoms, 21 bonds, 1 residue, 1 model selected
> color sel cornflower blue
> select #6/2:1412
23 atoms, 25 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 23 atom styles
> color sel cornflower blue
> select #6/2:1330
23 atoms, 25 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 23 atom styles
> color sel cornflower blue
> select #6/2:1329
20 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 20 atom styles
> color sel cornflower blue
> show sel atoms
> select #6/2:1328
20 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 20 atom styles
> show sel atoms
> color sel cornflower blue
> hide #!6 models
> show #!6 models
> hide #!1 models
> select #6/2:1409
23 atoms, 25 bonds, 1 residue, 1 model selected
> style sel stick
Changed 23 atom styles
> show sel atoms
> color sel cornflower blue
> select #6/2:1433
23 atoms, 25 bonds, 1 residue, 1 model selected
> style sel stick
Changed 23 atom styles
> show sel atoms
> color sel cornflower blue
> select #6/2:1434
24 atoms, 26 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel cornflower blue
> style sel stick
Changed 24 atom styles
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!6 models
> select #1/1:1747
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/1:1746
22 atoms, 24 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 22 atom styles
> hide sel atoms
> select #2/L5:3762
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/1:1791
20 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel atoms
> style sel stick
Changed 20 atom styles
> hide sel atoms
> select #1/1:1747
20 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 20 atom styles
> show sel atoms
> color (#!1 & sel) purple
> select #1/1:1749
22 atoms, 24 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color (#!1 & sel) purple
> select #1/1:1750
20 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 20 atom styles
> show sel atoms
> color (#!1 & sel) purple
> select #1/1:1751
20 atoms, 21 bonds, 1 residue, 1 model selected
> color (#!1 & sel) purple
> style sel stick
Changed 20 atom styles
> show sel atoms
> select #1/1:1752
20 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 20 atom styles
> show sel atoms
> color (#!1 & sel) purple
> select #1/1:1741
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/1:1742
22 atoms, 24 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 22 atom styles
> color (#!1 & sel) hot pink
> color (#!1 & sel) purple
> select clear
> hide #6.1 models
> hide #1.1 models
> hide #2.3 models
> hide #!2 models
> show #6.1 models
> hide #!6 models
> hide #6.1 models
> show #!6 models
> hide #!1 models
> select #6/2:1409-1412, 1433-1434, 1328-1330
196 atoms, 216 bonds, 9 residues, 1 model selected
> select ~sel
1050508 atoms, 1108675 bonds, 29961 pseudobonds, 94686 residues, 18 models
selected
> select #6/2:1409-1412, 1433-1434, 1328-1330
196 atoms, 216 bonds, 9 residues, 1 model selected
> select ~sel
1050508 atoms, 1108675 bonds, 29961 pseudobonds, 94686 residues, 18 models
selected
> select #6/2
28472 atoms, 31812 bonds, 48 pseudobonds, 1325 residues, 2 models selected
> hide sel cartoons
> select #6/2:1409-1412, 1433-1434, 1328-1330
196 atoms, 216 bonds, 9 residues, 1 model selected
> show sel cartoons
> select clear
> show #!1 models
> select #1/1:1749-1752, 1742, 1747
124 atoms, 135 bonds, 6 residues, 1 model selected
> select #1
104108 atoms, 111779 bonds, 96 pseudobonds, 8479 residues, 2 models selected
> hide sel cartoons
> select #1/1:1749-1752, 1742, 1747
124 atoms, 135 bonds, 6 residues, 1 model selected
> show sel cartoons
> select clear
> select clear
> select clear
Drag select of 230 atoms, 15 residues, 252 bonds
> ui tool show H-Bonds
> hbonds color #000000 reveal true
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.8/site-packages/chimerax/hbonds/tool.py",
line 52, in run_hbonds
run(self.session, " ".join(self.gui.get_command()))
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/opt/UCSF/ChimeraX/lib/python3.8/site-packages/chimerax/hbonds/cmd.py",
line 83, in cmd_hbonds
result = hb_func(session, struct_info, dist_slop=dist_slop,
angle_slop=angle_slop, **base_kw)
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/hbonds/hbond.py", line 494, in find_hbonds
acc_atoms, acc_data = _find_acceptors(structure, a_params,
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/hbonds/hbond.py", line 812, in _find_acceptors
bonded_geom = type_info[atom.neighbors[0].idatm_type].geometry
IndexError: list index out of range
IndexError: list index out of range
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/hbonds/hbond.py", line 812, in _find_acceptors
bonded_geom = type_info[atom.neighbors[0].idatm_type].geometry
See log for complete Python traceback.
