Opened 4 years ago

Last modified 4 years ago

#5684 feedback defect

AddH protonation issue

Reported by: Tristan Croll Owned by: pett
Priority: normal Milestone:
Component: Structure Editing Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.3rc202111182158 (2021-11-18 21:58:36 UTC)
Description
(very minor) AddH misses protonating the N1 atom of O-methyguanosine (OMG - good examples in 7o7y) - since this is a base-pairing atom it will make quite a difference. Interestingly, the base pairing pseudobond is still drawn between OMG-N1 and C-N3.

Log:
> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  
UCSF ChimeraX version: 1.3rc202111182158 (2021-11-18)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6xz7

Summary of feedback from opening 6xz7 fetched from pdb  
---  
notes | Fetching compressed mmCIF 6xz7 from
http://files.rcsb.org/download/6xz7.cif  
Fetching CCD DI0 from http://ligand-expo.rcsb.org/reports/D/DI0/DI0.cif  
Fetching CCD 31M from http://ligand-expo.rcsb.org/reports/3/31M/31M.cif  
  
6xz7 title:  
E. coli 50S ribosomal subunit in complex with dirithromycin, fMet-Phe-
tRNA(Phe) and deacylated tRNA(iMet). [more info...]  
  
Chain information for 6xz7 #1  
---  
Chain | Description | UniProt  
A | 23S rRNA |  
B | 5S rRNA |  
C | 50S ribosomal protein L2 | RL2_ECOLI  
D | 50S ribosomal protein L3 | RL3_ECOLI  
E | 50S ribosomal protein L4 | RL4_ECOLI  
F | 50S ribosomal protein L5 | RL5_ECOLI  
G | 50S ribosomal protein L6 | RL6_ECOLI  
H | 50S ribosomal protein L10 | RL10_ECOLI  
I | 50S ribosomal protein L11 | RL11_ECOLI  
J | 50S ribosomal protein L13 | RL13_ECOLI  
K | 50S ribosomal protein L14 | RL14_ECOLI  
L | 50S ribosomal protein L15 | RL15_ECOLI  
M | 50S ribosomal protein L16 | RL16_ECOLI  
N | 50S ribosomal protein L17 | RL17_ECOLI  
O | 50S ribosomal protein L18 | RL18_ECOLI  
P | 50S ribosomal protein L19 | RL19_ECOLI  
Q | 50S ribosomal protein L20 | RL20_ECOLI  
R | 50S ribosomal protein L21 | RL21_ECOLI  
S | 50S ribosomal protein L22 | RL22_ECOLI  
T | 50S ribosomal protein L23 | RL23_ECOLI  
U | 50S ribosomal protein L24 | RL24_ECOLI  
V | 50S ribosomal protein L25 | RL25_ECOLI  
W | 50S ribosomal protein L27 | RL27_ECOLI  
X | 50S ribosomal protein L28 | RL28_ECOLI  
Y | 50S ribosomal protein L29 | RL29_ECOLI  
Z | 50S ribosomal protein L30 | RL30_ECOLI  
a | 50S ribosomal protein L32 | RL32_ECOLI  
b | 50S ribosomal protein L33 | RL33_ECOLI  
c | 50S ribosomal protein L34 | RL34_ECOLI  
d | 50S ribosomal protein L35 | RL35_ECOLI  
e | 50S ribosomal protein L36 | RL36_ECOLI  
f | Deacylated tRNAi(Met) |  
g | fMet-Phe-tRNA(Phe) |  
  
Non-standard residues in 6xz7 #1  
---  
DI0 — Dirithromycin
((1R,2R,3R,6R,7S,8S,9R,10R,12R,13S,15R,17S)-3-ethyl-2,10-dihydroxy-15-[(2-methoxyethoxy)methyl]-2,6,8,10,12,17-hexamethy
l-5-oxo-9-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-
hexopyranosyl]oxy}-4,16-dioxa-14-azabicyclo[11.3.1]heptadecan-7 -yl
2,6-dideoxy-3-C-methyl-3-O-methyl-alpha-L-ribo-hexopyranoside)  
MG — magnesium ion  
  

> open 10655 fromDatabase emdb

Summary of feedback from opening 10655 fetched from emdb  
---  
note | Fetching compressed map 10655 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-10655/map/emd_10655.map.gz  
  
Opened emdb 10655 as #2, grid size 512,512,512, pixel 0.86, shown at level
0.0232, step 2, values float32  

> clipper associate #2 toModel #1

Opened emdb 10655 as #1.1.1.1, grid size 512,512,512, pixel 0.86, shown at
level 0.218, step 1, values float32  
6xz7 title:  
E. coli 50S ribosomal subunit in complex with dirithromycin, fMet-Phe-
tRNA(Phe) and deacylated tRNA(iMet). [more info...]  
  
Chain information for 6xz7  
---  
Chain | Description | UniProt  
1.2/A | 23S rRNA |  
1.2/B | 5S rRNA |  
1.2/C | 50S ribosomal protein L2 | RL2_ECOLI  
1.2/D | 50S ribosomal protein L3 | RL3_ECOLI  
1.2/E | 50S ribosomal protein L4 | RL4_ECOLI  
1.2/F | 50S ribosomal protein L5 | RL5_ECOLI  
1.2/G | 50S ribosomal protein L6 | RL6_ECOLI  
1.2/H | 50S ribosomal protein L10 | RL10_ECOLI  
1.2/I | 50S ribosomal protein L11 | RL11_ECOLI  
1.2/J | 50S ribosomal protein L13 | RL13_ECOLI  
1.2/K | 50S ribosomal protein L14 | RL14_ECOLI  
1.2/L | 50S ribosomal protein L15 | RL15_ECOLI  
1.2/M | 50S ribosomal protein L16 | RL16_ECOLI  
1.2/N | 50S ribosomal protein L17 | RL17_ECOLI  
1.2/O | 50S ribosomal protein L18 | RL18_ECOLI  
1.2/P | 50S ribosomal protein L19 | RL19_ECOLI  
1.2/Q | 50S ribosomal protein L20 | RL20_ECOLI  
1.2/R | 50S ribosomal protein L21 | RL21_ECOLI  
1.2/S | 50S ribosomal protein L22 | RL22_ECOLI  
1.2/T | 50S ribosomal protein L23 | RL23_ECOLI  
1.2/U | 50S ribosomal protein L24 | RL24_ECOLI  
1.2/V | 50S ribosomal protein L25 | RL25_ECOLI  
1.2/W | 50S ribosomal protein L27 | RL27_ECOLI  
1.2/X | 50S ribosomal protein L28 | RL28_ECOLI  
1.2/Y | 50S ribosomal protein L29 | RL29_ECOLI  
1.2/Z | 50S ribosomal protein L30 | RL30_ECOLI  
1.2/a | 50S ribosomal protein L32 | RL32_ECOLI  
1.2/b | 50S ribosomal protein L33 | RL33_ECOLI  
1.2/c | 50S ribosomal protein L34 | RL34_ECOLI  
1.2/d | 50S ribosomal protein L35 | RL35_ECOLI  
1.2/e | 50S ribosomal protein L36 | RL36_ECOLI  
1.2/f | Deacylated tRNAi(Met) |  
1.2/g | fMet-Phe-tRNA(Phe) |  
  
Non-standard residues in 6xz7 #1.2  
---  
DI0 — Dirithromycin
((1R,2R,3R,6R,7S,8S,9R,10R,12R,13S,15R,17S)-3-ethyl-2,10-dihydroxy-15-[(2-methoxyethoxy)methyl]-2,6,8,10,12,17-hexamethy
l-5-oxo-9-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-
hexopyranosyl]oxy}-4,16-dioxa-14-azabicyclo[11.3.1]heptadecan-7 -yl
2,6-dideoxy-3-C-methyl-3-O-methyl-alpha-L-ribo-hexopyranoside)  
MG — magnesium ion  
  

> addh

Summary of feedback from adding hydrogens to 6xz7 #1.2  
---  
warnings | Not adding hydrogens to /A G 1 P because it is missing heavy-atom
bond partners  
Not adding hydrogens to /B U 1 P because it is missing heavy-atom bond
partners  
Not adding hydrogens to /W THR 10 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /b ILE 54 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /f G 2 P because it is missing heavy-atom bond
partners  
notes | Termini for 6xz7 (#1.2) chain A determined from SEQRES records  
Termini for 6xz7 (#1.2) chain B determined from SEQRES records  
Termini for 6xz7 (#1.2) chain C determined from SEQRES records  
Termini for 6xz7 (#1.2) chain D determined from SEQRES records  
Termini for 6xz7 (#1.2) chain E determined from SEQRES records  
28 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /C ALA 2, /D MET 1, /E MET
1, /F ALA 2, /G SER 2, /H ALA 2, /I TYR 8, /J MET 1, /K MET 1, /L MET 1, /M
MET 1, /N MET 1, /O MET 1, /P SER 2, /Q ALA 2, /R MET 1, /S MET 1, /T MET 1,
/U ALA 2, /V MET 1, /W THR 10, /X SER 2, /Y LYS 2, /Z ALA 2, /a ALA 2, /b GLY
4, /c MET 1, /d PRO 2, /e MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /C SER 272, /D ALA 209, /E ALA
201, /F ARG 178, /G LYS 177, /H ILE 136, /I GLU 141, /J ILE 142, /K LEU 123,
/L GLU 144, /M MET 136, /N ALA 125, /O PHE 117, /P ASN 115, /Q ALA 118, /R ALA
103, /S ARG 110, /T LEU 93, /U ILE 103, /V ALA 94, /W GLU 85, /X TYR 78, /Y
ALA 63, /Z GLU 59, /a LYS 57, /b ILE 54, /c LYS 46, /d ALA 65, /e GLY 38  
Chain-final residues that are not actual C termini:  
Missing OXT added to C-terminal residue /H ILE 136  
Missing OXT added to C-terminal residue /I GLU 141  
Missing OXT added to C-terminal residue /K LEU 123  
Missing OXT added to C-terminal residue /N ALA 125  
Missing OXT added to C-terminal residue /b ILE 54  
12368 hydrogen bonds  
62895 hydrogens added  
  

