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Opened 4 years ago
Closed 3 years ago
#5687 closed defect (fixed)
AddH: spurious OXT
| Reported by: | Tristan Croll | Owned by: | pett |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Editing | Version: | |
| Keywords: | Cc: | Greg Couch | |
| 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
Addh adds a spurious OXT to the C of residue name 010 (/C:6) of 7bqy.
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
> isolde ignore :b*N
ISOLDE: currently ignoring 1 residues in model 1.2
> isolde ~ignore
> isolde ignore :B8N
ISOLDE: currently ignoring 1 residues in model 1.2
ISOLDE: stopped sim
> show sel
> cs 0.25
Deleted the following atoms from residue SPM A21909: H11, H12, H142, H141,
H51, H52, H101, H102, H13, H143
> delete sel
[Repeated 1 time(s)]
> isolde ignore :N
ISOLDE: currently ignoring 74 residues in model 1.2
Deleted the following atoms from residue G AT1: OP1
Fetching CCD ALA_LL from http://ligand-
expo.rcsb.org/reports/A/ALA_LL/ALA_LL.cif
Fetching CCD ALA_LEO2 from http://ligand-
expo.rcsb.org/reports/A/ALA_LEO2/ALA_LEO2.cif
Fetching CCD ALA_LFZW from http://ligand-
expo.rcsb.org/reports/A/ALA_LFZW/ALA_LFZW.cif
Deleted the following atoms from residue C B51: OP1
Traceback (most recent call last):
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\validation\unparameterised.py", line 198, in
_fix_selected_unparameterised_residue
indices = [i for i in range(table.rowCount()) if table.item(i,
0).data(USER_ROLE)[0].name == residue.name]
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\validation\unparameterised.py", line 198, in
<listcomp>
indices = [i for i in range(table.rowCount()) if table.item(i,
0).data(USER_ROLE)[0].name == residue.name]
File "atomic_cpp\cymol.pyx", line 1209, in
chimerax.atomic.cymol.CyResidue.name.__get__
RuntimeError: Residue already deleted
RuntimeError: Residue already deleted
File "atomic_cpp\cymol.pyx", line 1209, in
chimerax.atomic.cymol.CyResidue.name.__get__
See log for complete Python traceback.
Deleted the following atoms from residue SPM B54912: H51, H52, H143, H13,
H142, H11, H101, H141, H12, H102
Deleted the following atoms from residue SPM B54915: H51, H52, H101, H11, H12,
H102, H13, H141, H142, H143
> isolde ignore sel
ISOLDE: currently ignoring 75 residues in model 1.2
Deleted the following atoms from residue C B81: OP1
Deleted the following atoms from residue U B851: OP1
> isolde ignore sel
ISOLDE: currently ignoring 76 residues in model 1.2
> isolde ignore sel
ISOLDE: currently ignoring 77 residues in model 1.2
> select :7MG
76 atoms, 80 bonds, 2 residues, 1 model selected
> set bgColor white
ISOLDE: started sim
> select clear
> style sel ball
Changed 1 atom style
> style sel sphere
Changed 1 atom style
> style sel ball
Changed 1 atom style
> hide #1.2.4 models
> select clear
ISOLDE: paused sim
ISOLDE: resumed sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> close #1
> open 7bqy structureFactors true
Summary of feedback from opening 7bqy fetched from pdb
---
warning | WARNING: multiple experimental reflection datasets found:
F_meas_au, F_meas_sigma_au,
intensity_meas, intensity_sigma
Automatically choosing "F_meas_au, F_meas_sigma_au".
notes | Fetching compressed mmCIF 7bqy from
http://files.rcsb.org/download/7bqy.cif
Fetching CCD 02J from http://ligand-expo.rcsb.org/reports/0/02J/02J.cif
Fetching CCD PJE from http://ligand-expo.rcsb.org/reports/P/PJE/PJE.cif
Fetching CCD 010 from http://ligand-expo.rcsb.org/reports/0/010/010.cif
Fetching compressed 7bqy structure factors from
http://files.rcsb.org/download/7bqy-sf.cif
Resolution: 1.6967983026346858
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 70,46,50, pixel
0.535,0.559,0.543, shown at level 0.531, step 1, values float32
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 70,46,50, pixel
0.535,0.559,0.543, shown at level -0.123,0.123, step 1, values float32
Opened (LIVE) 2mFo-DFc_smooth_20 as #1.1.1.4, grid size 70,46,50, pixel
0.535,0.559,0.543, shown at level 0.4, step 1, values float32
7bqy title:
THE CRYSTAL STRUCTURE OF COVID-19 MAIN PROTEASE IN COMPLEX WITH AN INHIBITOR
N3 at 1.7 angstrom [more info...]
Chain information for 7bqy
---
Chain | Description | UniProt
1.2/A | 3C-like proteinase | R1AB_SARS2
1.2/C | N-[(5-methylisoxazol-3-yl)carbonyl]alanyl-L-
valyl-N~1~-((1R,2Z)-4-(benzyloxy)-4-oxo-1-{[(3R)-2-oxopyrrolidin-3-yl]methyl}but-2-enyl)-L-leucinamide
|
Non-standard residues in 7bqy #1.2
---
010 — phenylmethanol
02J — 5-methyl-1,2-oxazole-3-carboxylic acid
PJE — (E,4S)-4-azanyl-5-[(3S)-2-oxidanylidenepyrrolidin-3-yl]pent-2-enoic acid
7bqy mmCIF Assemblies
---
1| author_and_software_defined_assembly
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 20 residues in model #1.2 to IUPAC-IUB
standards.
Opened (LIVE) MDFF potential as #1.1.1.5, grid size 70,46,50, pixel
0.535,0.559,0.543, shown at level 0.386, step 1, values float32
> view :PJE
> select clear
> addh
Summary of feedback from adding hydrogens to 7bqy #1.2
---
notes | Termini for 7bqy (#1.2) chain A determined from SEQRES records
Termini for 7bqy (#1.2) chain C determined from SEQRES records
Chain-initial residues that are actual N termini: /A SER 1, /C 02J 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /C 010 6
Chain-final residues that are not actual C termini: /A SER 301
Missing OXT added to C-terminal residue /C 010 6
696 hydrogen bonds
/A SER 301 is not terminus, removing H atom from 'C'
2639 hydrogens added
> view ::name=010&@C
No objects specified.
> view :01O@C
No objects specified.
> select ::name="010"
14 atoms, 14 bonds, 1 residue, 1 model selected
> view sel
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)
comment:1 by , 4 years ago
| Component: | Unassigned → Structure Editing |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → AddH: spurious OXT |
comment:2 by , 4 years ago
| Cc: | added |
|---|
comment:3 by , 3 years ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
Not really sure if the mmCIF or PDB treatment is better (lean to PDB), but I've changed AddH to not try to "complete" a C-terminus that doesn't look like a carboxylate: https://github.com/RBVI/ChimeraX/commit/26956fbda6f937df3dc233daab57eeaa76d834c0
Committed to develop and 1.6 release branches.
Note:
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for help on using tickets.
Using the PDB format version, chain C correctly contains only the A-V-L residues and the others are treated as non-polymeric entities covalently bound to the peptide chain (and therefore addh works correctly) despite all the residues being in the SEQRES records (or equivalent). Will need to investigate how to make the mmCIF processing smarter in this regard.