The following bug report has been submitted:
Platform: macOS-12.5.1-arm64-arm-64bit
ChimeraX Version: 1.6rc202304252053 (2023-04-25 20:53:05 UTC)
Description
7jqm breaks AddH. :)
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: 1.6rc202304252053 (2023-04-25)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 6nak structureFactors true
Summary of feedback from opening 6nak fetched from pdb
---
warning | WARNING: multiple experimental reflection datasets found:
F_meas_au, F_meas_sigma_au,
phase_calc, fom
Automatically choosing "F_meas_au, F_meas_sigma_au".
notes | Fetching compressed mmCIF 6nak from
http://files.rcsb.org/download/6nak.cif
Fetching CCD TXA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/TXA/TXA.cif
Fetching CCD APC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/APC/APC.cif
Fetching compressed 6nak structure factors from
http://files.rcsb.org/download/6nak-sf.cif
Resolution: 3.1410925635747495
Launching live xmap mgr took 1.1173429489135742 seconds.
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 26,24,26, pixel 1,1.02,0.986,
shown at level 0.122, step 1, values float32
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 26,24,26, pixel 1,1.02,0.986,
shown at level -0.0739,0.0739, step 1, values float32
Opened (LIVE) 2mFo-DFc_sharp_34 as #1.1.1.4, grid size 26,24,26, pixel
1,1.02,0.986, shown at level 0.424, step 1, values float32
Opened (STATIC) F_calc_au, phase_calc as #1.1.1.5, grid size 26,24,26, pixel
1,1.02,0.986, shown at level -0.678,0.678, step 1, values float32
Opened (STATIC) pdbx_DELFWT, pdbx_DELPHWT as #1.1.1.6, grid size 26,24,26,
pixel 1,1.02,0.986, shown at level -0.121,0.121, step 1, values float32
Opened (STATIC) pdbx_FWT, pdbx_PHWT as #1.1.1.7, grid size 26,24,26, pixel
1,1.02,0.986, shown at level -0.38,0.38, step 1, values float32
6nak title:
BACTERIAL PROTEIN COMPLEX TM BDE complex [more info...]
Chain information for 6nak
---
Chain | Description | UniProt
1.2/A 1.2/C | tRNA threonylcarbamoyladenosine biosynthesis protein TsaB |
TSAB_THEMA 1-206
1.2/B 1.2/G | tRNA N6-adenosine threonylcarbamoyltransferase | TSAD_THEMA
1-327
1.2/D 1.2/E | TsaE | R4NRX5_THEMA -7-161
Non-standard residues in 6nak #1.2
---
APC — diphosphomethylphosphonic acid adenosyl ester
(α,β-methyleneadenosine-5'-triphosphate)
MG — magnesium ion
TXA — threonylcarbamoyladenylate
ZN — zinc ion
> addh
Summary of feedback from adding hydrogens to 6nak #1.2
---
warning | Not adding hydrogens to /G LYS 38 CB because it is missing heavy-
atom bond partners
notes | Termini for 6nak (#1.2) chain A determined from SEQRES records
Termini for 6nak (#1.2) chain B determined from SEQRES records
Termini for 6nak (#1.2) chain D determined from SEQRES records
Termini for 6nak (#1.2) chain C determined from SEQRES records
Termini for 6nak (#1.2) chain G determined from SEQRES records
1 messages similar to the above omitted
Chain-initial residues that are actual N termini: /A MET 1, /B MET 1, /C MET
1, /G MET 1
Chain-initial residues that are not actual N termini: /D GLU -3, /G GLU 45, /E
LYS 0
Chain-final residues that are actual C termini: /B VAL 327, /D THR 161, /C GLY
206, /G VAL 327
Chain-final residues that are not actual C termini: /A LYS 203, /G LYS 38, /E
ASN 160
Missing OXT added to C-terminal residue /D THR 161
1149 hydrogen bonds
Adding 'H' to /D GLU -3
Adding 'H' to /G GLU 45
Adding 'H' to /E LYS 0
/A LYS 203 is not terminus, removing H atom from 'C'
/E ASN 160 is not terminus, removing H atom from 'C'
11203 hydrogens added
> isolde start
> set selectionWidth 4
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 92 residues in model #1.2 to IUPAC-IUB
standards.
Opened (LIVE) MDFF potential as #1.1.1.8, grid size 26,24,26, pixel
1,1.02,0.986, shown at level 0.381, step 1, values float32
Loading residue template for APC from internal database
Loading residue template for TXA from internal database
> isolde sim start sel
ISOLDE: started sim
> select clear
> isolde report
4 models selected
[Repeated 1 time(s)]
> close #1.1.1
Deleting Crystallographic maps(6nak-sf.cif)
Deleting (LIVE) 2mFo-DFc
Deleting (LIVE) mFo-DFc
Deleting (LIVE) 2mFo-DFc_sharp_34
Deleting (LIVE) MDFF potential
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> close
> open 6nak structureFactors true
Summary of feedback from opening 6nak fetched from pdb
---
warning | WARNING: multiple experimental reflection datasets found:
F_meas_au, F_meas_sigma_au,
phase_calc, fom
Automatically choosing "F_meas_au, F_meas_sigma_au".
notes | Resolution: 3.1410925635747495
Launching live xmap mgr took 1.2058329582214355 seconds.
