The following bug report has been submitted:
Platform: Windows-10-10.0.22631
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
When saving a model loaded from mmCIF to PDB, the CRYST1 is still coming out slightly wrong. The attached file was saved from 5ewj fetched from the PDB with "open 5ewj", using "sel #2/A,B; save 5ewj_ab.pdb #2 sel t". Looks like it's missing a space... on reading back in the angles are interpreted as 90.0001, 16.22, 90.0 instead of 90.0, 116.22, 90.0.
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: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 5ewj structureFactors true
Summary of feedback from opening 5ewj fetched from pdb
---
warning | WARNING: multiple experimental reflection datasets found:
F_meas_au, F_meas_sigma_au,
pdbx_HL_A_iso, pdbx_HL_B_iso, pdbx_HL_C_iso, pdbx_HL_D_iso,
phase_calc, fom
Automatically choosing "F_meas_au, F_meas_sigma_au".
notes | Resolution: 2.770004960798391
Launching live xmap mgr took 2.285489082336426 seconds.
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 44,32,30, pixel
0.895,0.835,0.895, shown at level 0.133, step 1, values float32
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 44,32,30, pixel
0.895,0.835,0.895, shown at level -0.0732,0.0732, step 1, values float32
Opened (LIVE) 2mFo-DFc_sharp_21 as #1.1.1.4, grid size 44,32,30, pixel
0.895,0.835,0.895, shown at level 0.428, step 1, values float32
Opened (STATIC) F_calc, phase_calc as #1.1.1.5, grid size 44,32,30, pixel
0.895,0.835,0.895, shown at level -0.381,0.381, step 1, values float32
5ewj title:
Crystal structure of amino terminal domains of the NMDA receptor subunit GLUN1
and GLUN2B In complex with ifenprodil [more info...]
Chain information for 5ewj
---
Chain | Description | UniProt
1.2/A 1.2/C | NMDA glutamate receptor subunit | Q91977_XENLA 23-408
1.2/B 1.2/D | Glutamate receptor ionotropic, NMDA 2B | NMDE2_HUMAN 31-394
Non-standard residues in 5ewj #1.2
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NA — sodium ion
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
QEL — 4-[(1R,2S)-2-(4-benzylpiperidin-1-yl)-1-hydroxypropyl]phenol
(Ifenprodil)
5ewj mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> cd "C:/Users/Tristan
> Croll/Documents/Structures/Trazodone/glutamate_receptors/5ewj_nmdar_ifenprodil"
Current working directory is: C:\Users\Tristan
Croll\Documents\Structures\Trazodone\glutamate_receptors\5ewj_nmdar_ifenprodil
> addh
Summary of feedback from adding hydrogens to 5ewj #1.2
---
warnings | Not adding hydrogens to /A ASP 23 CB because it is missing heavy-atom bond partners
Not adding hydrogens to /A LYS 36 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A LYS 37 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A LEU 102 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A LYS 178 CB because it is missing heavy-atom bond
partners
55 messages similar to the above omitted
notes | Termini for 5ewj (#1.2) chain A determined from SEQRES records
Termini for 5ewj (#1.2) chain B determined from SEQRES records
Termini for 5ewj (#1.2) chain C determined from SEQRES records
Termini for 5ewj (#1.2) chain D determined from SEQRES records
Chain-initial residues that are actual N termini: /A ASP 23, /C ASP 23
Chain-initial residues that are not actual N termini: /A LEU 102, /A GLY 209,
/B PRO 32, /B LEU 62, /C LEU 102, /C GLY 209, /D PRO 32, /D PHE 59, /D ASP 348
Chain-final residues that are actual C termini: /D MET 394
Chain-final residues that are not actual C termini: /A PRO 96, /A GLU 185, /A
THR 407, /B ASP 52, /B ARG 393, /C PRO 95, /C GLU 185, /C THR 407, /D ASP 52,
/D GLU 345
Missing OXT added to C-terminal residue /D MET 394
1886 hydrogen bonds
Adding 'H' to /A LEU 102
Adding 'H' to /A GLY 209
Adding 'H' to /B LEU 62
Adding 'H' to /C LEU 102
Adding 'H' to /C GLY 209
2 messages similar to the above omitted
/A THR 407 is not terminus, removing H atom from 'C'
/B ARG 393 is not terminus, removing H atom from 'C'
/C THR 407 is not terminus, removing H atom from 'C'
11680 hydrogens added
> isolde select #1
> set selectionWidth 4
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 82 residues in model #1.2 to IUPAC-IUB
standards.