> view :7MG

> select :7MG

38 atoms, 40 bonds, 1 residue, 1 model selected  

> close #1

> open 7o7y

Summary of feedback from opening 7o7y fetched from pdb  
---  
notes | Fetching compressed mmCIF 7o7y from
http://files.rcsb.org/download/7o7y.cif  
Fetching CCD UNX from http://ligand-expo.rcsb.org/reports/U/UNX/UNX.cif  
Fetching CCD A2M from http://ligand-expo.rcsb.org/reports/A/A2M/A2M.cif  
Fetching CCD B8N from http://ligand-expo.rcsb.org/reports/B/B8N/B8N.cif  
Fetching CCD SAC from http://ligand-expo.rcsb.org/reports/S/SAC/SAC.cif  
Fetching CCD NMM from http://ligand-expo.rcsb.org/reports/N/NMM/NMM.cif  
Fetching CCD AME from http://ligand-expo.rcsb.org/reports/A/AME/AME.cif  
Fetching CCD HY3 from http://ligand-expo.rcsb.org/reports/H/HY3/HY3.cif  
Fetching CCD UY1 from http://ligand-expo.rcsb.org/reports/U/UY1/UY1.cif  
Fetching CCD GTP from http://ligand-expo.rcsb.org/reports/G/GTP/GTP.cif  
Fetching CCD V5N from http://ligand-expo.rcsb.org/reports/V/V5N/V5N.cif  
Fetching CCD AYA from http://ligand-expo.rcsb.org/reports/A/AYA/AYA.cif  
Fetching CCD AAC from http://ligand-expo.rcsb.org/reports/A/AAC/AAC.cif  
Fetching CCD M3L from http://ligand-expo.rcsb.org/reports/M/M3L/M3L.cif  
  
7o7y title:  
Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a
pseudoknot (high resolution) [more info...]  
  
Chain information for 7o7y #1  
---  
Chain | Description | UniProt  
A2 | 18S rRNA |  
AA | 40S ribosomal protein S27 | G1TZ76_RABIT  
AB | Ribosomal protein S28 | G1TIB4_RABIT  
AC | Ribosomal protein S27a | G1SK22_RABIT  
AD | 40S ribosomal protein S30 | G1T8A2_RABIT  
AE | Ribosomal protein eS26 |  
AF | RACK1 | G1SJB4_RABIT  
AG | uS14 | G1U7M4_RABIT  
AH | mRNA containing SARS-CoV-2 sequence |  
AI | E-site tRNA |  
AT | P-site Phe-tRNA(Phe) |  
AZ | 40S ribosomal protein SA | G1TLT8_RABIT  
Aa | 40S ribosomal protein S3a | G1SS70_RABIT  
Ab | Ribosomal protein uS5 |  
Ac | 40S ribosomal protein S3 | G1TNM3_RABIT  
Ad | Ribosomal protein eS4 |  
Ae | Ribosomal protein S5 | G1TFM5_RABIT  
Af | 40S ribosomal protein S6 | G1TM55_RABIT  
Ag | 40S ribosomal protein S7 | G1SVB0_RABIT  
Ah | 40S ribosomal protein S8 | G1TJW1_RABIT  
Ai | Ribosomal protein S9 (Predicted) | B7NZS8_RABIT  
Aj | eS10 | G1TPV3_RABIT  
Ak | 40S ribosomal protein S11 | G1TRM4_RABIT  
Al | 40S ribosomal protein S12 | G1SFR8_RABIT  
Am | uS15 | G1SP51_RABIT  
An | 40S ribosomal protein uS11 | G1T1F0_RABIT  
Ao | 40S ribosomal protein uS19 | G1U0Q2_RABIT  
Ap | uS9 | G1SGX4_RABIT  
Aq | 40S ribosomal protein eS17 | G1TU13_RABIT  
Ar | 40S ribosomal protein S18 | G1TPG3_RABIT  
As | Ribosomal protein eS19 |  
At | 40S ribosomal protein uS10 | G1SIZ2_RABIT  
Au | Ribosomal protein eS21 |  
Av | Ribosomal protein S15a | G1TG89_RABIT  
Aw | 40S ribosomal protein S23 | G1SZ47_RABIT  
Ax | 40S ribosomal protein S24 | G1T3D8_RABIT  
Ay | 40S ribosomal protein S25 | G1TDB3_RABIT  
Az | 60s ribosomal protein l41 | A0A087WNH4_RABIT  
B5 | 28S rRNA |  
B7 | 5S rRNA |  
B8 | 5.8S rRNA |  
BA | Ribosomal protein uL2 |  
BB | Ribosomal protein L3 | G1TL06_RABIT  
BC | 60S ribosomal protein L4 | G1SVW5_RABIT  
BD | Ribosomal_L18_c domain-containing protein | G1SYJ6_RABIT  
BE | 60S ribosomal protein L6 | G1SKF7_RABIT  
BF | Ribosomal Protein uL30 |  
BG | Ribosomal protein eL8 |  
BH | 60S ribosomal protein L9 | G1SWI6_RABIT  
BI | 60S ribosomal protein L10 | B7NZQ2_RABIT  
BJ | Ribosomal protein L11 | G1TUB8_RABIT  
BK | Replicase polyprotein 1ab | R1AB_SARS2  
BL | Ribosomal protein eL13 |  
BM | Ribosomal protein L14 | G1SZ12_RABIT  
BN | Ribosomal protein L15 | G1T0C1_RABIT  
BO | Ribosomal protein uL13 |  
BP | uL22 | G1TVT6_RABIT  
BQ | Ribosomal Protein eL18 |  
BR | 60S ribosomal protein L19 | RL19_BOVIN  
BS | Ribosomal protein eL20 |  
BT | eL21 | G1SHQ2_RABIT  
BU | Ribosomal protein eL22 |  
BV | Ribosomal protein L23 | G1T6D1_RABIT  
BW | eL24 | G1SE28_RABIT  
BX | uL23 | G1SE76_RABIT  
BY | Ribosomal protein L26 | G1SQH0_RABIT  
BZ | 60S ribosomal protein L27 | G1TXF6_RABIT  
Ba | 60S ribosomal protein L27a | G1SNY0_RABIT  
Bb | 60S ribosomal protein L29 | G1SGR6_RABIT  
Bc | eL30 | G1TDL2_RABIT  
Bd | eL31 | G1SHG0_RABIT  
Be | eL32 | G1U437_RABIT  
Bf | eL33 | G1SF08_RABIT  
Bg | 60S ribosomal protein L34 | G1TXG5_RABIT  
Bh | uL29 | G1SIT5_RABIT  
Bi | 60S ribosomal protein L36 | G1TTQ5_RABIT  
Bj | Ribosomal protein L37 | U3KPD5_RABIT  
Bk | eL38 | G1U001_RABIT  
Bl | eL39 | G1TTN1_RABIT  
Bm | 60S ribosomal protein L40 |  
Bo | eL42 | G1U344_RABIT  
Bp | eL43 | G1SY53_RABIT  
Br | Ribosomal protein eL28 |  
Bs | 60S acidic ribosomal protein P0 | G1SPK4_RABIT  
Bt | Ribosomal protein L12 | G1SMR7_RABIT  
Bv | Ribosomal protein uL1 | G1SKZ8_RABIT  
  
Non-standard residues in 7o7y #1  
---  
AAC — acetylamino-acetic acid  
B8N —
(2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic
acid  
GTP — guanosine-5'-triphosphate  
MG — magnesium ion  
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))  
SPM — spermine  
UNX — unknown atom or ion  
UY1 — 2'-O-methylpseudouridine-5'-monophosphate  
ZN — zinc ion  
  

> open 12756 fromDatabase emdb

Summary of feedback from opening 12756 fetched from emdb  
---  
note | Fetching compressed map 12756 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-12756/map/emd_12756.map.gz  
  
Opened emdb 12756 as #2, grid size 560,560,560, pixel 1.06, shown at level
0.779, step 4, values float32  