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 26,24,26, pixel 1,1.02,0.986,
shown at level 0.123, step 1, values float32
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 26,24,26, pixel 1,1.02,0.986,
shown at level -0.075,0.075, step 1, values float32
Opened (LIVE) 2mFo-DFc_sharp_34 as #1.1.1.4, grid size 26,24,26, pixel
1,1.02,0.986, shown at level 0.426, step 1, values float32
Opened (STATIC) F_calc_au, phase_calc as #1.1.1.5, grid size 26,24,26, pixel
1,1.02,0.986, shown at level -0.678,0.678, step 1, values float32
Opened (STATIC) pdbx_DELFWT, pdbx_DELPHWT as #1.1.1.6, grid size 26,24,26,
pixel 1,1.02,0.986, shown at level -0.121,0.121, step 1, values float32
Opened (STATIC) pdbx_FWT, pdbx_PHWT as #1.1.1.7, grid size 26,24,26, pixel
1,1.02,0.986, shown at level -0.38,0.38, step 1, values float32
6nak title:
BACTERIAL PROTEIN COMPLEX TM BDE complex [more info...]
Chain information for 6nak
---
Chain | Description | UniProt
1.2/A 1.2/C | tRNA threonylcarbamoyladenosine biosynthesis protein TsaB |
TSAB_THEMA 1-206
1.2/B 1.2/G | tRNA N6-adenosine threonylcarbamoyltransferase | TSAD_THEMA
1-327
1.2/D 1.2/E | TsaE | R4NRX5_THEMA -7-161
Non-standard residues in 6nak #1.2
---
APC — diphosphomethylphosphonic acid adenosyl ester
(α,β-methyleneadenosine-5'-triphosphate)
MG — magnesium ion
TXA — threonylcarbamoyladenylate
ZN — zinc ion
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 92 residues in model #1.2 to IUPAC-IUB
standards.
Opened (LIVE) MDFF potential as #1.1.1.8, grid size 26,24,26, pixel
1,1.02,0.986, shown at level 0.378, step 1, values float32
> close #1.1.1.5-7
> addh
Summary of feedback from adding hydrogens to 6nak #1.2
---
warning | Not adding hydrogens to /G LYS 38 CB because it is missing heavy-
atom bond partners
notes | Termini for 6nak (#1.2) chain A determined from SEQRES records
Termini for 6nak (#1.2) chain B determined from SEQRES records
Termini for 6nak (#1.2) chain D determined from SEQRES records
Termini for 6nak (#1.2) chain C determined from SEQRES records
Termini for 6nak (#1.2) chain G determined from SEQRES records
1 messages similar to the above omitted
Chain-initial residues that are actual N termini: /A MET 1, /B MET 1, /C MET
1, /G MET 1
Chain-initial residues that are not actual N termini: /D GLU -3, /G GLU 45, /E
LYS 0
Chain-final residues that are actual C termini: /B VAL 327, /D THR 161, /C GLY
206, /G VAL 327
Chain-final residues that are not actual C termini: /A LYS 203, /G LYS 38, /E
ASN 160
Missing OXT added to C-terminal residue /D THR 161
1149 hydrogen bonds
Adding 'H' to /D GLU -3
Adding 'H' to /G GLU 45
Adding 'H' to /E LYS 0
/A LYS 203 is not terminus, removing H atom from 'C'
/E ASN 160 is not terminus, removing H atom from 'C'
11203 hydrogens added
> select clear
> ui tool show "Ramachandran Plot"
> ui tool show Shell
> close
Deleting Crystallographic maps(6nak-sf.cif)
Deleting (LIVE) 2mFo-DFc
Deleting (LIVE) mFo-DFc
Deleting (LIVE) 2mFo-DFc_sharp_34
Deleting (LIVE) MDFF potential
> open 6nak structureFactors true
Summary of feedback from opening 6nak fetched from pdb
---
warning | WARNING: multiple experimental reflection datasets found:
F_meas_au, F_meas_sigma_au,
phase_calc, fom
Automatically choosing "F_meas_au, F_meas_sigma_au".
notes | Resolution: 3.1410925635747495
Launching live xmap mgr took 1.1217522621154785 seconds.
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 26,24,26, pixel 1,1.02,0.986,
shown at level 0.122, step 1, values float32
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 26,24,26, pixel 1,1.02,0.986,
shown at level -0.0742,0.0742, step 1, values float32
Opened (LIVE) 2mFo-DFc_sharp_34 as #1.1.1.4, grid size 26,24,26, pixel
1,1.02,0.986, shown at level 0.425, step 1, values float32
Opened (STATIC) F_calc_au, phase_calc as #1.1.1.5, grid size 26,24,26, pixel
1,1.02,0.986, shown at level -0.678,0.678, step 1, values float32
Opened (STATIC) pdbx_DELFWT, pdbx_DELPHWT as #1.1.1.6, grid size 26,24,26,
pixel 1,1.02,0.986, shown at level -0.121,0.121, step 1, values float32
Opened (STATIC) pdbx_FWT, pdbx_PHWT as #1.1.1.7, grid size 26,24,26, pixel
1,1.02,0.986, shown at level -0.38,0.38, step 1, values float32
6nak title:
BACTERIAL PROTEIN COMPLEX TM BDE complex [more info...]
Chain information for 6nak
---
Chain | Description | UniProt
1.2/A 1.2/C | tRNA threonylcarbamoyladenosine biosynthesis protein TsaB |
TSAB_THEMA 1-206
1.2/B 1.2/G | tRNA N6-adenosine threonylcarbamoyltransferase | TSAD_THEMA
1-327
1.2/D 1.2/E | TsaE | R4NRX5_THEMA -7-161
Non-standard residues in 6nak #1.2
---
APC — diphosphomethylphosphonic acid adenosyl ester
(α,β-methyleneadenosine-5'-triphosphate)
MG — magnesium ion
TXA — threonylcarbamoyladenylate
ZN — zinc ion
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 92 residues in model #1.2 to IUPAC-IUB
standards.