Opened (LIVE) MDFF potential as #1.1.1.6, grid size 44,32,30, pixel
0.895,0.835,0.895, shown at level 0.389, step 1, values float32
Done loading forcefield
> isolde set simFidelityMode Highest/Slowest
ISOLDE: setting sim fidelity mode to Highest/Slowest
nonbonded_cutoff_distance = 1.700000
use_gbsa = True
gbsa_cutoff = 2.000000
Loading residue template for QEL from internal database
Fetching CCD MEN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/MEN/MEN.cif
Fetching CCD QEL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/QEL/QEL.cif
Deleted the following atoms from residue QEL B503: HC9, HC11, HC10, HC1, HC2,
HC3, HC4, HC5, HC6, HC7, HC14, HC21, HC13, HO, HC20, HC24, HC8, HC, HO1, HC22,
HC15, HC19, HC17, HN, HC18, HC16, HC12, HC23
> select up
51 atoms, 53 bonds, 1 residue, 1 model selected
> show sel
> isolde parameterise sel override true
Running ANTECHAMBER command: C:/Program
Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\TRISTA~1\AppData\Local\Temp\tmpbzd1oawh\ante.in.mol2 -fi mol2 -o
C:\Users\TRISTA~1\AppData\Local\Temp\tmpbzd1oawh\ante.out.mol2 -fo mol2 -c bcc
-nc 1 -j 5 -s 2 -dr n
(QEL) ``
(QEL) `Welcome to antechamber 20.0: molecular input file processor.`
(QEL) ``
(QEL) `Info: Finished reading file
(C:\Users\TRISTA~1\AppData\Local\Temp\tmpbzd1oawh\ante.in.mol2); atoms read
(52), bonds read (54).`
(QEL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(QEL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(QEL) `bash.exe: warning: could not find /tmp, please create!`
(QEL) ``
(QEL) ``
(QEL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(QEL) `bash.exe: warning: could not find /tmp, please create!`
(QEL) `Info: Total number of electrons: 176; net charge: 1`
(QEL) ``
(QEL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`
(QEL) `bash.exe: warning: could not find /tmp, please create!`
(QEL) ``
(QEL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/am1bcc" -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program
Files/ChimeraX/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`
(QEL) `bash.exe: warning: could not find /tmp, please create!`
(QEL) ``
(QEL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(QEL) `bash.exe: warning: could not find /tmp, please create!`
(QEL) ``
Charges for residue QEL determined
OpenMM ffXML file QEL written to the current working directory.
New template added to forcefield as USER_QEL. This ligand should now work in
all remaining simulations for this session. To use in future sessions, load
the ffXML file with ISOLDE's Load Residue MD Definition(s) button.
> delete sel
[Repeated 2 time(s)]
> select :HOH
1026 atoms, 684 bonds, 342 residues, 1 model selected
> delete :HOH
> ui tool show "Ramachandran Plot"
> select #1
22199 atoms, 22453 bonds, 11 pseudobonds, 1436 residues, 35 models selected
> isolde sim start /A-E
ISOLDE: started sim
> select clear
> isolde sim pause
> alphafold match #1 trim false
Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json
Fetching compressed AlphaFold Q13224 from
https://alphafold.ebi.ac.uk/files/AF-Q13224-F1-model_v4.cif
1 UniProt id does not have an AlphaFold database model: Q91977 (chains A,C)
1 AlphaFold model found using UniProt identifier: Q13224 (chains B,D)
Fetching compressed AlphaFold A0A6I8QSJ4 from
https://alphafold.ebi.ac.uk/files/AF-A0A6I8QSJ4-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A0A6I8QSJ4 (chains
A,C)
AlphaFold prediction matching 5ewj
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
A | A0A6I8QSJ4 | A0A6I8QSJ4_XENTR | 0.78 | 904 | 357 | 97
C | A0A6I8QSJ4 | A0A6I8QSJ4_XENTR | 0.65 | 904 | 356 | 97
B | Q13224 | NMDE2_HUMAN | 1.57 | 1484 | 353 | 100
D | Q13224 | NMDE2_HUMAN | 1.58 | 1484 | 355 | 100
Opened 4 AlphaFold models
> matchmaker #2.1 to #1.2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5ewj, chain D (#1.2) with AlphaFold NMDE2_HUMAN chain B, chain B
(#2.1), sequence alignment score = 1787.4
RMSD between 318 pruned atom pairs is 0.899 angstroms; (across all 355 pairs:
1.582)
> color #2.1 bychain
> color #2.1 byhetero
> color modify #2.1 hue + 50
ISOLDE: attempting to load PAE matrix for model #2.1 from the AlphaFold-EBI
database. If this fails or you wish to use a different PAE matrix, use the
"Load PAE matrix" button in ISOLDE's reference model restraints widget.