> addh

Summary of feedback from adding hydrogens to 7o7y #1  
---  
warnings | Not adding hydrogens to /AH A 3456 O3' because it is missing heavy-
atom bond partners  
Not adding hydrogens to /AI N 1 C1' because it is missing heavy-atom bond
partners  
Not adding hydrogens to /AI N 2 C1' because it is missing heavy-atom bond
partners  
Not adding hydrogens to /AI N 3 C1' because it is missing heavy-atom bond
partners  
Not adding hydrogens to /AI N 4 C1' because it is missing heavy-atom bond
partners  
70 messages similar to the above omitted  
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /AH A 3456 O3'  
notes | Termini for 7o7y (#1) chain A2 determined from SEQRES records  
Termini for 7o7y (#1) chain AA determined from SEQRES records  
Termini for 7o7y (#1) chain AB determined from SEQRES records  
Termini for 7o7y (#1) chain AC determined from SEQRES records  
Termini for 7o7y (#1) chain AD determined from SEQRES records  
81 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /Af MET 1, /Aj MET 1, /Au
AME 1, /Az MET 1, /BH MET 1, /BS MET 1, /BW MET 1, /BY MET 1, /Bf MET 1  
Chain-initial residues that are not actual N termini: /AA PRO 2, /AB VAL 6,
/AC LYS 78, /AD HIS 77, /AE THR 2, /AF THR 2, /AG GLY 2, /AZ SAC 2, /Aa ALA 2,
/Aa LYS 20, /Ab ASP 57, /Ac VAL 3, /Ad ALA 2, /Ae THR 14, /Ag SER 5, /Ah GLY
2, /Ai PRO 2, /Ak ASP 3, /Al GLY 9, /Am GLY 2, /An SER 16, /Ao THR 11, /Ap PRO
6, /Aq GLY 2, /Ar SAC 2, /As PRO 2, /At ALA 16, /Av VAL 2, /Aw GLY 2, /Ax THR
4, /Ay LYS 31, /BA GLY 2, /BB SER 2, /BC AYA 2, /BD AAC 2, /BE PRO 39, /BE GLU
239, /BF ARG 22, /BG VAL 27, /BG LYS 131, /BI GLY 2, /BJ LYS 8, /BK LEU 4365,
/BL ALA 2, /BM VAL 2, /BN GLY 2, /BO GLN 5, /BP VAL 2, /BQ GLY 2, /BR SER 2,
/BT THR 2, /BU GLN 17, /BV SER 2, /BX LYS 39, /BZ GLY 2, /Ba PRO 2, /Bb ALA 2,
/Bb VAL 89, /Bc VAL 2, /Bd ASN 18, /Be ALA 2, /Bg VAL 2, /Bh ALA 2, /Bi ALA 2,
/Bj THR 2, /Bk PRO 2, /Bl SER 2, /Bm ILE 77, /Bo VAL 2, /Bp ALA 2, /Br SAC 2,
/Bs ASP 5, /Bt GLU 9, /Bv SER 6  
Chain-final residues that are actual C termini: /AA HIS 84, /AD SER 133, /AG
ASP 56, /Ad GLY 263, /Ae ARG 204, /Ag LEU 194, /Al LYS 132, /Am ALA 151, /An
LEU 151, /Ap ARG 146, /Aq VAL 135, /At ALA 119, /Au PHE 83, /Av PHE 130, /Az
LYS 25, /BE PHE 291, /BF ASN 247, /BG GLY 266, /BI SER 214, /BL LYS 211, /BN
ARG 204, /BO VAL 203, /BQ ASN 188, /BS PHE 176, /BT ALA 160, /BV ALA 140, /BX
ILE 156, /BZ PHE 136, /Ba ALA 148, /Bf ILE 110, /Bh ALA 123, /Bk LYS 70, /Bl
LEU 51, /Bm LYS 128, /Bo PHE 106, /Bp GLN 92, /Bv TYR 217  
Chain-final residues that are not actual C termini: /AB LEU 68, /AC ASN 151,
/AE ARG 102, /AF ILE 314, /AZ VAL 222, /Aa LYS 11, /Aa GLY 233, /Ab THR 276,
/Ac LYS 227, /Af LEU 237, /Ah GLY 207, /Ai GLY 186, /Aj ARG 96, /Ak GLN 156,
/Ao SER 138, /Ar SER 149, /As LYS 144, /Aw ARG 142, /Ax GLY 128, /Ay GLY 115,
/BA GLU 254, /BB LYS 399, /BC ASP 363, /BD ALA 295, /BE PRO 228, /BG ALA 123,
/BH ALA 190, /BJ GLY 177, /BK PHE 4399, /BM SER 139, /BP PRO 160, /BR LYS 181,
/BU PHE 115, /BW ALA 121, /BY LYS 134, /Bb VAL 76, /Bb PRO 121, /Bc PRO 109,
/Bd GLU 124, /Be SER 131, /Bg LYS 115, /Bi LYS 103, /Bj LYS 87, /Br LYS 127,
/Bs ASN 200, /Bt ALA 164  
Chain-initial residues that are not actual 5' termini: /AH A 3456  
Missing OXT added to C-terminal residue /Ag LEU 194  
Missing OXT added to C-terminal residue /Aq VAL 135  
Missing OXT added to C-terminal residue /Au PHE 83  
Missing OXT added to C-terminal residue /Az LYS 25  
Missing OXT added to C-terminal residue /Bo PHE 106  
1 messages similar to the above omitted  
66494 hydrogen bonds  
Adding 'H' to /AB VAL 6  
Adding 'H' to /AC LYS 78  
Adding 'H' to /AD HIS 77  
Adding 'H' to /AE THR 2  
Adding 'H' to /AF THR 2  
56 messages similar to the above omitted  
/AB LEU 68 is not terminus, removing H atom from 'C'  
/AC ASN 151 is not terminus, removing H atom from 'C'  
/AE ARG 102 is not terminus, removing H atom from 'C'  
/AF ILE 314 is not terminus, removing H atom from 'C'  
/AZ VAL 222 is not terminus, removing H atom from 'C'  
36 messages similar to the above omitted  
190814 hydrogens added  
  

> clipper associate #2 toModel #1

Opened emdb 12756 as #1.1.1.1, grid size 560,560,560, pixel 1.06, shown at
level 1.54, step 1, values float32  
7o7y title:  
Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a
pseudoknot (high resolution) [more info...]  
  
Chain information for 7o7y  
---  
Chain | Description | UniProt  
1.2/A2 | 18S rRNA |  
1.2/AA | 40S ribosomal protein S27 | G1TZ76_RABIT  
1.2/AB | Ribosomal protein S28 | G1TIB4_RABIT  
1.2/AC | Ribosomal protein S27a | G1SK22_RABIT  
1.2/AD | 40S ribosomal protein S30 | G1T8A2_RABIT  
1.2/AE | Ribosomal protein eS26 |  
1.2/AF | RACK1 | G1SJB4_RABIT  
1.2/AG | uS14 | G1U7M4_RABIT  
1.2/AH | mRNA containing SARS-CoV-2 sequence |  
1.2/AI | E-site tRNA |  
1.2/AT | P-site Phe-tRNA(Phe) |  
1.2/AZ | 40S ribosomal protein SA | G1TLT8_RABIT  
1.2/Aa | 40S ribosomal protein S3a | G1SS70_RABIT  
1.2/Ab | Ribosomal protein uS5 |  
1.2/Ac | 40S ribosomal protein S3 | G1TNM3_RABIT  
1.2/Ad | Ribosomal protein eS4 |  
1.2/Ae | Ribosomal protein S5 | G1TFM5_RABIT  
1.2/Af | 40S ribosomal protein S6 | G1TM55_RABIT  
1.2/Ag | 40S ribosomal protein S7 | G1SVB0_RABIT  
1.2/Ah | 40S ribosomal protein S8 | G1TJW1_RABIT  
1.2/Ai | Ribosomal protein S9 (Predicted) | B7NZS8_RABIT  
1.2/Aj | eS10 | G1TPV3_RABIT  
1.2/Ak | 40S ribosomal protein S11 | G1TRM4_RABIT  
1.2/Al | 40S ribosomal protein S12 | G1SFR8_RABIT  
1.2/Am | uS15 | G1SP51_RABIT  
1.2/An | 40S ribosomal protein uS11 | G1T1F0_RABIT  
1.2/Ao | 40S ribosomal protein uS19 | G1U0Q2_RABIT  
1.2/Ap | uS9 | G1SGX4_RABIT  
1.2/Aq | 40S ribosomal protein eS17 | G1TU13_RABIT  
1.2/Ar | 40S ribosomal protein S18 | G1TPG3_RABIT  
1.2/As | Ribosomal protein eS19 |  
1.2/At | 40S ribosomal protein uS10 | G1SIZ2_RABIT  
1.2/Au | Ribosomal protein eS21 |  
1.2/Av | Ribosomal protein S15a | G1TG89_RABIT  
1.2/Aw | 40S ribosomal protein S23 | G1SZ47_RABIT  
1.2/Ax | 40S ribosomal protein S24 | G1T3D8_RABIT  
1.2/Ay | 40S ribosomal protein S25 | G1TDB3_RABIT  
1.2/Az | 60s ribosomal protein l41 | A0A087WNH4_RABIT  
1.2/B5 | 28S rRNA |  
1.2/B7 | 5S rRNA |  
1.2/B8 | 5.8S rRNA |  
1.2/BA | Ribosomal protein uL2 |  
1.2/BB | Ribosomal protein L3 | G1TL06_RABIT  
1.2/BC | 60S ribosomal protein L4 | G1SVW5_RABIT  
1.2/BD | Ribosomal_L18_c domain-containing protein | G1SYJ6_RABIT  
1.2/BE | 60S ribosomal protein L6 | G1SKF7_RABIT  
1.2/BF | Ribosomal Protein uL30 |  
1.2/BG | Ribosomal protein eL8 |  
1.2/BH | 60S ribosomal protein L9 | G1SWI6_RABIT  
1.2/BI | 60S ribosomal protein L10 | B7NZQ2_RABIT  
1.2/BJ | Ribosomal protein L11 | G1TUB8_RABIT  
1.2/BK | Replicase polyprotein 1ab | R1AB_SARS2  
1.2/BL | Ribosomal protein eL13 |  
1.2/BM | Ribosomal protein L14 | G1SZ12_RABIT  
1.2/BN | Ribosomal protein L15 | G1T0C1_RABIT  
1.2/BO | Ribosomal protein uL13 |  
1.2/BP | uL22 | G1TVT6_RABIT  
1.2/BQ | Ribosomal Protein eL18 |  
1.2/BR | 60S ribosomal protein L19 | RL19_BOVIN  
1.2/BS | Ribosomal protein eL20 |  
1.2/BT | eL21 | G1SHQ2_RABIT  
1.2/BU | Ribosomal protein eL22 |  
1.2/BV | Ribosomal protein L23 | G1T6D1_RABIT  
1.2/BW | eL24 | G1SE28_RABIT  
1.2/BX | uL23 | G1SE76_RABIT  
1.2/BY | Ribosomal protein L26 | G1SQH0_RABIT  
1.2/BZ | 60S ribosomal protein L27 | G1TXF6_RABIT  
1.2/Ba | 60S ribosomal protein L27a | G1SNY0_RABIT  
1.2/Bb | 60S ribosomal protein L29 | G1SGR6_RABIT  
1.2/Bc | eL30 | G1TDL2_RABIT  
1.2/Bd | eL31 | G1SHG0_RABIT  
1.2/Be | eL32 | G1U437_RABIT  
1.2/Bf | eL33 | G1SF08_RABIT  
1.2/Bg | 60S ribosomal protein L34 | G1TXG5_RABIT  
1.2/Bh | uL29 | G1SIT5_RABIT  
1.2/Bi | 60S ribosomal protein L36 | G1TTQ5_RABIT  
1.2/Bj | Ribosomal protein L37 | U3KPD5_RABIT  
1.2/Bk | eL38 | G1U001_RABIT  
1.2/Bl | eL39 | G1TTN1_RABIT  
1.2/Bm | 60S ribosomal protein L40 |  
1.2/Bo | eL42 | G1U344_RABIT  
1.2/Bp | eL43 | G1SY53_RABIT  
1.2/Br | Ribosomal protein eL28 |  
1.2/Bs | 60S acidic ribosomal protein P0 | G1SPK4_RABIT  
1.2/Bt | Ribosomal protein L12 | G1SMR7_RABIT  
1.2/Bv | Ribosomal protein uL1 | G1SKZ8_RABIT  
  