Opened (LIVE) MDFF potential as #1.1.1.8, grid size 26,24,26, pixel
1,1.02,0.986, shown at level 0.379, step 1, values float32
> select #1
10983 atoms, 11176 bonds, 12 pseudobonds, 1395 residues, 33 models selected
> close
Deleting Crystallographic maps(6nak-sf.cif)
Deleting (LIVE) 2mFo-DFc
Deleting (LIVE) mFo-DFc
Deleting (LIVE) 2mFo-DFc_sharp_34
Deleting (LIVE) MDFF potential
> open 8hkj structureFactors true
Summary of feedback from opening 8hkj fetched from pdb
---
warning | WARNING: multiple experimental reflection datasets found:
F_meas_au, F_meas_sigma_au,
pdbx_F_plus, pdbx_F_plus_sigma, pdbx_F_minus, pdbx_F_minus_sigma,
pdbx_anom_difference, pdbx_anom_difference_sigma,
intensity_meas, intensity_sigma,
pdbx_I_plus, pdbx_I_plus_sigma, pdbx_I_minus, pdbx_I_minus_sigma
Automatically choosing "F_meas_au, F_meas_sigma_au".
notes | Fetching compressed mmCIF 8hkj from
http://files.rcsb.org/download/8hkj.cif
Fetching CCD PLM from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/PLM/PLM.cif
Fetching compressed 8hkj structure factors from
http://files.rcsb.org/download/8hkj-sf.cif
Resolution: 2.800001345548072
Launching live xmap mgr took 1.8189010620117188 seconds.
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 36,30,28, pixel
0.895,0.875,0.873, shown at level 0.131, step 1, values float32
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 36,30,28, pixel
0.895,0.875,0.873, shown at level -0.0883,0.0883, step 1, values float32
Opened (LIVE) 2mFo-DFc_sharp_22 as #1.1.1.4, grid size 36,30,28, pixel
0.895,0.875,0.873, shown at level 0.416, step 1, values float32
8hkj title:
Crystal structure of the CYP102A5 haem Domain isolated from Bacillus cereus
[more info...]
Chain information for 8hkj
---
Chain | Description | UniProt
1.2/A 1.2/B 1.2/C 1.2/D 1.2/E 1.2/F 1.2/G 1.2/H 1.2/I 1.2/J 1.2/K 1.2/L |
Bifunctional cytochrome P450/NADPH--P450 reductase | A0A853ZNE6_BACCE 1-458
Non-standard residues in 8hkj #1.2
---
HEM — protoporphyrin IX containing Fe (HEME)
PLM — palmitic acid
8hkj mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
4| author_and_software_defined_assembly
5| author_and_software_defined_assembly
6| author_and_software_defined_assembly
7| author_and_software_defined_assembly
8| author_and_software_defined_assembly
9| author_and_software_defined_assembly
10| author_and_software_defined_assembly
11| author_and_software_defined_assembly
12| author_and_software_defined_assembly
> view #1
> addh
Summary of feedback from adding hydrogens to 8hkj #1.2
---
warning | Not adding hydrogens to /L ARG 182 CB because it is missing heavy-
atom bond partners
notes | Termini for 8hkj (#1.2) chain A determined from SEQRES records
Termini for 8hkj (#1.2) chain B determined from SEQRES records
Termini for 8hkj (#1.2) chain C determined from SEQRES records
Termini for 8hkj (#1.2) chain D determined from SEQRES records
Termini for 8hkj (#1.2) chain E determined from SEQRES records
7 messages similar to the above omitted
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: /A ALA 7, /A GLN 209, /B
ILE 8, /B GLN 209, /C ILE 8, /C HIS 210, /C GLU 234, /D VAL 5, /D HIS 210, /D
GLU 234, /E ILE 8, /E GLN 209, /E ASN 235, /F SER 6, /F HIS 210, /F ASP 236,
/G SER 6, /G SER 214, /G ASP 236, /G ASP 254, /H ILE 8, /H ASP 211, /H ASN
235, /I ILE 8, /I SER 214, /I PRO 247, /J ALA 7, /J ILE 212, /J ASP 236, /K
SER 6, /K GLN 213, /K ASN 235, /L ILE 8, /L ILE 212, /L ASP 236
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A ALA 187, /A ARG 456, /B
HIS 189, /B ARG 456, /C GLU 186, /C SER 229, /C PRO 455, /D LEU 184, /D GLU
225, /D ARG 456, /E ASP 185, /E GLY 230, /E ARG 456, /F LEU 184, /F SER 228,
/F ARG 456, /G LEU 184, /G GLU 225, /G LEU 242, /G ARG 456, /H LEU 184, /H ARG
226, /H ARG 456, /I LEU 184, /I ARG 226, /I PRO 455, /J ASP 185, /J ARG 226,
/J ARG 456, /K ASP 185, /K ARG 226, /K ARG 456, /L ALA 183, /L ARG 226, /L LEU
454
4856 hydrogen bonds
Adding 'H' to /A ALA 7
Adding 'H' to /A GLN 209
Adding 'H' to /B ILE 8
Adding 'H' to /B GLN 209
Adding 'H' to /C ILE 8
29 messages similar to the above omitted
/A ARG 456 is not terminus, removing H atom from 'C'
/B ARG 456 is not terminus, removing H atom from 'C'
/C PRO 455 is not terminus, removing H atom from 'C'
/D ARG 456 is not terminus, removing H atom from 'C'
/E ARG 456 is not terminus, removing H atom from 'C'
7 messages similar to the above omitted
40987 hydrogens added
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 236 residues in model #1.2 to IUPAC-IUB
standards.