> alphafold pae #2.1 uniprotId Q13224 plot false
Fetching compressed AlphaFold PAE Q13224 from
https://alphafold.ebi.ac.uk/files/AF-Q13224-F1-predicted_aligned_error_v4.json
s1:
..............................DPKIVNIGAVLSTKKHEQIFREAVNQANKRHFT..RKIQLQATSVTHRPNAIQMALSVCEDLISSQVYAILVSHPPAPTD.HLTPTPISYTAGFYRIPVIGL.TTRMSIYSDKSIHLSFLRTVPPYSHQALVWFEMMRLFNWNHVILIVSDDHEGRAAQKKLETLLEGKESKSKKRNYENLDQLSYDNK.RGPKADKVLQFEPGTKN.LTALLLEAKELEARVIILSASEDDATAVYKSAAMLDMTGAGYVWLVGEREISGSALRYA..PDGIIGLQLIN.GKNESAHISDAVAVVAQAIHELFEMENITDPPRGCVGNTNIWKTGPLFKRVLMS...SKYPDGVT..GR.IEFNEDGDRKFAQYSIMNLQ.NRKLVQVGIFNGSYIIQNDRKIIWPGGETELVPR...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
s2:
MKPRAECCSPKFWLVLAVLAVSGSRARSQKSPPSIGIAVILVGTSDEVAIKDAHEKDDFHHLSVVPRVELVAMNET...DPKSIITRICDLMSDRKIQGVVFADD...TDQEAIAQILDFISAQTLTPILGIHGGSSMIMADKDESSMFFQFGPSIEQQASVMLNIMEEYDW.YIFSIVTTYFPG...................YQDFVNKIRSTIENSFVGWELEEVLLLDMSLDDGDSKIQNQLKKLQSPIILLYCTKEEATYIFEVANSVGLTGYGYTWIVPSLVAGDTDTVPAEFPTGLISVSYDEWDYGLPARVRDGIAIITTAASDMLSEHSFIPEPKSSCYNTH.......EKRIYQSNMLNRYLINVTFEGRNLSFSEDGYQMHPKLVIILLNKERKWERVGKWKDKSLQM..KYYVWP....RMCPETEEQEDDHLSIVTLEEAPFVIVESVDPLSGTCMRNTVPCQKRIVTENKTDEEPGYIKKCCKGFCIDILKKISKSVKFTYDLYLVTNGKHGKKINGTWNGMIGEVVMKRAYMAVGSLTINEERSEVVDFSVPFIETGISVMVSRSNGTVSPSAFLEPFSADVWVMMFVMLLIVSAVAVFVFEYFSPVGYNRCLADGREPGGPSFTIGKAIWLLWGLVFNNSVPVQNPKGTTSKIMVSVWAFFAVIFLASYTANLAAFMIQEEYVDQVSGLSDKKFQRPNDFSPPFRFGTVPNGSTERNIRNNYAEMHAYMGKFNQRGVDDALLSLKTGKLDAFIYDAAVLNYMAGRDEGCKLVTIGSGKVFASTGYGIAIQKDSGWKRQVDLAILQLFGDGEMEELEALWLTGICHNEKNEVMSSQLDIDNMAGVFYMLGAAMALSLITFICEHLFYWQFRHCFMGVCSGKPGMVFSISRGIYSCIHGVAIEERQSVMNSPTATMNNTHSNILRLLRTAKNMANLSGVNGSPQSALDFIRRESSVYDISEHRRSFTHSDCKSYNNPPCEENLFSDYISEVERTFGNLQLKDSNVYQDHYHHHHRPHSIGSASSIDGLYDCDNPPFTTQSRSISKKPLDIGLPSSKHSQLSDLYGKFSFKSDRYSGHDDLIRSDVSDISTHTVTYGNIEGNAAKRRKQQYKDSLKKRPASAKSRREFDEIELAYRRRPPRSPDHKRYFRDKEGLRDFYLDQFRTKENSPHWEHVDLTDIYKERSDDFKRDSVSGGGPCTNRSHIKHGTGDKHGVVSGVPAPWEKNLTNVEWEDRSGGNFCRSCPSKLHNYSTTVTGQNSGRQACIRCEACKKAGNLYDISEDNSLQELDQPAAPVAVTSNASTTKYPQSPTNSKAQKKNRNKLRRQHSYDTFVDLQKEEAALAPRSVSLKDKGRFMDGSPYAHMFEMSAGESTFANNKSSVPTAGHHHHNNPGGGYMLSKSLYPDRVTQNPFIPTFGDDQCLLHGSKSYFFRQPTVAGASKARPDFRALVTNKPVVSALHGAVPARFQKDICIGNQSNPCVPNNKNPRAFNGSSNGHVYEKLSSIESDV