> select clear
> show #!2 models
> select clear
> save
> /yonath_group/disha/Giardia_DH_AR_AB/Final_model_map/chimera/new/Inter_subunit/B2a.cxs
> select #1
104108 atoms, 111779 bonds, 96 pseudobonds, 8479 residues, 2 models selected
> hide sel atoms
> select #6
58253 atoms, 62084 bonds, 98 pseudobonds, 5116 residues, 2 models selected
> hide sel cartoons
> select #2
218776 atoms, 234864 bonds, 4237 pseudobonds, 17789 residues, 4 models
selected
> hide sel atoms
> select #1
104108 atoms, 111779 bonds, 96 pseudobonds, 8479 residues, 2 models selected
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> undo
> undo
> select #2
218776 atoms, 234864 bonds, 4237 pseudobonds, 17789 residues, 4 models
selected
> show sel cartoons
> hide sel atoms
> select #6
58253 atoms, 62084 bonds, 98 pseudobonds, 5116 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> select #1
104108 atoms, 111779 bonds, 96 pseudobonds, 8479 residues, 2 models selected
> show sel cartoons
> color (#!1 & sel) dark gray
> select clear
> select #6/2
28472 atoms, 31812 bonds, 48 pseudobonds, 1325 residues, 2 models selected
> select ~sel
1022232 atoms, 1077079 bonds, 29913 pseudobonds, 93370 residues, 18 models
selected
> hide sel & #!1-2,6 cartoons
> select #1/1
52552 atoms, 58724 bonds, 68 pseudobonds, 2446 residues, 2 models selected
> show sel cartoons
> select #2/L5
80333 atoms, 89642 bonds, 2751 pseudobonds, 3925 residues, 4 models selected
> show sel cartoons
> select #2/S2
36966 atoms, 41243 bonds, 1121 pseudobonds, 1808 residues, 4 models selected
> show sel cartoons
> select clear
> select #2/S2:1051
23 atoms, 25 bonds, 1 residue, 1 model selected
> style sel stick
Changed 23 atom styles
> show sel atoms
> hide #!1 models
> hide #!6 models
> color (#!2 & sel) lime
> select clear
> select clear
> select #2/S2:1051
23 atoms, 25 bonds, 1 residue, 1 model selected
> color (#!2 & sel) red
> select #2/L5:3699
20 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 20 atom styles
> color (#!2 & sel) lime
> select #2/L5:3699
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #2
218776 atoms, 234864 bonds, 4237 pseudobonds, 17789 residues, 4 models
selected
> hide sel cartoons
> select #2/L5:3699
20 atoms, 21 bonds, 1 residue, 1 model selected
> show sel cartoons
> select #2/S2:1051
23 atoms, 25 bonds, 1 residue, 1 model selected
> show sel cartoons
> show #!6 models
> select #6/2:746
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #2/S2:1051
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #6/2:745
23 atoms, 25 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 23 atom styles
> color sel purple
> show #!1 models
> select #1/1:1682
20 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 20 atom styles
> show sel atoms
> color (#!1 & sel) cornflower blue
> color (#!1 & sel) purple
> select #6/2:746
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #6/2:745
23 atoms, 25 bonds, 1 residue, 1 model selected
> color sel cornflower blue
> hide #!6 models
> show #!6 models
> select #6
58253 atoms, 62084 bonds, 98 pseudobonds, 5116 residues, 2 models selected
> hide sel cartoons
> select #1
104108 atoms, 111779 bonds, 96 pseudobonds, 8479 residues, 2 models selected
> hide sel cartoons
> select #1/1:1682
20 atoms, 21 bonds, 1 residue, 1 model selected
> show sel cartoons
> select #6/2:745
23 atoms, 25 bonds, 1 residue, 1 model selected
> show sel cartoons
> select clear
> save
> /yonath_group/disha/Giardia_DH_AR_AB/Final_model_map/chimera/new/Inter_subunit/B2b.cxs
> select #2/S2:1180
20 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 20 atom styles
> show sel atoms
> show sel cartoons
> color (#!2 & sel) lime
> select #2/L5:3694-3695
40 atoms, 43 bonds, 2 residues, 1 model selected
> show sel cartoons
> show sel atoms
> style sel stick
Changed 40 atom styles
> color (#!2 & sel) cornflower blue