Opened (LIVE) MDFF potential as #1.1.1.5, grid size 36,30,28, pixel
0.895,0.875,0.873, shown at level 0.377, step 1, values float32
Loading residue template for PLM from internal database
> close
Deleting Crystallographic maps(8hkj-sf.cif)
Deleting (LIVE) 2mFo-DFc
Deleting (LIVE) mFo-DFc
Deleting (LIVE) 2mFo-DFc_sharp_22
Deleting (LIVE) MDFF potential
> open 8cjh structureFactors true
Summary of feedback from opening 8cjh 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 8cjh from
http://files.rcsb.org/download/8cjh.cif
Fetching compressed 8cjh structure factors from
http://files.rcsb.org/download/8cjh-sf.cif
Resolution: 2.981685584195263
Launching live xmap mgr took 2.118582010269165 seconds.
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 28,26,26, pixel
0.977,0.972,0.972, shown at level 0.1, step 1, values float32
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 28,26,26, pixel
0.977,0.972,0.972, shown at level -0.0632,0.0632, step 1, values float32
Opened (LIVE) 2mFo-DFc_sharp_29 as #1.1.1.4, grid size 28,26,26, pixel
0.977,0.972,0.972, shown at level 0.336, step 1, values float32
8cjh title:
Architecture of a PKS-NRPS hybrid megaenzyme involved in the biosynthesis of
the genotoxin colibactin [more info...]
Chain information for 8cjh
---
Chain | Description | UniProt
1.2/A 1.2/B 1.2/C 1.2/D 1.2/E 1.2/F | Colibactin hybrid non-ribosomal peptide
synthetase/type I polyketide synthase ClbK | Q0P7K1_ECOLX 1-787
8cjh mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> addh
Summary of feedback from adding hydrogens to 8cjh #1.2
---
notes | Termini for 8cjh (#1.2) chain A determined from SEQRES records
Termini for 8cjh (#1.2) chain B determined from SEQRES records
Termini for 8cjh (#1.2) chain C determined from SEQRES records
Termini for 8cjh (#1.2) chain D determined from SEQRES records
Termini for 8cjh (#1.2) chain E determined from SEQRES records
1 messages similar to the above omitted
Chain-initial residues that are actual N termini: /A MET 1, /B MET 1, /C MET
1, /D MET 1
Chain-initial residues that are not actual N termini: /A CYS 632, /B CYS 632,
/C CYS 632, /D CYS 632, /E ASN 706, /F ASN 706
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A ASP 619, /A ARG 696, /B
ASP 619, /B ARG 696, /C ASP 619, /C ARG 696, /D ASP 619, /D ARG 696, /E LEU
783, /F LEU 783
2715 hydrogen bonds
Adding 'H' to /A CYS 632
Adding 'H' to /B CYS 632
Adding 'H' to /C CYS 632
Adding 'H' to /D CYS 632
Adding 'H' to /E ASN 706
1 messages similar to the above omitted
/A ARG 696 is not terminus, removing H atom from 'C'
/B ARG 696 is not terminus, removing H atom from 'C'
/C ARG 696 is not terminus, removing H atom from 'C'
/D ARG 696 is not terminus, removing H atom from 'C'
/E LEU 783 is not terminus, removing H atom from 'C'
1 messages similar to the above omitted
21604 hydrogens added
> view #1&protein
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 189 residues in model #1.2 to IUPAC-IUB
standards.
Opened (LIVE) MDFF potential as #1.1.1.5, grid size 28,26,26, pixel
0.977,0.972,0.972, shown at level 0.298, step 1, values float32
> isolde sim start sel
ISOLDE: started sim
> select clear
> alphafold match \1/E
Missing or invalid "sequences" argument: Sequences argument "\1/E" is not a
chain specifier, alignment id, UniProt id, or sequence characters
> alphafold match #1/E
1 UniProt id does not have an AlphaFold database model: Q0P7K1 (chain E)
Fetching compressed AlphaFold A0A7B5G0N4 from
https://alphafold.ebi.ac.uk/files/AF-A0A7B5G0N4-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A0A7B5G0N4 (chain
E)
AlphaFold prediction matching 8cjh
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
E | A0A7B5G0N4 | A0A7B5G0N4_ECOLX | 0.88 | 787 | 78 | 100
Opened 1 AlphaFold model
> show #2
> hide #!2 models
> isolde sim pause
> close
Sim termination reason: model deleted
ISOLDE: model deleted during running simulation.