s1:
..............................SPPSIGIAVILVGTSDEVAIKDAHEKDDFHHLSVVPRVELVAMNETDPKSIITRICDLMSDRKIQGVVFADDTDQEAIAQILDFISAQTLTPILGIHGGSSMIMADKDESSMFFQFGPSIEQQASVMLNIMEEYDWYIFSIVTTYFPGYQDFVNKIRSTIENSFVGWELEEVLLLDMSLDDGDSKIQNQLKKLQSPIILLYCTKEEATYIFEVANSVGLTGYGYTWIVPSLVAGDTDTVPAEFPTGLISVSYDEWDYGLPARVRDGIAIITTAASDMLSEHSFIPEPKSSCYNTHEKRIYQSNMLNRYLINVTFEGRDLSFSEDGYQMHPKLVIILLNKERKWERVGKWKDKSLQMKYYVWPRM..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
s2:
MKPRAECCSPKFWLVLAVLAVSGSRARSQKSPPSIGIAVILVGTSDEVAIKDAHEKDDFHHLSVVPRVELVAMNETDPKSIITRICDLMSDRKIQGVVFADDTDQEAIAQILDFISAQTLTPILGIHGGSSMIMADKDESSMFFQFGPSIEQQASVMLNIMEEYDWYIFSIVTTYFPGYQDFVNKIRSTIENSFVGWELEEVLLLDMSLDDGDSKIQNQLKKLQSPIILLYCTKEEATYIFEVANSVGLTGYGYTWIVPSLVAGDTDTVPAEFPTGLISVSYDEWDYGLPARVRDGIAIITTAASDMLSEHSFIPEPKSSCYNTHEKRIYQSNMLNRYLINVTFEGRNLSFSEDGYQMHPKLVIILLNKERKWERVGKWKDKSLQMKYYVWPRMCPETEEQEDDHLSIVTLEEAPFVIVESVDPLSGTCMRNTVPCQKRIVTENKTDEEPGYIKKCCKGFCIDILKKISKSVKFTYDLYLVTNGKHGKKINGTWNGMIGEVVMKRAYMAVGSLTINEERSEVVDFSVPFIETGISVMVSRSNGTVSPSAFLEPFSADVWVMMFVMLLIVSAVAVFVFEYFSPVGYNRCLADGREPGGPSFTIGKAIWLLWGLVFNNSVPVQNPKGTTSKIMVSVWAFFAVIFLASYTANLAAFMIQEEYVDQVSGLSDKKFQRPNDFSPPFRFGTVPNGSTERNIRNNYAEMHAYMGKFNQRGVDDALLSLKTGKLDAFIYDAAVLNYMAGRDEGCKLVTIGSGKVFASTGYGIAIQKDSGWKRQVDLAILQLFGDGEMEELEALWLTGICHNEKNEVMSSQLDIDNMAGVFYMLGAAMALSLITFICEHLFYWQFRHCFMGVCSGKPGMVFSISRGIYSCIHGVAIEERQSVMNSPTATMNNTHSNILRLLRTAKNMANLSGVNGSPQSALDFIRRESSVYDISEHRRSFTHSDCKSYNNPPCEENLFSDYISEVERTFGNLQLKDSNVYQDHYHHHHRPHSIGSASSIDGLYDCDNPPFTTQSRSISKKPLDIGLPSSKHSQLSDLYGKFSFKSDRYSGHDDLIRSDVSDISTHTVTYGNIEGNAAKRRKQQYKDSLKKRPASAKSRREFDEIELAYRRRPPRSPDHKRYFRDKEGLRDFYLDQFRTKENSPHWEHVDLTDIYKERSDDFKRDSVSGGGPCTNRSHIKHGTGDKHGVVSGVPAPWEKNLTNVEWEDRSGGNFCRSCPSKLHNYSTTVTGQNSGRQACIRCEACKKAGNLYDISEDNSLQELDQPAAPVAVTSNASTTKYPQSPTNSKAQKKNRNKLRRQHSYDTFVDLQKEEAALAPRSVSLKDKGRFMDGSPYAHMFEMSAGESTFANNKSSVPTAGHHHHNNPGGGYMLSKSLYPDRVTQNPFIPTFGDDQCLLHGSKSYFFRQPTVAGASKARPDFRALVTNKPVVSALHGAVPARFQKDICIGNQSNPCVPNNKNPRAFNGSSNGHVYEKLSSIESDV