> select #2/L5:3694-3695
40 atoms, 43 bonds, 2 residues, 1 model selected
> color (#!2 & sel) lime
> select #2/S2:1180
20 atoms, 21 bonds, 1 residue, 1 model selected
> color (#!2 & sel) red
> select clear
> select #1
104108 atoms, 111779 bonds, 96 pseudobonds, 8479 residues, 2 models selected
> show sel cartoons
> show #6.1 models
> hide #6.1 models
> select #6
58253 atoms, 62084 bonds, 98 pseudobonds, 5116 residues, 2 models selected
> show sel cartoons
> undo
> show sel cartoons
> select #6/2:864
20 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 20 atom styles
> color sel cornflower blue
> select #1/1:1676
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/1:1677
20 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 20 atom styles
> color (#!1 & sel) purple
> select #1/1:1676
20 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 20 atom styles
> show sel atoms
> hide sel atoms
> select #1/1:1679
20 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 20 atom styles
> show sel atoms
> color (#!1 & sel) purple
> hide sel atoms
> color (#!1 & sel) dim gray
> select #1/1:1678
20 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 20 atom styles
> show sel atoms
> color (#!1 & sel) purple
> select #1
104108 atoms, 111779 bonds, 96 pseudobonds, 8479 residues, 2 models selected
> hide sel cartoons
> select #6
58253 atoms, 62084 bonds, 98 pseudobonds, 5116 residues, 2 models selected
> hide sel cartoons
> select #6/2:864@C5'
1 atom, 1 residue, 1 model selected
> select #6/2:864@OP2
1 atom, 1 residue, 1 model selected
> select clear
> select clear
> select clear
> select #6/2:864
20 atoms, 21 bonds, 1 residue, 1 model selected
> show sel cartoons
> select #1/1:1677-1678
40 atoms, 43 bonds, 2 residues, 1 model selected
> show sel cartoons
> select clear
> save
> /yonath_group/disha/Giardia_DH_AR_AB/Final_model_map/chimera/new/Inter_subunit/B2c.cxs
> style #!1-2,6 stick
Changed 381137 atom styles
> show #!1-2,6 atoms
> undo
> select #2/S2:938-939
42 atoms, 46 bonds, 2 residues, 1 model selected
> show sel atoms
> color (#!2 & sel) red
> show sel cartoons
> select clear
> select #2/Lp
709 atoms, 718 bonds, 4 pseudobonds, 92 residues, 2 models selected
> show sel cartoons
> color (#!2 & sel) lime
> select clear
> select #2/Lp:85
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> show sel atoms
> hide #!6 models
> show #!6 models
> select #6/2
28472 atoms, 31812 bonds, 48 pseudobonds, 1325 residues, 2 models selected
> show sel cartoons
> select #6/2:632
22 atoms, 24 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel cornflower blue
> select #6/2:633
20 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 20 atom styles
> show sel atoms
> color sel cornflower blue
> select #6/2
28472 atoms, 31812 bonds, 48 pseudobonds, 1325 residues, 2 models selected
> hide sel cartoons
> select clear
> select #6/2:632-633
42 atoms, 46 bonds, 2 residues, 1 model selected
> show sel cartoons
> select clear
> select #1/p
708 atoms, 720 bonds, 91 residues, 1 model selected
> show sel cartoons
> color (#!1 & sel) purple
> select clear
> select #1/p:85
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> save
> /yonath_group/disha/Giardia_DH_AR_AB/Final_model_map/chimera/new/Inter_subunit/B2e.cxs
> select #2
218776 atoms, 234864 bonds, 4237 pseudobonds, 17789 residues, 4 models
selected
> hide sel cartoons
> hide sel atoms
> select #1
104108 atoms, 111779 bonds, 96 pseudobonds, 8479 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select #6
58253 atoms, 62084 bonds, 98 pseudobonds, 5116 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select #6/2:1815-1819, 1719-1721
Nothing selected
> show #!1-2,6 atoms
> undo
> select #6/2:1815-1819, 1719-1721
Nothing selected
> select #6/2:1815-1819, 1719-1721
Nothing selected
> select #2/S2:1815-1819, 1719-1721