Deleting Crystallographic maps(8cjh-sf.cif)
Deleting (LIVE) 2mFo-DFc
Deleting (LIVE) mFo-DFc
Deleting (LIVE) 2mFo-DFc_sharp_29
Deleting (LIVE) MDFF potential
> open 7jqm structureFactors true
Summary of feedback from opening 7jqm fetched from pdb
---
notes | Fetching compressed mmCIF 7jqm from
http://files.rcsb.org/download/7jqm.cif
Fetching CCD 5MU from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/5MU/5MU.cif
Fetching CCD 4OC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/4OC/4OC.cif
Fetching CCD 5MC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/5MC/5MC.cif
Fetching CCD OMG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/OMG/OMG.cif
Fetching CCD 2MA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/2MA/2MA.cif
Fetching CCD 2MU from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/2MU/2MU.cif
Fetching CCD 7MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/7MG/7MG.cif
Fetching CCD M2G from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/M2G/M2G.cif
Fetching CCD 2MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/2MG/2MG.cif
Fetching CCD UR3 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/3/UR3/UR3.cif
Fetching CCD MA6 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/6/MA6/MA6.cif
Fetching CCD 0TD from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/0TD/0TD.cif
Fetching CCD 4SU from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/4SU/4SU.cif
Fetching compressed 7jqm structure factors from
http://files.rcsb.org/download/7jqm-sf.cif
Resolution: 3.050001149974444
Launching live xmap mgr took 10.615027904510498 seconds.
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 28,26,26, pixel
0.966,0.999,0.956, shown at level 0.176, step 1, values float32
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 28,26,26, pixel
0.966,0.999,0.956, shown at level -0.124,0.124, step 1, values float32
Opened (LIVE) 2mFo-DFc_sharp_31 as #1.1.1.4, grid size 28,26,26, pixel
0.966,0.999,0.956, shown at level 0.611, step 1, values float32
7jqm title:
Crystal structure of the Thermus thermophilus 70S ribosome in complex with
Bac7-002, mRNA, and deacylated P-site tRNA at 3.05A resolution [more info...]
Chain information for 7jqm
---
Chain | Description | UniProt
1.2/10 1.2/20 | 50S ribosomal protein L27 | RL27_THET8 1-85
1.2/11 1.2/21 | 50S ribosomal protein L28 | RL28_THET8 1-98
1.2/12 1.2/22 | 50S ribosomal protein L29 | RL29_THET8 1-72
1.2/13 1.2/23 | 50S ribosomal protein L30 | RL30_THET8 1-60
1.2/14 1.2/24 | 50S ribosomal protein L31 | RL31_THET8 1-71
1.2/15 1.2/25 | 50S ribosomal protein L32 | RL32_THET8 1-60
1.2/16 1.2/26 | 50S ribosomal protein L33 | RL33_THET8 1-54
1.2/17 1.2/27 | 50S ribosomal protein L34 | RL34_THET8 1-49
1.2/18 1.2/28 | 50S ribosomal protein L35 | RL35_THET8 1-65
1.2/19 1.2/29 | 50S ribosomal protein L36 | RL36_THET8 1-37
1.2/1A 1.2/2A | 23S Ribosomal RNA |
1.2/1B 1.2/2B | 5S Ribosomal RNA |
1.2/1D 1.2/2D | 50S ribosomal protein L2 | RL2_THET8 1-276
1.2/1E 1.2/2E | 50S ribosomal protein L3 | RL3_THET8 1-206
1.2/1F 1.2/2F | 50S ribosomal protein L4 | RL4_THET8 1-210
1.2/1G 1.2/2G | 50S ribosomal protein L5 | RL5_THET8 1-182
1.2/1H 1.2/2H | 50S ribosomal protein L6 | RL6_THET8 1-180
1.2/1I 1.2/2I | 50S ribosomal protein L9 | RL9_THET8 1-148
1.2/1N 1.2/2N | 50S ribosomal protein L13 | RL13_THET8 1-140
1.2/1O 1.2/2O | 50S ribosomal protein L14 | RL14_THET8 1-122
1.2/1P 1.2/2P | 50S ribosomal protein L15 | RL15_THET8 1-150
1.2/1Q 1.2/2Q | 50S ribosomal protein L16 | RL16_THET8 1-141
1.2/1R 1.2/2R | 50S ribosomal protein L17 | RL17_THET8 1-118
1.2/1S 1.2/2S | 50S ribosomal protein L18 | RL18_THET8 1-112
1.2/1T 1.2/2T | 50S ribosomal protein L19 | RL19_THET8 1-146
1.2/1U 1.2/2U | 50S ribosomal protein L20 | RL20_THET8 1-118
1.2/1V 1.2/2V | 50S ribosomal protein L21 | RL21_THET8 1-101
1.2/1W 1.2/2W | 50S ribosomal protein L22 | RL22_THET8 1-113
1.2/1X 1.2/2X | 50S ribosomal protein L23 | RL23_THET8 1-96
1.2/1Y 1.2/2Y | 50S ribosomal protein L24 | RL24_THET8 1-110
1.2/1Z 1.2/2Z | 50S ribosomal protein L25 | RL25_THET8 1-206
1.2/1a 1.2/2a | 16S Ribosomal RNA |
