Opened 4 years ago

Last modified 4 years ago

#4763 feedback defect

H-bonds: acceptor not bonded to any atoms

Reported by: disha-gajanan.hiregange@… 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/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.  
  




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       4.8Gi       417Mi        37Gi        41Gi
	Swap:          31Gi        76Mi        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 pett, 4 years ago

Component: Unassigned → Structure Analysis
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → H-bonds: acceptor not bonded to any atoms

comment:2 by pett, 4 years ago

Status: accepted → feedback

Hi Disha,

Thanks for reporting this problem. In order to understand how it's happening I would need the structure(s) it's failing on. Could you provide a session file?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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