174 atoms, 194 bonds, 8 residues, 1 model selected
> show sel cartoons
> show sel atoms
> color (#!2 & sel) red
> select #2/L5:3805-3807, 3794-3796, 3628-3629, 3834
192 atoms, 211 bonds, 5 pseudobonds, 9 residues, 2 models selected
> show sel cartoons
> show sel atoms
> color (#!2 & sel) lime
> select #2/Ln
230 atoms, 231 bonds, 24 residues, 1 model selected
> show sel cartoons
> color (#!2 & sel) lime
Drag select of 262 atoms, 41 residues, 6 pseudobonds, 290 bonds
> ui tool show H-Bonds
> hbonds sel color #000000 restrict both reveal true
33 hydrogen bonds found
> select clear
> select #1/1
52552 atoms, 58724 bonds, 68 pseudobonds, 2446 residues, 2 models selected
> show sel cartoons
> select #1/1:1779
23 atoms, 25 bonds, 1 residue, 1 model selected
> style sel stick
Changed 23 atom styles
> show sel atoms
> color (#!1 & sel) purple
> select #1/1:1778
23 atoms, 25 bonds, 1 residue, 1 model selected
> color (#!1 & sel) purple
> style sel stick
Changed 23 atom styles
> show sel atoms
> select #1/1:1777
20 atoms, 21 bonds, 1 residue, 1 model selected
> color (#!1 & sel) purple
> style sel stick
Changed 20 atom styles
> show sel atoms
> select #1/1:1790
22 atoms, 24 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color (#!1 & sel) purple
> select #1/1:1789
23 atoms, 25 bonds, 1 residue, 1 model selected
> style sel stick
Changed 23 atom styles
> show sel atoms
> color (#!1 & sel) purple
> select #1/1:1788
20 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!1 & sel) purple
> select #1/1:1817
20 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!1 & sel) purple
> select #1/1:1612
23 atoms, 25 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!1 & sel) purple
> select #1/1:1613
22 atoms, 24 bonds, 1 residue, 1 model selected
> color (#!1 & sel) purple
> hide #!1 models
> select #6/2
28472 atoms, 31812 bonds, 48 pseudobonds, 1325 residues, 2 models selected
> show sel cartoons
> select clear
> select clear
> select #6/2:1342
20 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel cornflower blue
> select #6/2:1340
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #6/2:1341
20 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 20 atom styles
> show sel atoms
> color sel cornflower blue
> select #6/2:1340
22 atoms, 24 bonds, 1 residue, 1 model selected
> color sel cornflower blue
> style sel stick
Changed 22 atom styles
> show sel atoms
> select #6/2:1399
23 atoms, 25 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> color sel cornflower blue
> select #6/2:1398
22 atoms, 24 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel cornflower blue
> select #6/2:1400
23 atoms, 25 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel cornflower blue
> select #6/2:1401
22 atoms, 24 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel cornflower blue
> select #6/2:1402
22 atoms, 24 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel cornflower blue
> select clear
> select #6/N
1195 atoms, 1218 bonds, 152 residues, 1 model selected
> select #6/n
217 atoms, 219 bonds, 24 residues, 1 model selected
> show sel cartoons
> color sel purple
> select clear
> select #6
58253 atoms, 62084 bonds, 98 pseudobonds, 5116 residues, 2 models selected
> ~select #6
Nothing selected
> select #6
58253 atoms, 62084 bonds, 98 pseudobonds, 5116 residues, 2 models selected
> ~select #6
Nothing selected
> select #6/2
28472 atoms, 31812 bonds, 48 pseudobonds, 1325 residues, 2 models selected
> hide sel cartoons
> select clear
> show #!1 models
> select #1/1
52552 atoms, 58724 bonds, 68 pseudobonds, 2446 residues, 2 models selected
> hide sel cartoons
> select clear
> select #1/1:1788-1790, 1612-1613, 1817, 1777-1779
196 atoms, 216 bonds, 9 residues, 1 model selected
> show sel atoms
> show sel cartoons
> select clear
> select #6/2:1398-1402, 1340-1342