1.2/1b 1.2/2b | 30S ribosomal protein S2 | RS2_THET8 1-256
1.2/1c 1.2/2c | 30S ribosomal protein S3 | RS3_THET8 1-239
1.2/1d 1.2/2d | 30S ribosomal protein S4 | RS4_THET8 1-209
1.2/1e 1.2/2e | 30S ribosomal protein S5 | RS5_THET8 1-162
1.2/1f 1.2/2f | 30S ribosomal protein S6 | RS6_THET8 1-101
1.2/1g 1.2/2g | 30S ribosomal protein S7 | RS7_THET8 1-156
1.2/1h 1.2/2h | 30S ribosomal protein S8 | RS8_THET8 1-138
1.2/1i 1.2/2i | 30S ribosomal protein S9 | RS9_THET8 1-128
1.2/1j 1.2/2j | 30S ribosomal protein S10 | RS10_THET8 1-105
1.2/1k 1.2/2k | 30S ribosomal protein S11 | RS11_THET8 1-129
1.2/1l 1.2/2l | 30S ribosomal protein S12 | RS12_THET8 4-135
1.2/1m 1.2/2m | 30S ribosomal protein S13 | RS13_THET8 1-126
1.2/1n 1.2/2n | 30S ribosomal protein S14 type Z | RS14Z_THET8 1-61
1.2/1o 1.2/2o | 30S ribosomal protein S15 | RS15_THET8 1-89
1.2/1p 1.2/2p | 30S ribosomal protein S16 | RS16_THET8 1-88
1.2/1q 1.2/2q | 30S ribosomal protein S17 | RS17_THET8 1-105
1.2/1r 1.2/2r | 30S ribosomal protein S18 | RS18_THET8 1-88
1.2/1s 1.2/2s | 30S ribosomal protein S19 | RS19_THET8 1-93
1.2/1t 1.2/2t | 30S ribosomal protein S20 | RS20_THET8 1-106
1.2/1u 1.2/2u | 30S ribosomal protein Thx | RSHX_THET8 1-27
1.2/1v 1.2/2v | mRNA |
1.2/1x 1.2/2x | P-site tRNA |
1.2/1z 1.2/2z | Bac7-002 |
Non-standard residues in 7jqm #1.2
---
K — potassium ion
MG — magnesium ion
SF4 — iron/sulfur cluster
ZN — zinc ion
7jqm mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> view #1
> addh
Summary of feedback from adding hydrogens to 7jqm #1.2
---
warnings | Not adding hydrogens to /1A A 6 P because it is missing heavy-atom
bond partners
Not adding hydrogens to /1D ARG 262 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /1D ARG 268 NE because it is missing heavy-atom bond
partners
Not adding hydrogens to /1E LYS 57 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /1F VAL 6 CB because it is missing heavy-atom bond
partners
347 messages similar to the above omitted
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /1F GLY 208 N; /1D ARG 268 NE; /1g ARG 149 NE; /1f ARG 3 NE;
/2F GLY 208 N; /2D ARG 268 NE; /2f ARG 3 NE; /2g ARG 149 NE
notes | Termini for 7jqm (#1.2) chain 1A determined from SEQRES records
Termini for 7jqm (#1.2) chain 1B determined from SEQRES records
Termini for 7jqm (#1.2) chain 1D determined from SEQRES records
Termini for 7jqm (#1.2) chain 1E determined from SEQRES records
Termini for 7jqm (#1.2) chain 1F determined from SEQRES records
105 messages similar to the above omitted
Chain-initial residues that are actual N termini: /1E MET 1, /1I MET 1, /1N
MET 1, /1O MET 1, /1P MET 1, /1Q MET 1, /1R MET 1, /1T MET 1, /1V MET 1, /1W
MET 1, /1X MET 1, /1Y MET 1, /1Z MET 1, /12 MET 1, /14 MET 1, /17 MET 1, /19
MET 1, /1f MET 1, /1p MET 1, /1z ARG 1, /2E MET 1, /2I MET 1, /2N MET 1, /2O
MET 1, /2P MET 1, /2Q MET 1, /2R MET 1, /2T MET 1, /2V MET 1, /2W MET 1, /2X
MET 1, /2Y MET 1, /2Z MET 1, /22 MET 1, /24 MET 1, /27 MET 1, /29 MET 1, /2f
MET 1, /2p MET 1, /2z ARG 1
Chain-initial residues that are not actual N termini: /1D ALA 2, /1F VAL 6,
/1G PRO 2, /1H SER 2, /1S ARG 3, /1U PRO 2, /1Z GLU 119, /1Z ILE 146, /10 SER
9, /11 SER 2, /13 PRO 2, /15 ALA 2, /16 ALA 2, /18 PRO 2, /1b VAL 7, /1c GLY
2, /1d GLY 2, /1e ASP 5, /1g ALA 2, /1h LEU 2, /1i GLU 2, /1j ILE 4, /1k GLN
13, /1l PRO 5, /1m ALA 2, /1n ALA 2, /1o PRO 2, /1q PRO 2, /1r ALA 20, /1s PRO
2, /1t ARG 8, /1u GLY 2, /2D ALA 2, /2F VAL 6, /2G PRO 2, /2H SER 2, /2S ARG
3, /2U PRO 2, /2Z HIS 121, /20 SER 9, /21 SER 2, /23 PRO 2, /25 ALA 2, /26 ALA
2, /28 PRO 2, /2b VAL 7, /2c GLY 2, /2d GLY 2, /2e ASP 5, /2g ALA 2, /2h LEU
2, /2i GLU 2, /2j ARG 5, /2k GLN 13, /2l PRO 5, /2m ARG 3, /2n ALA 2, /2o PRO
2, /2q PRO 2, /2r ALA 20, /2s PRO 2, /2t ARG 8, /2u GLY 2
Chain-final residues that are actual C termini: /1D LYS 276, /1G LYS 182, /1N
VAL 140, /1O LEU 122, /1Q GLN 141, /1R GLU 118, /1S PHE 112, /1V GLY 101, /11
LEU 98, /13 GLU 60, /15 VAL 60, /16 ILE 54, /18 GLU 65, /19 GLY 37, /1d ARG
209, /1g TRP 156, /1h TRP 138, /1i ARG 128, /1n TRP 61, /1o GLY 89, /1z ARG