Non-standard residues in 7o7y #1.2  
---  
AAC — acetylamino-acetic acid  
B8N —
(2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic
acid  
GTP — guanosine-5'-triphosphate  
MG — magnesium ion  
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))  
SPM — spermine  
UY1 — 2'-O-methylpseudouridine-5'-monophosphate  
ZN — zinc ion  
  

> view :7MG

> select :7MG

76 atoms, 80 bonds, 2 residues, 1 model selected  

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1218 residues in model #1.2 to IUPAC-
IUB standards.  
Forcefield cache not found or out of date. Regenerating from ffXML files. This
is normal if running ISOLDE for the first time, or after upgrading OpenMM.  
Done loading forcefield  
ISOLDE: stopped sim  
Loading residue template for SPD from internal database  
Loading residue template for SPM from internal database  
Deleted the following atoms from residue U A21: OP1  




OpenGL version: 3.3.0 NVIDIA 471.11
OpenGL renderer: NVIDIA GeForce RTX 2080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Notebook                        
Model: P7xxTM1
OS: Microsoft Windows 10 Education (Build 19041)
Memory: 68,654,501,888
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz
OSLanguage: en-GB
Locale: ('en_GB', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    -himerax-clipper: 0.17.0
    -himerax-isolde: 1.3.dev33
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.7
    ChimeraX-AddCharge: 1.2
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.30.2
    ChimeraX-AtomicLibrary: 4.1.5
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3rc202111182158
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.3.dev33
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.7.3
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.2
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.22
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    python-igraph: 0.9.7
    pytz: 2021.3
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.2
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    texttable: 1.6.4
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    versioneer: 0.21
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (3)

in reply to:  1 ; comment:1 by Tristan Croll, 4 years ago 

Actually, pretty much all of the modified guanosine variants have the same issue. Lots in that model: 7MG, 2MG, M2G, etc.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 25 November 2021 19:49
To: Tristan Croll <tic20@cam.ac.uk>
Subject: [ChimeraX] #5684: ChimeraX bug report submission

#5684: ChimeraX bug report submission
---------------------------+-----------------------------
 Reporter:  Tristan Croll  |                Type:  defect
   Status:  new            |            Priority:  normal
Component:  Unassigned     |          Blocked By:
 Blocking:                 |  Notify when closed:
---------------------------+-----------------------------
 {{{
 The following bug report has been submitted:
 Platform:        Windows-10-10.0.19041
 ChimeraX Version: 1.3rc202111182158 (2021-11-18 21:58:36 UTC)
 Description
 (very minor) AddH misses protonating the N1 atom of O-methyguanosine (OMG
 - good examples in 7o7y) - since this is a base-pairing atom it will make
 quite a difference. Interestingly, the base pairing pseudobond is still
 drawn between OMG-N1 and C-N3.

 Log:
 > isolde shorthand


     Initialising ISOLDE-specific command aliases:
     Alias       Equivalent full command
     -------------------------------------------------
     st  isolde step {arguments}
     aw  isolde add water {arguments}
     awsf        isolde add water {arguments} sim false
     al  isolde add ligand {arguments}
     aa  isolde add aa $1 sel {arguments}
     ht  isolde mod his sel {arguments}
     so  setattr sel atoms occupancy {arguments}
     ab  isolde adjust bfactors {arguments}
     ss  isolde sim start sel
     rt  isolde release torsions sel {arguments}
     rd  isolde release distances sel {arguments}
     ra  rd; rt
     pf  isolde pepflip sel
     cf  isolde cisflip sel
     cbb color bfactor {arguments}
     cbo color byattr occupancy {arguments}
     cbc color {arguments} bychain; color {arguments} byhet
     cs  clipper set contourSensitivity {arguments}



 UCSF ChimeraX version: 1.3rc202111182158 (2021-11-18)
 © 2016-2021 Regents of the University of California. All rights reserved.
 How to cite UCSF ChimeraX

 > open 6xz7

 Summary of feedback from opening 6xz7 fetched from pdb
 ---
 notes | Fetching compressed mmCIF 6xz7 from
 http://files.rcsb.org/download/6xz7.cif
 Fetching CCD DI0 from http://ligand-expo.rcsb.org/reports/D/DI0/DI0.cif
 Fetching CCD 31M from http://ligand-expo.rcsb.org/reports/3/31M/31M.cif

 6xz7 title:
 E. coli 50S ribosomal subunit in complex with dirithromycin, fMet-Phe-
 tRNA(Phe) and deacylated tRNA(iMet). [more info...]

 Chain information for 6xz7 #1
 ---
 Chain | Description | UniProt
 A | 23S rRNA |
 B | 5S rRNA |
 C | 50S ribosomal protein L2 | RL2_ECOLI
 D | 50S ribosomal protein L3 | RL3_ECOLI
 E | 50S ribosomal protein L4 | RL4_ECOLI
 F | 50S ribosomal protein L5 | RL5_ECOLI
 G | 50S ribosomal protein L6 | RL6_ECOLI
 H | 50S ribosomal protein L10 | RL10_ECOLI
 I | 50S ribosomal protein L11 | RL11_ECOLI
 J | 50S ribosomal protein L13 | RL13_ECOLI
 K | 50S ribosomal protein L14 | RL14_ECOLI
 L | 50S ribosomal protein L15 | RL15_ECOLI
 M | 50S ribosomal protein L16 | RL16_ECOLI
 N | 50S ribosomal protein L17 | RL17_ECOLI
 O | 50S ribosomal protein L18 | RL18_ECOLI
 P | 50S ribosomal protein L19 | RL19_ECOLI
 Q | 50S ribosomal protein L20 | RL20_ECOLI
 R | 50S ribosomal protein L21 | RL21_ECOLI
 S | 50S ribosomal protein L22 | RL22_ECOLI
 T | 50S ribosomal protein L23 | RL23_ECOLI
 U | 50S ribosomal protein L24 | RL24_ECOLI
 V | 50S ribosomal protein L25 | RL25_ECOLI
 W | 50S ribosomal protein L27 | RL27_ECOLI
 X | 50S ribosomal protein L28 | RL28_ECOLI
 Y | 50S ribosomal protein L29 | RL29_ECOLI
 Z | 50S ribosomal protein L30 | RL30_ECOLI
 a | 50S ribosomal protein L32 | RL32_ECOLI
 b | 50S ribosomal protein L33 | RL33_ECOLI
 c | 50S ribosomal protein L34 | RL34_ECOLI
 d | 50S ribosomal protein L35 | RL35_ECOLI
 e | 50S ribosomal protein L36 | RL36_ECOLI
 f | Deacylated tRNAi(Met) |
 g | fMet-Phe-tRNA(Phe) |

 Non-standard residues in 6xz7 #1
 ---
 DI0 — Dirithromycin
 ((1R,2R,3R,6R,7S,8S,9R,10R,12R,13S,15R,17S)-3-ethyl-2,10-dihydroxy-15-[(2-methoxyethoxy)methyl]-2,6,8,10,12,17-hexamethy
 l-5-oxo-9-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-
 hexopyranosyl]oxy}-4,16-dioxa-14-azabicyclo[11.3.1]heptadecan-7 -yl
 2,6-dideoxy-3-C-methyl-3-O-methyl-alpha-L-ribo-hexopyranoside)
 MG — magnesium ion


 > open 10655 fromDatabase emdb

 Summary of feedback from opening 10655 fetched from emdb
 ---
 note | Fetching compressed map 10655 from
 ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-10655/map/emd_10655.map.gz

 Opened emdb 10655 as #2, grid size 512,512,512, pixel 0.86, shown at level
 0.0232, step 2, values float32

 > clipper associate #2 toModel #1

 Opened emdb 10655 as #1.1.1.1, grid size 512,512,512, pixel 0.86, shown at
 level 0.218, step 1, values float32
 6xz7 title:
 E. coli 50S ribosomal subunit in complex with dirithromycin, fMet-Phe-
 tRNA(Phe) and deacylated tRNA(iMet). [more info...]