174 atoms, 194 bonds, 8 residues, 1 model selected
> show sel cartoons
> select clear
> hide #!2 models
> select clear
Drag select of 268 atoms, 41 residues, 297 bonds
> ui tool show H-Bonds
> hbonds sel color #000000 restrict both reveal true
44 hydrogen bonds found
> show #!2 models
> select #6/n:17
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #6/n:20
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> hide #!2 models
> select clear
Drag select of 292 atoms, 41 residues, 317 bonds, 44 pseudobonds
> ui tool show H-Bonds
> hbonds sel color #000000 restrict both reveal true
44 hydrogen bonds found
> show #!2 models
> hide #!2 models
> select clear
> save
> /yonath_group/disha/Giardia_DH_AR_AB/Final_model_map/chimera/new/Inter_subunit/B3.cxs
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> show #!3 models
> hide #!3 models
> hide #!1 models
> hide #7 models
> show #7 models
> show #6.1 models
> hide #6.1 models
> hide #!6 models
> select #2/S2
36966 atoms, 41243 bonds, 71 pseudobonds, 1808 residues, 4 models selected
> hide sel atoms
> show sel cartoons
> select #2/L5
80333 atoms, 89642 bonds, 174 pseudobonds, 3925 residues, 4 models selected
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> hide sel cartoons
> hide sel cartoons
> select #2/S2
36966 atoms, 41243 bonds, 71 pseudobonds, 1808 residues, 4 models selected
> hide sel cartoons
> select #2/Ln
230 atoms, 231 bonds, 12 pseudobonds, 24 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select #2/S2:1028-1029, 677-678
88 atoms, 97 bonds, 4 residues, 1 model selected
> show sel cartoons
> show sel atoms
> color (#!2 & sel) red
> select #2/L5:1563-1564
44 atoms, 49 bonds, 2 residues, 1 model selected
> show sel atoms
> show sel cartoons
> color (#!2 & sel) lime
Drag select of 96 atoms, 6 residues, 107 bonds
> ui tool show H-Bonds
> hbonds sel color #000000 restrict both reveal true
11 hydrogen bonds found
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #1/1
52552 atoms, 58724 bonds, 77 pseudobonds, 2446 residues, 3 models selected
> show #!2 cartoons
> undo
> show #!1 models
> select #1/1
52552 atoms, 58724 bonds, 77 pseudobonds, 2446 residues, 3 models selected
> hide sel atoms
> hide sel cartoons
> show sel cartoons
> select clear
> select #1/1:563
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #1/1:564
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #1/1:563
22 atoms, 24 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/1:562
22 atoms, 24 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/1:563
22 atoms, 24 bonds, 1 residue, 1 model selected
> color (#!1 & sel) purple
> select #1/1:562
22 atoms, 24 bonds, 1 residue, 1 model selected
> color (#!1 & sel) purple
> select #6/2
28472 atoms, 31812 bonds, 51 pseudobonds, 1325 residues, 3 models selected
> show #!1-2 cartoons
> show #6.1 models
> select #6/2
28472 atoms, 31812 bonds, 51 pseudobonds, 1325 residues, 3 models selected
> hide sel cartoons
> hide sel atoms
> show sel cartoons
> hide #!1 models
> select #6/2:509
23 atoms, 25 bonds, 1 residue, 1 model selected
> show sel atoms
> select #6/2:510
20 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select #6/2:723
23 atoms, 25 bonds, 1 residue, 1 model selected
> show sel atoms
> select #6/2:722
22 atoms, 24 bonds, 1 residue, 1 model selected
> show sel atoms
> select #6/2:723
23 atoms, 25 bonds, 1 residue, 1 model selected
> color sel cornflower blue
> select #6/2:722
22 atoms, 24 bonds, 1 residue, 1 model selected
> color sel cornflower blue
> select #6/2:510
20 atoms, 21 bonds, 1 residue, 1 model selected
> color sel cornflower blue
> select clear
> select #6/2:509
23 atoms, 25 bonds, 1 residue, 1 model selected
> select clear
> select #6/2:509
23 atoms, 25 bonds, 1 residue, 1 model selected
> color sel cornflower blue
> select #6/2
28472 atoms, 31812 bonds, 51 pseudobonds, 1325 residues, 3 models selected