16, /2D LYS 276, /2G LYS 182, /2N VAL 140, /2O LEU 122, /2Q GLN 141, /2R GLU
118, /2S PHE 112, /2V GLY 101, /21 LEU 98, /23 GLU 60, /25 VAL 60, /26 ILE 54,
/28 GLU 65, /29 GLY 37, /2d ARG 209, /2g TRP 156, /2h TRP 138, /2i ARG 128,
/2n TRP 61, /2o GLY 89, /2z ARG 16
Chain-final residues that are not actual C termini: /1E ALA 204, /1F GLY 208,
/1H LYS 175, /1I ALA 146, /1P GLU 149, /1T ALA 131, /1U GLN 117, /1W GLY 112,
/1X LEU 95, /1Y ASP 107, /1Z VAL 105, /1Z VAL 141, /1Z ILE 171, /10 LEU 84,
/12 GLN 70, /14 LYS 69, /17 LYS 48, /1b ALA 237, /1c VAL 207, /1e ARG 152, /1f
ASN 100, /1j THR 100, /1k ARG 126, /1l LYS 126, /1m PRO 124, /1p GLN 82, /1q
LYS 100, /1r ARG 87, /1s GLY 84, /1t GLY 103, /1u ARG 24, /2E ALA 204, /2F GLY
208, /2H LYS 175, /2I ALA 146, /2P GLU 149, /2T ALA 131, /2U GLN 117, /2W GLY
112, /2X LEU 95, /2Y ASP 107, /2Z GLY 106, /2Z VAL 174, /20 LEU 84, /22 GLN
70, /24 LYS 69, /27 LYS 48, /2b ALA 237, /2c VAL 207, /2e ARG 152, /2f ASN
100, /2j THR 100, /2k ARG 126, /2l LYS 126, /2m PRO 124, /2p GLN 82, /2q LYS
100, /2r ARG 87, /2s GLY 84, /2t GLY 103, /2u ARG 24
Chain-initial residues that are not actual 5' termini: /1A A 6, /1a U 4, /1v A
12, /1x G 2, /2A A 6, /2a U 4, /2v A 12, /2x G 2
Missing OXT added to C-terminal residue /1z ARG 16
Missing OXT added to C-terminal residue /23 GLU 60
Missing OXT added to C-terminal residue /2z ARG 16
35457 hydrogen bonds
Adding 'H' to /1D ALA 2
Adding 'H' to /1F VAL 6
Adding 'H' to /1H SER 2
Adding 'H' to /1S ARG 3
Adding 'H' to /1Z GLU 119
42 messages similar to the above omitted
/1E ALA 204 is not terminus, removing H atom from 'C'
/1H LYS 175 is not terminus, removing H atom from 'C'
/1I ALA 146 is not terminus, removing H atom from 'C'
/1P GLU 149 is not terminus, removing H atom from 'C'
/1T ALA 131 is not terminus, removing H atom from 'C'
51 messages similar to the above omitted
/1A U 2897 is not terminus, removing H atom from O3'
/1B A 120 is not terminus, removing H atom from O3'
/2A U 2897 is not terminus, removing H atom from O3'
/2B A 120 is not terminus, removing H atom from O3'
/2a U 1532 is not terminus, removing H atom from O3'
197376 hydrogens added
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1447 residues in model #1.2 to IUPAC-
IUB standards.
Opened (LIVE) MDFF potential as #1.1.1.5, grid size 28,26,26, pixel
0.966,0.999,0.956, shown at level 0.529, step 1, values float32
> addh #1.2
Summary of feedback from adding hydrogens to 7jqm #1.2
---
warnings | Not adding hydrogens to /1A A 6 P because it is missing heavy-atom
bond partners
Not adding hydrogens to /1D ARG 262 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /1D ARG 268 NE because it is missing heavy-atom bond
partners
Not adding hydrogens to /1E LYS 57 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /1F VAL 6 CB because it is missing heavy-atom bond
partners
347 messages similar to the above omitted
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /2F GLY 208 N; /1D ARG 268 NE; /1g ARG 149 NE; /1f ARG 3 NE;
/1F GLY 208 N; /2D ARG 268 NE; /2f ARG 3 NE; /2g ARG 149 NE
notes | Termini for 7jqm (#1.2) chain 1A determined from SEQRES records
Termini for 7jqm (#1.2) chain 1B determined from SEQRES records
Termini for 7jqm (#1.2) chain 1D determined from SEQRES records
Termini for 7jqm (#1.2) chain 1E determined from SEQRES records
Termini for 7jqm (#1.2) chain 1F determined from SEQRES records
105 messages similar to the above omitted
Chain-initial residues that are actual N termini: /1E MET 1, /1I MET 1, /1N
MET 1, /1O MET 1, /1P MET 1, /1Q MET 1, /1R MET 1, /1T MET 1, /1V MET 1, /1W
MET 1, /1X MET 1, /1Y MET 1, /1Z MET 1, /12 MET 1, /14 MET 1, /17 MET 1, /19
MET 1, /1f MET 1, /1p MET 1, /1z ARG 1, /2E MET 1, /2I MET 1, /2N MET 1, /2O
MET 1, /2P MET 1, /2Q MET 1, /2R MET 1, /2T MET 1, /2V MET 1, /2W MET 1, /2X
MET 1, /2Y MET 1, /2Z MET 1, /22 MET 1, /24 MET 1, /27 MET 1, /29 MET 1, /2f
MET 1, /2p MET 1, /2z ARG 1
Chain-initial residues that are not actual N termini: /1D ALA 2, /1F VAL 6,
/1G PRO 2, /1H SER 2, /1S ARG 3, /1U PRO 2, /1Z GLU 119, /1Z ILE 146, /10 SER