 Chain information for 6xz7
 ---
 Chain | Description | UniProt
 1.2/A | 23S rRNA |
 1.2/B | 5S rRNA |
 1.2/C | 50S ribosomal protein L2 | RL2_ECOLI
 1.2/D | 50S ribosomal protein L3 | RL3_ECOLI
 1.2/E | 50S ribosomal protein L4 | RL4_ECOLI
 1.2/F | 50S ribosomal protein L5 | RL5_ECOLI
 1.2/G | 50S ribosomal protein L6 | RL6_ECOLI
 1.2/H | 50S ribosomal protein L10 | RL10_ECOLI
 1.2/I | 50S ribosomal protein L11 | RL11_ECOLI
 1.2/J | 50S ribosomal protein L13 | RL13_ECOLI
 1.2/K | 50S ribosomal protein L14 | RL14_ECOLI
 1.2/L | 50S ribosomal protein L15 | RL15_ECOLI
 1.2/M | 50S ribosomal protein L16 | RL16_ECOLI
 1.2/N | 50S ribosomal protein L17 | RL17_ECOLI
 1.2/O | 50S ribosomal protein L18 | RL18_ECOLI
 1.2/P | 50S ribosomal protein L19 | RL19_ECOLI
 1.2/Q | 50S ribosomal protein L20 | RL20_ECOLI
 1.2/R | 50S ribosomal protein L21 | RL21_ECOLI
 1.2/S | 50S ribosomal protein L22 | RL22_ECOLI
 1.2/T | 50S ribosomal protein L23 | RL23_ECOLI
 1.2/U | 50S ribosomal protein L24 | RL24_ECOLI
 1.2/V | 50S ribosomal protein L25 | RL25_ECOLI
 1.2/W | 50S ribosomal protein L27 | RL27_ECOLI
 1.2/X | 50S ribosomal protein L28 | RL28_ECOLI
 1.2/Y | 50S ribosomal protein L29 | RL29_ECOLI
 1.2/Z | 50S ribosomal protein L30 | RL30_ECOLI
 1.2/a | 50S ribosomal protein L32 | RL32_ECOLI
 1.2/b | 50S ribosomal protein L33 | RL33_ECOLI
 1.2/c | 50S ribosomal protein L34 | RL34_ECOLI
 1.2/d | 50S ribosomal protein L35 | RL35_ECOLI
 1.2/e | 50S ribosomal protein L36 | RL36_ECOLI
 1.2/f | Deacylated tRNAi(Met) |
 1.2/g | fMet-Phe-tRNA(Phe) |

 Non-standard residues in 6xz7 #1.2
 ---
 DI0 — Dirithromycin
 ((1R,2R,3R,6R,7S,8S,9R,10R,12R,13S,15R,17S)-3-ethyl-2,10-dihydroxy-15-[(2-methoxyethoxy)methyl]-2,6,8,10,12,17-hexamethy
 l-5-oxo-9-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-
 hexopyranosyl]oxy}-4,16-dioxa-14-azabicyclo[11.3.1]heptadecan-7 -yl
 2,6-dideoxy-3-C-methyl-3-O-methyl-alpha-L-ribo-hexopyranoside)
 MG — magnesium ion


 > addh

 Summary of feedback from adding hydrogens to 6xz7 #1.2
 ---
 warnings | Not adding hydrogens to /A G 1 P because it is missing heavy-
 atom
 bond partners
 Not adding hydrogens to /B U 1 P because it is missing heavy-atom bond
 partners
 Not adding hydrogens to /W THR 10 CB because it is missing heavy-atom bond
 partners
 Not adding hydrogens to /b ILE 54 CB because it is missing heavy-atom bond
 partners
 Not adding hydrogens to /f G 2 P because it is missing heavy-atom bond
 partners
 notes | Termini for 6xz7 (#1.2) chain A determined from SEQRES records
 Termini for 6xz7 (#1.2) chain B determined from SEQRES records
 Termini for 6xz7 (#1.2) chain C determined from SEQRES records
 Termini for 6xz7 (#1.2) chain D determined from SEQRES records
 Termini for 6xz7 (#1.2) chain E determined from SEQRES records
 28 messages similar to the above omitted
 Chain-initial residues that are actual N termini: /C ALA 2, /D MET 1, /E
 MET
 1, /F ALA 2, /G SER 2, /H ALA 2, /I TYR 8, /J MET 1, /K MET 1, /L MET 1,
 /M
 MET 1, /N MET 1, /O MET 1, /P SER 2, /Q ALA 2, /R MET 1, /S MET 1, /T MET
 1,
 /U ALA 2, /V MET 1, /W THR 10, /X SER 2, /Y LYS 2, /Z ALA 2, /a ALA 2, /b
 GLY
 4, /c MET 1, /d PRO 2, /e MET 1
 Chain-initial residues that are not actual N termini:
 Chain-final residues that are actual C termini: /C SER 272, /D ALA 209, /E
 ALA
 201, /F ARG 178, /G LYS 177, /H ILE 136, /I GLU 141, /J ILE 142, /K LEU
 123,
 /L GLU 144, /M MET 136, /N ALA 125, /O PHE 117, /P ASN 115, /Q ALA 118, /R
 ALA
 103, /S ARG 110, /T LEU 93, /U ILE 103, /V ALA 94, /W GLU 85, /X TYR 78,
 /Y
 ALA 63, /Z GLU 59, /a LYS 57, /b ILE 54, /c LYS 46, /d ALA 65, /e GLY 38
 Chain-final residues that are not actual C termini:
 Missing OXT added to C-terminal residue /H ILE 136
 Missing OXT added to C-terminal residue /I GLU 141
 Missing OXT added to C-terminal residue /K LEU 123
 Missing OXT added to C-terminal residue /N ALA 125
 Missing OXT added to C-terminal residue /b ILE 54
 12368 hydrogen bonds
 62895 hydrogens added


 > view :7MG

 > select :7MG

 38 atoms, 40 bonds, 1 residue, 1 model selected

 > close #1

 > open 7o7y

 Summary of feedback from opening 7o7y fetched from pdb
 ---
 notes | Fetching compressed mmCIF 7o7y from
 http://files.rcsb.org/download/7o7y.cif
 Fetching CCD UNX from http://ligand-expo.rcsb.org/reports/U/UNX/UNX.cif
 Fetching CCD A2M from http://ligand-expo.rcsb.org/reports/A/A2M/A2M.cif
 Fetching CCD B8N from http://ligand-expo.rcsb.org/reports/B/B8N/B8N.cif
 Fetching CCD SAC from http://ligand-expo.rcsb.org/reports/S/SAC/SAC.cif
 Fetching CCD NMM from http://ligand-expo.rcsb.org/reports/N/NMM/NMM.cif
 Fetching CCD AME from http://ligand-expo.rcsb.org/reports/A/AME/AME.cif
 Fetching CCD HY3 from http://ligand-expo.rcsb.org/reports/H/HY3/HY3.cif
 Fetching CCD UY1 from http://ligand-expo.rcsb.org/reports/U/UY1/UY1.cif
 Fetching CCD GTP from http://ligand-expo.rcsb.org/reports/G/GTP/GTP.cif
 Fetching CCD V5N from http://ligand-expo.rcsb.org/reports/V/V5N/V5N.cif
 Fetching CCD AYA from http://ligand-expo.rcsb.org/reports/A/AYA/AYA.cif
 Fetching CCD AAC from http://ligand-expo.rcsb.org/reports/A/AAC/AAC.cif
 Fetching CCD M3L from http://ligand-expo.rcsb.org/reports/M/M3L/M3L.cif

 7o7y title:
 Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site
 by a
 pseudoknot (high resolution) [more info...]

 Chain information for 7o7y #1
 ---
 Chain | Description | UniProt
 A2 | 18S rRNA |
 AA | 40S ribosomal protein S27 | G1TZ76_RABIT
 AB | Ribosomal protein S28 | G1TIB4_RABIT
 AC | Ribosomal protein S27a | G1SK22_RABIT
 AD | 40S ribosomal protein S30 | G1T8A2_RABIT
 AE | Ribosomal protein eS26 |
 AF | RACK1 | G1SJB4_RABIT
 AG | uS14 | G1U7M4_RABIT
 AH | mRNA containing SARS-CoV-2 sequence |
 AI | E-site tRNA |
 AT | P-site Phe-tRNA(Phe) |
 AZ | 40S ribosomal protein SA | G1TLT8_RABIT
 Aa | 40S ribosomal protein S3a | G1SS70_RABIT
 Ab | Ribosomal protein uS5 |
 Ac | 40S ribosomal protein S3 | G1TNM3_RABIT
 Ad | Ribosomal protein eS4 |
 Ae | Ribosomal protein S5 | G1TFM5_RABIT
 Af | 40S ribosomal protein S6 | G1TM55_RABIT
 Ag | 40S ribosomal protein S7 | G1SVB0_RABIT
 Ah | 40S ribosomal protein S8 | G1TJW1_RABIT
 Ai | Ribosomal protein S9 (Predicted) | B7NZS8_RABIT
 Aj | eS10 | G1TPV3_RABIT
 Ak | 40S ribosomal protein S11 | G1TRM4_RABIT
 Al | 40S ribosomal protein S12 | G1SFR8_RABIT
 Am | uS15 | G1SP51_RABIT
 An | 40S ribosomal protein uS11 | G1T1F0_RABIT
 Ao | 40S ribosomal protein uS19 | G1U0Q2_RABIT
 Ap | uS9 | G1SGX4_RABIT
 Aq | 40S ribosomal protein eS17 | G1TU13_RABIT
 Ar | 40S ribosomal protein S18 | G1TPG3_RABIT
 As | Ribosomal protein eS19 |
 At | 40S ribosomal protein uS10 | G1SIZ2_RABIT
 Au | Ribosomal protein eS21 |
 Av | Ribosomal protein S15a | G1TG89_RABIT
 Aw | 40S ribosomal protein S23 | G1SZ47_RABIT
 Ax | 40S ribosomal protein S24 | G1T3D8_RABIT
 Ay | 40S ribosomal protein S25 | G1TDB3_RABIT
 Az | 60s ribosomal protein l41 | A0A087WNH4_RABIT
 B5 | 28S rRNA |
 B7 | 5S rRNA |
 B8 | 5.8S rRNA |
 BA | Ribosomal protein uL2 |
 BB | Ribosomal protein L3 | G1TL06_RABIT
 BC | 60S ribosomal protein L4 | G1SVW5_RABIT
 BD | Ribosomal_L18_c domain-containing protein | G1SYJ6_RABIT
 BE | 60S ribosomal protein L6 | G1SKF7_RABIT
 BF | Ribosomal Protein uL30 |
 BG | Ribosomal protein eL8 |
 BH | 60S ribosomal protein L9 | G1SWI6_RABIT
 BI | 60S ribosomal protein L10 | B7NZQ2_RABIT
 BJ | Ribosomal protein L11 | G1TUB8_RABIT
 BK | Replicase polyprotein 1ab | R1AB_SARS2
 BL | Ribosomal protein eL13 |
 BM | Ribosomal protein L14 | G1SZ12_RABIT
 BN | Ribosomal protein L15 | G1T0C1_RABIT
 BO | Ribosomal protein uL13 |
 BP | uL22 | G1TVT6_RABIT
 BQ | Ribosomal Protein eL18 |
 BR | 60S ribosomal protein L19 | RL19_BOVIN
 BS | Ribosomal protein eL20 |
 BT | eL21 | G1SHQ2_RABIT
 BU | Ribosomal protein eL22 |
 BV | Ribosomal protein L23 | G1T6D1_RABIT
 BW | eL24 | G1SE28_RABIT
 BX | uL23 | G1SE76_RABIT
 BY | Ribosomal protein L26 | G1SQH0_RABIT
 BZ | 60S ribosomal protein L27 | G1TXF6_RABIT
 Ba | 60S ribosomal protein L27a | G1SNY0_RABIT
 Bb | 60S ribosomal protein L29 | G1SGR6_RABIT
 Bc | eL30 | G1TDL2_RABIT
 Bd | eL31 | G1SHG0_RABIT
 Be | eL32 | G1U437_RABIT
 Bf | eL33 | G1SF08_RABIT
 Bg | 60S ribosomal protein L34 | G1TXG5_RABIT
 Bh | uL29 | G1SIT5_RABIT
 Bi | 60S ribosomal protein L36 | G1TTQ5_RABIT
 Bj | Ribosomal protein L37 | U3KPD5_RABIT
 Bk | eL38 | G1U001_RABIT
 Bl | eL39 | G1TTN1_RABIT
 Bm | 60S ribosomal protein L40 |
 Bo | eL42 | G1U344_RABIT
 Bp | eL43 | G1SY53_RABIT
 Br | Ribosomal protein eL28 |
 Bs | 60S acidic ribosomal protein P0 | G1SPK4_RABIT
 Bt | Ribosomal protein L12 | G1SMR7_RABIT
 Bv | Ribosomal protein uL1 | G1SKZ8_RABIT