> hide sel cartoons
> select clear
> select #6/2:722-723, 509-510
88 atoms, 97 bonds, 4 residues, 1 model selected
> show sel cartoons
> select #1/1:562-563
44 atoms, 49 bonds, 2 residues, 1 model selected
> show #!2,6 cartoons
> undo
> show #!1 models
> hide sel cartoons
> select #1/1
52552 atoms, 58724 bonds, 77 pseudobonds, 2446 residues, 3 models selected
> hide sel cartoons
> select #1/1:562-563
44 atoms, 49 bonds, 2 residues, 1 model selected
> show sel cartoons
> select clear
> hide #!2 models
Drag select of 96 atoms, 6 residues, 107 bonds
> ui tool show H-Bonds
> hbonds sel color #000000 restrict both reveal true
8 hydrogen bonds found
> select clear
> graphics silhouettes true
> graphics silhouettes false
QXcbConnection: XCB error: 3 (BadWindow), sequence: 5225, resource id:
31468131, major code: 40 (TranslateCoords), minor code: 0
> save
> /yonath_group/disha/Giardia_DH_AR_AB/Final_model_map/chimera/new/Inter_subunit/B4.cxs
——— End of log from Mon Jun 14 14:22:23 2021 ———
opened ChimeraX session
> select #2/L5
80333 atoms, 89642 bonds, 169 pseudobonds, 3925 residues, 4 models selected
> show #!2 models
> hide sel atoms
> select #2/S2
36966 atoms, 41243 bonds, 74 pseudobonds, 1808 residues, 4 models selected
> hide sel atoms
> select clear
> select #1/1
52552 atoms, 58724 bonds, 68 pseudobonds, 2446 residues, 2 models selected
> hide sel atoms
> select #6/2
28472 atoms, 31812 bonds, 51 pseudobonds, 1325 residues, 3 models selected
> hide sel atoms
> select #2/S2:1731-1732
45 atoms, 50 bonds, 2 residues, 1 model selected
> show sel cartoons
> show sel atoms
> color (#!2 & sel) red
> select #2/Ln
230 atoms, 231 bonds, 24 residues, 1 model selected
> hide sel cartoons
> select #6/n
217 atoms, 219 bonds, 24 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #2/L5:2884-2885
45 atoms, 50 bonds, 2 residues, 1 model selected
> show sel atoms
> show sel cartoons
> color (#!2 & sel) lime
Drag select of 66 atoms, 4 residues, 74 bonds
> ui tool show H-Bonds
> hbonds sel color #000000 restrict both reveal true
3 hydrogen bonds found
> hide #!1 models
> show #!1 models
> select #6/2
28472 atoms, 31812 bonds, 51 pseudobonds, 1325 residues, 3 models selected
> show sel cartoons
> select #6/2:1353
23 atoms, 25 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel cornflower blue
> select #6/2:1352
23 atoms, 25 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel cornflower blue
> select #6/2
28472 atoms, 31812 bonds, 51 pseudobonds, 1325 residues, 3 models selected
> hide sel cartoons
> select #1/1
52552 atoms, 58724 bonds, 68 pseudobonds, 2446 residues, 2 models selected
> show sel cartoons
> select #1/1:1567
22 atoms, 24 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!1 & sel) purple
> select #1/1:1566
23 atoms, 25 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!1 & sel) purple
> select #1/1
52552 atoms, 58724 bonds, 68 pseudobonds, 2446 residues, 2 models selected
> hide sel cartoons
> select #1/1:1566-1567
45 atoms, 50 bonds, 2 residues, 1 model selected
> show sel cartoons
> select #6/2:1352-1353
46 atoms, 51 bonds, 2 residues, 1 model selected
> show sel cartoons
> select clear
> hide #!2 models
Drag select of 67 atoms, 4 residues, 75 bonds
> ui tool show H-Bonds
> hbonds sel color #000000 restrict both reveal true
2 hydrogen bonds found
> show #!2 models
> hide #!2 models
> select clear
QXcbConnection: XCB error: 3 (BadWindow), sequence: 7684, resource id:
31468201, major code: 40 (TranslateCoords), minor code: 0
> save
> /yonath_group/disha/Giardia_DH_AR_AB/Final_model_map/chimera/new/Inter_subunit/B5.cxs
——— End of log from Mon Jun 14 15:26:28 2021 ———
opened ChimeraX session
> select #2/S2
36966 atoms, 41243 bonds, 70 pseudobonds, 1808 residues, 3 models selected
> show #!2 models
> hide sel cartoons