9, /11 SER 2, /13 PRO 2, /15 ALA 2, /16 ALA 2, /18 PRO 2, /1b VAL 7, /1c GLY
2, /1d GLY 2, /1e ASP 5, /1g ALA 2, /1h LEU 2, /1i GLU 2, /1j ILE 4, /1k GLN
13, /1l PRO 5, /1m ALA 2, /1n ALA 2, /1o PRO 2, /1q PRO 2, /1r ALA 20, /1s PRO
2, /1t ARG 8, /1u GLY 2, /2D ALA 2, /2F VAL 6, /2G PRO 2, /2H SER 2, /2S ARG
3, /2U PRO 2, /2Z HIS 121, /20 SER 9, /21 SER 2, /23 PRO 2, /25 ALA 2, /26 ALA
2, /28 PRO 2, /2b VAL 7, /2c GLY 2, /2d GLY 2, /2e ASP 5, /2g ALA 2, /2h LEU
2, /2i GLU 2, /2j ARG 5, /2k GLN 13, /2l PRO 5, /2m ARG 3, /2n ALA 2, /2o PRO
2, /2q PRO 2, /2r ALA 20, /2s PRO 2, /2t ARG 8, /2u GLY 2
Chain-final residues that are actual C termini: /1D LYS 276, /1G LYS 182, /1N
VAL 140, /1O LEU 122, /1Q GLN 141, /1R GLU 118, /1S PHE 112, /1V GLY 101, /11
LEU 98, /13 GLU 60, /15 VAL 60, /16 ILE 54, /18 GLU 65, /19 GLY 37, /1d ARG
209, /1g TRP 156, /1h TRP 138, /1i ARG 128, /1n TRP 61, /1o GLY 89, /1z ARG
16, /2D LYS 276, /2G LYS 182, /2N VAL 140, /2O LEU 122, /2Q GLN 141, /2R GLU
118, /2S PHE 112, /2V GLY 101, /21 LEU 98, /23 GLU 60, /25 VAL 60, /26 ILE 54,
/28 GLU 65, /29 GLY 37, /2d ARG 209, /2g TRP 156, /2h TRP 138, /2i ARG 128,
/2n TRP 61, /2o GLY 89, /2z ARG 16
Chain-final residues that are not actual C termini: /1E ALA 204, /1F GLY 208,
/1H LYS 175, /1I ALA 146, /1P GLU 149, /1T ALA 131, /1U GLN 117, /1W GLY 112,
/1X LEU 95, /1Y ASP 107, /1Z VAL 105, /1Z VAL 141, /1Z ILE 171, /10 LEU 84,
/12 GLN 70, /14 LYS 69, /17 LYS 48, /1b ALA 237, /1c VAL 207, /1e ARG 152, /1f
ASN 100, /1j THR 100, /1k ARG 126, /1l LYS 126, /1m PRO 124, /1p GLN 82, /1q
LYS 100, /1r ARG 87, /1s GLY 84, /1t GLY 103, /1u ARG 24, /2E ALA 204, /2F GLY
208, /2H LYS 175, /2I ALA 146, /2P GLU 149, /2T ALA 131, /2U GLN 117, /2W GLY
112, /2X LEU 95, /2Y ASP 107, /2Z GLY 106, /2Z VAL 174, /20 LEU 84, /22 GLN
70, /24 LYS 69, /27 LYS 48, /2b ALA 237, /2c VAL 207, /2e ARG 152, /2f ASN
100, /2j THR 100, /2k ARG 126, /2l LYS 126, /2m PRO 124, /2p GLN 82, /2q LYS
100, /2r ARG 87, /2s GLY 84, /2t GLY 103, /2u ARG 24
Chain-initial residues that are not actual 5' termini: /1A A 6, /1a U 4, /1v A
12, /1x G 2, /2A A 6, /2a U 4, /2v A 12, /2x G 2
29185 hydrogen bonds
Traceback (most recent call last):
File "/Users/tcroll/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 76, in
_populate_unparameterised_residue_table
self._ask_to_add_hydrogens_if_necessary(residues)
File "/Users/tcroll/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 224, in
_ask_to_add_hydrogens_if_necessary
run(self.session, f'addh #{residues.unique_structures[0].id_string}')
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/addh/cmd.py", line 66, in cmd_addh
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/addh/cmd.py", line 173, in hbond_add_hydrogens
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/addh/hbond.py", line 673, in add_hydrogens
rooms = roomiest(remaining, a, _room_dist, bonding_info)
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/addh/cmd.py", line 846, in roomiest
return list(zip(*pos_info))[1]
IndexError: list index out of range
IndexError: list index out of range
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/addh/cmd.py", line 846, in roomiest
return list(zip(*pos_info))[1]
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,1
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 GB
System Firmware Version: 7459.141.1
OS Loader Version: 7459.141.1
Software:
System Software Overview:
System Version: macOS 12.5.1 (21G83)
Kernel Version: Darwin 21.6.0
Time since boot: 78 days 23:02
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
HP Z27k G3:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.4
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.20.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6rc202304252053
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.6.0
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-QScore: 1.0
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.4.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
This only happens if you run addh *twice* on the structure. Investigating. I wish it weren't such a huge structure. :-)