 Non-standard residues in 7o7y #1
 ---
 AAC — acetylamino-acetic acid
 B8N —
 (2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic
 acid
 GTP — guanosine-5'-triphosphate
 MG — magnesium ion
 SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))
 SPM — spermine
 UNX — unknown atom or ion
 UY1 — 2'-O-methylpseudouridine-5'-monophosphate
 ZN — zinc ion


 > open 12756 fromDatabase emdb

 Summary of feedback from opening 12756 fetched from emdb
 ---
 note | Fetching compressed map 12756 from
 ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-12756/map/emd_12756.map.gz

 Opened emdb 12756 as #2, grid size 560,560,560, pixel 1.06, shown at level
 0.779, step 4, values float32

 > addh

 Summary of feedback from adding hydrogens to 7o7y #1
 ---
 warnings | Not adding hydrogens to /AH A 3456 O3' because it is missing
 heavy-
 atom bond partners
 Not adding hydrogens to /AI N 1 C1' because it is missing heavy-atom bond
 partners
 Not adding hydrogens to /AI N 2 C1' because it is missing heavy-atom bond
 partners
 Not adding hydrogens to /AI N 3 C1' because it is missing heavy-atom bond
 partners
 Not adding hydrogens to /AI N 4 C1' because it is missing heavy-atom bond
 partners
 70 messages similar to the above omitted
 The following atoms were skipped as donors/acceptors due to missing heavy-
 atom
 bond partners: /AH A 3456 O3'
 notes | Termini for 7o7y (#1) chain A2 determined from SEQRES records
 Termini for 7o7y (#1) chain AA determined from SEQRES records
 Termini for 7o7y (#1) chain AB determined from SEQRES records
 Termini for 7o7y (#1) chain AC determined from SEQRES records
 Termini for 7o7y (#1) chain AD determined from SEQRES records
 81 messages similar to the above omitted
 Chain-initial residues that are actual N termini: /Af MET 1, /Aj MET 1,
 /Au
 AME 1, /Az MET 1, /BH MET 1, /BS MET 1, /BW MET 1, /BY MET 1, /Bf MET 1
 Chain-initial residues that are not actual N termini: /AA PRO 2, /AB VAL
 6,
 /AC LYS 78, /AD HIS 77, /AE THR 2, /AF THR 2, /AG GLY 2, /AZ SAC 2, /Aa
 ALA 2,
 /Aa LYS 20, /Ab ASP 57, /Ac VAL 3, /Ad ALA 2, /Ae THR 14, /Ag SER 5, /Ah
 GLY
 2, /Ai PRO 2, /Ak ASP 3, /Al GLY 9, /Am GLY 2, /An SER 16, /Ao THR 11, /Ap
 PRO
 6, /Aq GLY 2, /Ar SAC 2, /As PRO 2, /At ALA 16, /Av VAL 2, /Aw GLY 2, /Ax
 THR
 4, /Ay LYS 31, /BA GLY 2, /BB SER 2, /BC AYA 2, /BD AAC 2, /BE PRO 39, /BE
 GLU
 239, /BF ARG 22, /BG VAL 27, /BG LYS 131, /BI GLY 2, /BJ LYS 8, /BK LEU
 4365,
 /BL ALA 2, /BM VAL 2, /BN GLY 2, /BO GLN 5, /BP VAL 2, /BQ GLY 2, /BR SER
 2,
 /BT THR 2, /BU GLN 17, /BV SER 2, /BX LYS 39, /BZ GLY 2, /Ba PRO 2, /Bb
 ALA 2,
 /Bb VAL 89, /Bc VAL 2, /Bd ASN 18, /Be ALA 2, /Bg VAL 2, /Bh ALA 2, /Bi
 ALA 2,
 /Bj THR 2, /Bk PRO 2, /Bl SER 2, /Bm ILE 77, /Bo VAL 2, /Bp ALA 2, /Br SAC
 2,
 /Bs ASP 5, /Bt GLU 9, /Bv SER 6
 Chain-final residues that are actual C termini: /AA HIS 84, /AD SER 133,
 /AG
 ASP 56, /Ad GLY 263, /Ae ARG 204, /Ag LEU 194, /Al LYS 132, /Am ALA 151,
 /An
 LEU 151, /Ap ARG 146, /Aq VAL 135, /At ALA 119, /Au PHE 83, /Av PHE 130,
 /Az
 LYS 25, /BE PHE 291, /BF ASN 247, /BG GLY 266, /BI SER 214, /BL LYS 211,
 /BN
 ARG 204, /BO VAL 203, /BQ ASN 188, /BS PHE 176, /BT ALA 160, /BV ALA 140,
 /BX
 ILE 156, /BZ PHE 136, /Ba ALA 148, /Bf ILE 110, /Bh ALA 123, /Bk LYS 70,
 /Bl
 LEU 51, /Bm LYS 128, /Bo PHE 106, /Bp GLN 92, /Bv TYR 217
 Chain-final residues that are not actual C termini: /AB LEU 68, /AC ASN
 151,
 /AE ARG 102, /AF ILE 314, /AZ VAL 222, /Aa LYS 11, /Aa GLY 233, /Ab THR
 276,
 /Ac LYS 227, /Af LEU 237, /Ah GLY 207, /Ai GLY 186, /Aj ARG 96, /Ak GLN
 156,
 /Ao SER 138, /Ar SER 149, /As LYS 144, /Aw ARG 142, /Ax GLY 128, /Ay GLY
 115,
 /BA GLU 254, /BB LYS 399, /BC ASP 363, /BD ALA 295, /BE PRO 228, /BG ALA
 123,
 /BH ALA 190, /BJ GLY 177, /BK PHE 4399, /BM SER 139, /BP PRO 160, /BR LYS
 181,
 /BU PHE 115, /BW ALA 121, /BY LYS 134, /Bb VAL 76, /Bb PRO 121, /Bc PRO
 109,
 /Bd GLU 124, /Be SER 131, /Bg LYS 115, /Bi LYS 103, /Bj LYS 87, /Br LYS
 127,
 /Bs ASN 200, /Bt ALA 164
 Chain-initial residues that are not actual 5' termini: /AH A 3456
 Missing OXT added to C-terminal residue /Ag LEU 194
 Missing OXT added to C-terminal residue /Aq VAL 135
 Missing OXT added to C-terminal residue /Au PHE 83
 Missing OXT added to C-terminal residue /Az LYS 25
 Missing OXT added to C-terminal residue /Bo PHE 106
 1 messages similar to the above omitted
 66494 hydrogen bonds
 Adding 'H' to /AB VAL 6
 Adding 'H' to /AC LYS 78
 Adding 'H' to /AD HIS 77
 Adding 'H' to /AE THR 2
 Adding 'H' to /AF THR 2
 56 messages similar to the above omitted
 /AB LEU 68 is not terminus, removing H atom from 'C'
 /AC ASN 151 is not terminus, removing H atom from 'C'
 /AE ARG 102 is not terminus, removing H atom from 'C'
 /AF ILE 314 is not terminus, removing H atom from 'C'
 /AZ VAL 222 is not terminus, removing H atom from 'C'
 36 messages similar to the above omitted
 190814 hydrogens added


 > clipper associate #2 toModel #1

 Opened emdb 12756 as #1.1.1.1, grid size 560,560,560, pixel 1.06, shown at
 level 1.54, step 1, values float32
 7o7y title:
 Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site
 by a
 pseudoknot (high resolution) [more info...]