> hide sel atoms
> select #2/S2:1793
22 atoms, 24 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel cartoons
> color (#!2 & sel) red
> select #1/1
52552 atoms, 58724 bonds, 68 pseudobonds, 2446 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> select #6/2
28472 atoms, 31812 bonds, 48 pseudobonds, 1325 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> select #2/L5
80333 atoms, 89642 bonds, 168 pseudobonds, 3925 residues, 3 models selected
> hide sel atoms
> hide sel cartoons
> select #2/LW
1015 atoms, 1030 bonds, 124 residues, 1 model selected
> show sel cartoons
> color (#!2 & sel) lime
> select #2/LW:47
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #2/LW:47
11 atoms, 10 bonds, 1 residue, 1 model selected
Drag select of 13 atoms, 3 residues, 13 bonds
> ui tool show H-Bonds
> hbonds sel color #000000 restrict both reveal true
0 hydrogen bonds found
Drag select of 22 atoms, 3 residues, 24 bonds
> ui tool show H-Bonds
> hbonds sel color #000000 restrict both reveal true
0 hydrogen bonds found
> ui tool show H-Bonds
> hbonds sel color #000000 restrict both distSlop 0.6 reveal true
0 hydrogen bonds found
Drag select of 24 atoms, 12 residues, 25 bonds
> ui tool show H-Bonds
> hbonds sel color #000000 restrict both distSlop 0.6 reveal true
6 hydrogen bonds found
Drag select of 14 atoms, 1 residues, 16 bonds
> undo
> undo
Drag select of 29 atoms, 29 residues, 6 pseudobonds, 29 bonds
> hide #7 models
> show #7 models
> hide #2.1 models
> hide sel atoms
> select #2/S2:1793
22 atoms, 24 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/LW:47
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
Drag select of 2 atoms
> ui tool show H-Bonds
> hbonds sel color #000000 distSlop 0.6 reveal true
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.8/site-packages/chimerax/hbonds/tool.py",
line 52, in run_hbonds
run(self.session, " ".join(self.gui.get_command()))
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/opt/UCSF/ChimeraX/lib/python3.8/site-packages/chimerax/hbonds/cmd.py",
line 83, in cmd_hbonds
result = hb_func(session, struct_info, dist_slop=dist_slop,
angle_slop=angle_slop, **base_kw)
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/hbonds/hbond.py", line 494, in find_hbonds
acc_atoms, acc_data = _find_acceptors(structure, a_params,
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/hbonds/hbond.py", line 812, in _find_acceptors
bonded_geom = type_info[atom.neighbors[0].idatm_type].geometry
IndexError: list index out of range
IndexError: list index out of range
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/hbonds/hbond.py", line 812, in _find_acceptors
bonded_geom = type_info[atom.neighbors[0].idatm_type].geometry
See log for complete Python traceback.
> ui tool show H-Bonds
> hbonds sel color #000000 restrict cross distSlop 0.6 reveal true
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.8/site-packages/chimerax/hbonds/tool.py",
line 52, in run_hbonds
run(self.session, " ".join(self.gui.get_command()))
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/opt/UCSF/ChimeraX/lib/python3.8/site-packages/chimerax/hbonds/cmd.py",
line 83, in cmd_hbonds
result = hb_func(session, struct_info, dist_slop=dist_slop,
angle_slop=angle_slop, **base_kw)
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/hbonds/hbond.py", line 494, in find_hbonds
acc_atoms, acc_data = _find_acceptors(structure, a_params,
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/hbonds/hbond.py", line 812, in _find_acceptors
bonded_geom = type_info[atom.neighbors[0].idatm_type].geometry
IndexError: list index out of range
IndexError: list index out of range
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/hbonds/hbond.py", line 812, in _find_acceptors
bonded_geom = type_info[atom.neighbors[0].idatm_type].geometry
See log for complete Python traceback.