 Chain information for 7o7y
 ---
 Chain | Description | UniProt
 1.2/A2 | 18S rRNA |
 1.2/AA | 40S ribosomal protein S27 | G1TZ76_RABIT
 1.2/AB | Ribosomal protein S28 | G1TIB4_RABIT
 1.2/AC | Ribosomal protein S27a | G1SK22_RABIT
 1.2/AD | 40S ribosomal protein S30 | G1T8A2_RABIT
 1.2/AE | Ribosomal protein eS26 |
 1.2/AF | RACK1 | G1SJB4_RABIT
 1.2/AG | uS14 | G1U7M4_RABIT
 1.2/AH | mRNA containing SARS-CoV-2 sequence |
 1.2/AI | E-site tRNA |
 1.2/AT | P-site Phe-tRNA(Phe) |
 1.2/AZ | 40S ribosomal protein SA | G1TLT8_RABIT
 1.2/Aa | 40S ribosomal protein S3a | G1SS70_RABIT
 1.2/Ab | Ribosomal protein uS5 |
 1.2/Ac | 40S ribosomal protein S3 | G1TNM3_RABIT
 1.2/Ad | Ribosomal protein eS4 |
 1.2/Ae | Ribosomal protein S5 | G1TFM5_RABIT
 1.2/Af | 40S ribosomal protein S6 | G1TM55_RABIT
 1.2/Ag | 40S ribosomal protein S7 | G1SVB0_RABIT
 1.2/Ah | 40S ribosomal protein S8 | G1TJW1_RABIT
 1.2/Ai | Ribosomal protein S9 (Predicted) | B7NZS8_RABIT
 1.2/Aj | eS10 | G1TPV3_RABIT
 1.2/Ak | 40S ribosomal protein S11 | G1TRM4_RABIT
 1.2/Al | 40S ribosomal protein S12 | G1SFR8_RABIT
 1.2/Am | uS15 | G1SP51_RABIT
 1.2/An | 40S ribosomal protein uS11 | G1T1F0_RABIT
 1.2/Ao | 40S ribosomal protein uS19 | G1U0Q2_RABIT
 1.2/Ap | uS9 | G1SGX4_RABIT
 1.2/Aq | 40S ribosomal protein eS17 | G1TU13_RABIT
 1.2/Ar | 40S ribosomal protein S18 | G1TPG3_RABIT
 1.2/As | Ribosomal protein eS19 |
 1.2/At | 40S ribosomal protein uS10 | G1SIZ2_RABIT
 1.2/Au | Ribosomal protein eS21 |
 1.2/Av | Ribosomal protein S15a | G1TG89_RABIT
 1.2/Aw | 40S ribosomal protein S23 | G1SZ47_RABIT
 1.2/Ax | 40S ribosomal protein S24 | G1T3D8_RABIT
 1.2/Ay | 40S ribosomal protein S25 | G1TDB3_RABIT
 1.2/Az | 60s ribosomal protein l41 | A0A087WNH4_RABIT
 1.2/B5 | 28S rRNA |
 1.2/B7 | 5S rRNA |
 1.2/B8 | 5.8S rRNA |
 1.2/BA | Ribosomal protein uL2 |
 1.2/BB | Ribosomal protein L3 | G1TL06_RABIT
 1.2/BC | 60S ribosomal protein L4 | G1SVW5_RABIT
 1.2/BD | Ribosomal_L18_c domain-containing protein | G1SYJ6_RABIT
 1.2/BE | 60S ribosomal protein L6 | G1SKF7_RABIT
 1.2/BF | Ribosomal Protein uL30 |
 1.2/BG | Ribosomal protein eL8 |
 1.2/BH | 60S ribosomal protein L9 | G1SWI6_RABIT
 1.2/BI | 60S ribosomal protein L10 | B7NZQ2_RABIT
 1.2/BJ | Ribosomal protein L11 | G1TUB8_RABIT
 1.2/BK | Replicase polyprotein 1ab | R1AB_SARS2
 1.2/BL | Ribosomal protein eL13 |
 1.2/BM | Ribosomal protein L14 | G1SZ12_RABIT
 1.2/BN | Ribosomal protein L15 | G1T0C1_RABIT
 1.2/BO | Ribosomal protein uL13 |
 1.2/BP | uL22 | G1TVT6_RABIT
 1.2/BQ | Ribosomal Protein eL18 |
 1.2/BR | 60S ribosomal protein L19 | RL19_BOVIN
 1.2/BS | Ribosomal protein eL20 |
 1.2/BT | eL21 | G1SHQ2_RABIT
 1.2/BU | Ribosomal protein eL22 |
 1.2/BV | Ribosomal protein L23 | G1T6D1_RABIT
 1.2/BW | eL24 | G1SE28_RABIT
 1.2/BX | uL23 | G1SE76_RABIT
 1.2/BY | Ribosomal protein L26 | G1SQH0_RABIT
 1.2/BZ | 60S ribosomal protein L27 | G1TXF6_RABIT
 1.2/Ba | 60S ribosomal protein L27a | G1SNY0_RABIT
 1.2/Bb | 60S ribosomal protein L29 | G1SGR6_RABIT
 1.2/Bc | eL30 | G1TDL2_RABIT
 1.2/Bd | eL31 | G1SHG0_RABIT
 1.2/Be | eL32 | G1U437_RABIT
 1.2/Bf | eL33 | G1SF08_RABIT
 1.2/Bg | 60S ribosomal protein L34 | G1TXG5_RABIT
 1.2/Bh | uL29 | G1SIT5_RABIT
 1.2/Bi | 60S ribosomal protein L36 | G1TTQ5_RABIT
 1.2/Bj | Ribosomal protein L37 | U3KPD5_RABIT
 1.2/Bk | eL38 | G1U001_RABIT
 1.2/Bl | eL39 | G1TTN1_RABIT
 1.2/Bm | 60S ribosomal protein L40 |
 1.2/Bo | eL42 | G1U344_RABIT
 1.2/Bp | eL43 | G1SY53_RABIT
 1.2/Br | Ribosomal protein eL28 |
 1.2/Bs | 60S acidic ribosomal protein P0 | G1SPK4_RABIT
 1.2/Bt | Ribosomal protein L12 | G1SMR7_RABIT
 1.2/Bv | Ribosomal protein uL1 | G1SKZ8_RABIT

 Non-standard residues in 7o7y #1.2
 ---
 AAC — acetylamino-acetic acid
 B8N —
 (2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic
 acid
 GTP — guanosine-5'-triphosphate
 MG — magnesium ion
 SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))
 SPM — spermine
 UY1 — 2'-O-methylpseudouridine-5'-monophosphate
 ZN — zinc ion


 > view :7MG

 > select :7MG

 76 atoms, 80 bonds, 2 residues, 1 model selected

 > isolde start

 > set selectionWidth 4

 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
 chains...
 ISOLDE: Corrected atom nomenclature of 1218 residues in model #1.2 to
 IUPAC-
 IUB standards.
 Forcefield cache not found or out of date. Regenerating from ffXML files.
 This
 is normal if running ISOLDE for the first time, or after upgrading OpenMM.
 Done loading forcefield
 ISOLDE: stopped sim
 Loading residue template for SPD from internal database
 Loading residue template for SPM from internal database
 Deleted the following atoms from residue U A21: OP1