> ui tool show H-Bonds
Restriction atom specifier must not be blank
> hbonds sel color #000000 radius 0.135 restrict both distSlop 0.6 select true
> reveal true
0 hydrogen bonds found
> select #6/2
28472 atoms, 31812 bonds, 48 pseudobonds, 1325 residues, 2 models selected
> show sel cartoons
> select #6/2:1377
23 atoms, 25 bonds, 1 residue, 1 model selected
> show sel atoms
> select #6/2:1376
23 atoms, 25 bonds, 1 residue, 1 model selected
> show sel atoms
> select #6/2:1377
23 atoms, 25 bonds, 1 residue, 1 model selected
> color sel medium blue
> color sel cornflower blue
> select #6/2:1376
23 atoms, 25 bonds, 1 residue, 1 model selected
> color sel cornflower blue
> select #6/2
28472 atoms, 31812 bonds, 48 pseudobonds, 1325 residues, 2 models selected
> hide sel cartoons
> select #1/W
522 atoms, 534 bonds, 64 residues, 1 model selected
> show sel cartoons
> color (#!1 & sel) purple
> select #1/W:48
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/W:49
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide #!2 models
Drag select of 55 atoms, 9 residues, 59 bonds
Drag select of 59 atoms, 6 residues, 62 bonds
> ui tool show H-Bonds
> hbonds reveal true
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.8/site-packages/chimerax/hbonds/tool.py",
line 52, in run_hbonds
run(self.session, " ".join(self.gui.get_command()))
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/opt/UCSF/ChimeraX/lib/python3.8/site-packages/chimerax/hbonds/cmd.py",
line 83, in cmd_hbonds
result = hb_func(session, struct_info, dist_slop=dist_slop,
angle_slop=angle_slop, **base_kw)
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/hbonds/hbond.py", line 494, in find_hbonds
acc_atoms, acc_data = _find_acceptors(structure, a_params,
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/hbonds/hbond.py", line 812, in _find_acceptors
bonded_geom = type_info[atom.neighbors[0].idatm_type].geometry
IndexError: list index out of range
IndexError: list index out of range
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/hbonds/hbond.py", line 812, in _find_acceptors
bonded_geom = type_info[atom.neighbors[0].idatm_type].geometry
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 418.113
OpenGL renderer: Quadro RTX 4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: ASUS
Model: System Product Name
OS: CentOS Stream 8
Architecture: 64bit ELF
Virutal Machine: none
CPU: 24 AMD Ryzen 9 5900X 12-Core Processor
Cache Size: 512 KB
Memory:
total used free shared buff/cache available
Mem: 62Gi 20Gi 4.5Gi 445Mi 38Gi 41Gi
Swap: 31Gi 87Mi 31Gi
Graphics:
05:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU104GL [Quadro RTX 4000] [10de:1eb1] (rev a1)
Subsystem: NVIDIA Corporation Device [10de:12a0]
Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.12.5
cftime: 1.4.1
chardet: 3.0.4
ChimeraX-AddCharge: 1.0
ChimeraX-AddH: 2.1.6
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.13.3
ChimeraX-AtomicLibrary: 3.1.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.2.1
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.1.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.1
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: 2.1
ChimeraX-Help: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-Label: 1.0
ChimeraX-LinuxSupport: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.0.2
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: 1.2
ChimeraX-MDcrds: 2.2
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.3
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0.1
ChimeraX-ModelPanel: 1.0.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.1
ChimeraX-OpenCommand: 1.5
ChimeraX-PDB: 2.4.1
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.4
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.3
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: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.3.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.7.3
ChimeraX-uniprot: 2.1
ChimeraX-UnitCell: 1.0
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-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.21
decorator: 5.0.7
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: 0.17
imagecodecs: 2020.5.30
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.7.1
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.6.2
lz4: 3.1.0
MarkupSafe: 1.1.1
matplotlib: 3.3.2
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.3
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.9
ParmEd: 3.2.0
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 21.0.1
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.18
psutil: 5.7.2
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.7.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pyzmq: 22.0.3
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.2
sfftk-rw: 0.6.7.dev1
six: 1.15.0
snowballstemmer: 2.1.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
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: 2020.9.3
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.0
wheel-filename: 1.2.0
Change History (2)
comment:1 by , 4 years ago
| Component: | Unassigned → Structure Analysis |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → 4v88: acceptor has no neighbors |
comment:2 by , 4 years ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
Note:
See TracTickets
for help on using tickets.
Hi Disha,
--Eric