 OpenGL version: 3.3.0 NVIDIA 471.11
 OpenGL renderer: NVIDIA GeForce RTX 2080/PCIe/SSE2
 OpenGL vendor: NVIDIA Corporation
 Manufacturer: Notebook
 Model: P7xxTM1
 OS: Microsoft Windows 10 Education (Build 19041)
 Memory: 68,654,501,888
 MaxProcessMemory: 137,438,953,344
 CPU: 16 Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz
 OSLanguage: en-GB
 Locale: ('en_GB', 'cp1252')
 PyQt5 5.15.2, Qt 5.15.2
 Installed Packages:
     -himerax-clipper: 0.17.0
     -himerax-isolde: 1.3.dev33
     alabaster: 0.7.12
     appdirs: 1.4.4
     Babel: 2.9.1
     backcall: 0.2.0
     blockdiag: 2.0.1
     certifi: 2021.10.8
     cftime: 1.5.1.1
     charset-normalizer: 2.0.7
     ChimeraX-AddCharge: 1.2
     ChimeraX-AddH: 2.1.10
     ChimeraX-AlignmentAlgorithms: 2.0
     ChimeraX-AlignmentHdrs: 3.2
     ChimeraX-AlignmentMatrices: 2.0
     ChimeraX-Alignments: 2.2.3
     ChimeraX-AlphaFold: 1.0
     ChimeraX-AltlocExplorer: 1.0.1
     ChimeraX-AmberInfo: 1.0
     ChimeraX-Arrays: 1.0
     ChimeraX-Atomic: 1.30.2
     ChimeraX-AtomicLibrary: 4.1.5
     ChimeraX-AtomSearch: 2.0
     ChimeraX-AtomSearchLibrary: 1.0
     ChimeraX-AxesPlanes: 2.0
     ChimeraX-BasicActions: 1.1
     ChimeraX-BILD: 1.0
     ChimeraX-BlastProtein: 2.0
     ChimeraX-BondRot: 2.0
     ChimeraX-BugReporter: 1.0
     ChimeraX-BuildStructure: 2.6
     ChimeraX-Bumps: 1.0
     ChimeraX-BundleBuilder: 1.1
     ChimeraX-ButtonPanel: 1.0
     ChimeraX-CageBuilder: 1.0
     ChimeraX-CellPack: 1.0
     ChimeraX-Centroids: 1.2
     ChimeraX-ChemGroup: 2.0
     ChimeraX-Clashes: 2.2.2
     ChimeraX-Clipper: 0.17.0
     ChimeraX-ColorActions: 1.0
     ChimeraX-ColorGlobe: 1.0
     ChimeraX-ColorKey: 1.5
     ChimeraX-CommandLine: 1.1.5
     ChimeraX-ConnectStructure: 2.0
     ChimeraX-Contacts: 1.0
     ChimeraX-Core: 1.3rc202111182158
     ChimeraX-CoreFormats: 1.1
     ChimeraX-coulombic: 1.3.1
     ChimeraX-Crosslinks: 1.0
     ChimeraX-Crystal: 1.0
     ChimeraX-CrystalContacts: 1.0
     ChimeraX-DataFormats: 1.2.2
     ChimeraX-Dicom: 1.0
     ChimeraX-DistMonitor: 1.1.5
     ChimeraX-DistUI: 1.0
     ChimeraX-Dssp: 2.0
     ChimeraX-EMDB-SFF: 1.0
     ChimeraX-ExperimentalCommands: 1.0
     ChimeraX-FileHistory: 1.0
     ChimeraX-FunctionKey: 1.0
     ChimeraX-Geometry: 1.1
     ChimeraX-gltf: 1.0
     ChimeraX-Graphics: 1.1
     ChimeraX-Hbonds: 2.1.2
     ChimeraX-Help: 1.2
     ChimeraX-HKCage: 1.3
     ChimeraX-IHM: 1.1
     ChimeraX-ImageFormats: 1.2
     ChimeraX-IMOD: 1.0
     ChimeraX-IO: 1.0.1
     ChimeraX-ISOLDE: 1.3.dev33
     ChimeraX-ItemsInspection: 1.0
     ChimeraX-Label: 1.1
     ChimeraX-ListInfo: 1.1.1
     ChimeraX-Log: 1.1.4
     ChimeraX-LookingGlass: 1.1
     ChimeraX-Maestro: 1.8.1
     ChimeraX-Map: 1.1
     ChimeraX-MapData: 2.0
     ChimeraX-MapEraser: 1.0
     ChimeraX-MapFilter: 2.0
     ChimeraX-MapFit: 2.0
     ChimeraX-MapSeries: 2.1
     ChimeraX-Markers: 1.0
     ChimeraX-Mask: 1.0
     ChimeraX-MatchMaker: 2.0.4
     ChimeraX-MDcrds: 2.6
     ChimeraX-MedicalToolbar: 1.0.1
     ChimeraX-Meeting: 1.0
     ChimeraX-MLP: 1.1
     ChimeraX-mmCIF: 2.4
     ChimeraX-MMTF: 2.1
     ChimeraX-Modeller: 1.2.6
     ChimeraX-ModelPanel: 1.2.1
     ChimeraX-ModelSeries: 1.0
     ChimeraX-Mol2: 2.0
     ChimeraX-Morph: 1.0
     ChimeraX-MouseModes: 1.1
     ChimeraX-Movie: 1.0
     ChimeraX-Neuron: 1.0
     ChimeraX-Nucleotides: 2.0.2
     ChimeraX-OpenCommand: 1.7
     ChimeraX-PDB: 2.6.5
     ChimeraX-PDBBio: 1.0
     ChimeraX-PDBLibrary: 1.0.2
     ChimeraX-PDBMatrices: 1.0
     ChimeraX-PickBlobs: 1.0
     ChimeraX-Positions: 1.0
     ChimeraX-PresetMgr: 1.0.1
     ChimeraX-PubChem: 2.1
     ChimeraX-ReadPbonds: 1.0.1
     ChimeraX-Registration: 1.1
     ChimeraX-RemoteControl: 1.0
     ChimeraX-ResidueFit: 1.0
     ChimeraX-RestServer: 1.1
     ChimeraX-RNALayout: 1.0
     ChimeraX-RotamerLibMgr: 2.0.1
     ChimeraX-RotamerLibsDunbrack: 2.0
     ChimeraX-RotamerLibsDynameomics: 2.0
     ChimeraX-RotamerLibsRichardson: 2.0
     ChimeraX-SaveCommand: 1.5
     ChimeraX-SchemeMgr: 1.0
     ChimeraX-SDF: 2.0
     ChimeraX-Segger: 1.0
     ChimeraX-Segment: 1.0
     ChimeraX-SelInspector: 1.0
     ChimeraX-SeqView: 2.4.6
     ChimeraX-Shape: 1.0.1
     ChimeraX-Shell: 1.0
     ChimeraX-Shortcuts: 1.1
     ChimeraX-ShowAttr: 1.0
     ChimeraX-ShowSequences: 1.0
     ChimeraX-SideView: 1.0
     ChimeraX-Smiles: 2.1
     ChimeraX-SmoothLines: 1.0
     ChimeraX-SpaceNavigator: 1.0
     ChimeraX-StdCommands: 1.6.1
     ChimeraX-STL: 1.0
     ChimeraX-Storm: 1.0
     ChimeraX-Struts: 1.0
     ChimeraX-Surface: 1.0
     ChimeraX-SwapAA: 2.0
     ChimeraX-SwapRes: 2.1
     ChimeraX-TapeMeasure: 1.0
     ChimeraX-Test: 1.0
     ChimeraX-Toolbar: 1.1
     ChimeraX-ToolshedUtils: 1.2
     ChimeraX-Tug: 1.0
     ChimeraX-UI: 1.13.7
     ChimeraX-uniprot: 2.2
     ChimeraX-UnitCell: 1.0
     ChimeraX-ViewDockX: 1.0.1
     ChimeraX-VIPERdb: 1.0
     ChimeraX-Vive: 1.1
     ChimeraX-VolumeMenu: 1.0
     ChimeraX-VTK: 1.0
     ChimeraX-WavefrontOBJ: 1.0
     ChimeraX-WebCam: 1.0
     ChimeraX-WebServices: 1.0
     ChimeraX-Zone: 1.0
     colorama: 0.4.4
     comtypes: 1.1.10
     cxservices: 1.1
     cycler: 0.11.0
     Cython: 0.29.24
     decorator: 5.1.0
     docutils: 0.17.1
     filelock: 3.0.12
     funcparserlib: 0.3.6
     grako: 3.16.5
     h5py: 3.6.0
     html2text: 2020.1.16
     idna: 3.3
     ihm: 0.21
     imagecodecs: 2021.4.28
     imagesize: 1.3.0
     ipykernel: 5.5.5
     ipython: 7.23.1
     ipython-genutils: 0.2.0
     jedi: 0.18.0
     Jinja2: 3.0.1
     jupyter-client: 6.1.12
     jupyter-core: 4.9.1
     kiwisolver: 1.3.2
     lxml: 4.6.3
     lz4: 3.1.3
     MarkupSafe: 2.0.1
     matplotlib: 3.4.3
     matplotlib-inline: 0.1.3
     msgpack: 1.0.2
     netCDF4: 1.5.7
     networkx: 2.6.3
     numexpr: 2.7.3
     numpy: 1.21.2
     openvr: 1.16.801
     packaging: 21.3
     ParmEd: 3.4.3
     parso: 0.8.2
     pickleshare: 0.7.5
     Pillow: 8.3.2
     pip: 21.2.4
     pkginfo: 1.7.1
     prompt-toolkit: 3.0.22
     psutil: 5.8.0
     pycollada: 0.7.1
     pydicom: 2.1.2
     Pygments: 2.10.0
     PyOpenGL: 3.1.5
     PyOpenGL-accelerate: 3.1.5
     pyparsing: 3.0.6
     PyQt5-commercial: 5.15.2
     PyQt5-sip: 12.8.1
     PyQtWebEngine-commercial: 5.15.2
     python-dateutil: 2.8.2
     python-igraph: 0.9.7
     pytz: 2021.3
     pywin32: 228
     pyzmq: 22.3.0
     qtconsole: 5.1.1
     QtPy: 1.11.2
     RandomWords: 0.3.0
     requests: 2.26.0
     scipy: 1.7.1
     setuptools: 57.5.0
     sfftk-rw: 0.7.1
     six: 1.16.0
     snowballstemmer: 2.2.0
     sortedcontainers: 2.4.0
     Sphinx: 4.2.0
     sphinx-autodoc-typehints: 1.12.0
     sphinxcontrib-applehelp: 1.0.2
     sphinxcontrib-blockdiag: 2.0.0
     sphinxcontrib-devhelp: 1.0.2
     sphinxcontrib-htmlhelp: 2.0.0
     sphinxcontrib-jsmath: 1.0.1
     sphinxcontrib-qthelp: 1.0.3
     sphinxcontrib-serializinghtml: 1.1.5
     suds-jurko: 0.6
     tables: 3.6.1
     texttable: 1.6.4
     tifffile: 2021.4.8
     tinyarray: 1.2.3
     tornado: 6.1
     traitlets: 5.1.1
     urllib3: 1.26.7
     versioneer: 0.21
     wcwidth: 0.2.5
     webcolors: 1.11.1
     wheel: 0.37.0
     wheel-filename: 1.3.0
     WMI: 1.5.1

 }}}

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5684>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:2 by pett, 4 years ago

Component: Unassigned → Structure Editing
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → AddH protonation issue

comment:3 by pett, 4 years ago

Status: accepted → feedback

The base-pairing pseudobonds are added by the mmCIF reader based on records from the input file. They aren't necessarily the H-bonds you would get if you ran the hbond command.

As you may be aware, the keto form of guanine can be protonated at either the N3 or N1 positions, but is almost always protonated at the N1 position due to its base-pairing hydrogen bonds with cytosine. This is enforced for non-modified nucleic acids by the IDATM templates for G/DG. There is no template for OMG, so the atom typing / protonation is based on internal bonds and distances and not possible hydrogen bonding possibilities.

For the first example of OMG protonation I looked at, it's questionable that N1 should be the protonated position. The example is OMG 3676 in chain B5 (mis)pairing with U 3797 in chain B5. Protonating N1 puts a hydrogen in very close proximity to the mandatory hydrogen for atom N3 in the U residue -- 1.7 angstroms.

Conversely, not protonating the N1 when base pairing with C (/B5: 15 residues, /B8: 1 residue) is clearly wrong, or when H-bonding to the phosphate backbone (/B5:1580), or when the N3 interacts with the aniline of a G (/B5:4245).

For a higher resolution structure (e.g. 1jbs) all the base pairing OMG N1s are protonated, since the greater accuracy of the bond lengths allows the typing to get the right tautomer.

Are you not using "template true" when running addh? "template true" will always protonate the N1.

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