s1:
..............................DPKIVNIGAVLSTKKHEQIFREAVNQANKRHFT..RKIQLQATSVTHRPNAIQMALSVCEDLISSQVYAILVSHPPAPTD.HLTPTPISYTAGFYRIPVIGL.TTRMSIYSDKSIHLSFLRTVPPYSHQALVWFEMMRLFNWNHVILIVSDDHEGRAAQKKLETLLEGKESKSKKRNYENLDQLSYDNK.RGPKADKVLQFEPGTKN.LTALLLEAKELEARVIILSASEDDATAVYKSAAMLDMTGAGYVWLVGEREISGSALRYA..PDGIIGLQLIN.GKNESAHISDAVAVVAQAIHELFEMENITDPPRGCVGNTNIWKTGPLFKRVLMS...SKYPDGVT..GR.IEFNEDGDRKFAQYSIMNLQ.NRKLVQVGIFNGSYIIQNDRKIIWPGGETELVPR...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
s2:
MKPRAECCSPKFWLVLAVLAVSGSRARSQKSPPSIGIAVILVGTSDEVAIKDAHEKDDFHHLSVVPRVELVAMNET...DPKSIITRICDLMSDRKIQGVVFADD...TDQEAIAQILDFISAQTLTPILGIHGGSSMIMADKDESSMFFQFGPSIEQQASVMLNIMEEYDW.YIFSIVTTYFPG...................YQDFVNKIRSTIENSFVGWELEEVLLLDMSLDDGDSKIQNQLKKLQSPIILLYCTKEEATYIFEVANSVGLTGYGYTWIVPSLVAGDTDTVPAEFPTGLISVSYDEWDYGLPARVRDGIAIITTAASDMLSEHSFIPEPKSSCYNTH.......EKRIYQSNMLNRYLINVTFEGRNLSFSEDGYQMHPKLVIILLNKERKWERVGKWKDKSLQM..KYYVWP....RMCPETEEQEDDHLSIVTLEEAPFVIVESVDPLSGTCMRNTVPCQKRIVTENKTDEEPGYIKKCCKGFCIDILKKISKSVKFTYDLYLVTNGKHGKKINGTWNGMIGEVVMKRAYMAVGSLTINEERSEVVDFSVPFIETGISVMVSRSNGTVSPSAFLEPFSADVWVMMFVMLLIVSAVAVFVFEYFSPVGYNRCLADGREPGGPSFTIGKAIWLLWGLVFNNSVPVQNPKGTTSKIMVSVWAFFAVIFLASYTANLAAFMIQEEYVDQVSGLSDKKFQRPNDFSPPFRFGTVPNGSTERNIRNNYAEMHAYMGKFNQRGVDDALLSLKTGKLDAFIYDAAVLNYMAGRDEGCKLVTIGSGKVFASTGYGIAIQKDSGWKRQVDLAILQLFGDGEMEELEALWLTGICHNEKNEVMSSQLDIDNMAGVFYMLGAAMALSLITFICEHLFYWQFRHCFMGVCSGKPGMVFSISRGIYSCIHGVAIEERQSVMNSPTATMNNTHSNILRLLRTAKNMANLSGVNGSPQSALDFIRRESSVYDISEHRRSFTHSDCKSYNNPPCEENLFSDYISEVERTFGNLQLKDSNVYQDHYHHHHRPHSIGSASSIDGLYDCDNPPFTTQSRSISKKPLDIGLPSSKHSQLSDLYGKFSFKSDRYSGHDDLIRSDVSDISTHTVTYGNIEGNAAKRRKQQYKDSLKKRPASAKSRREFDEIELAYRRRPPRSPDHKRYFRDKEGLRDFYLDQFRTKENSPHWEHVDLTDIYKERSDDFKRDSVSGGGPCTNRSHIKHGTGDKHGVVSGVPAPWEKNLTNVEWEDRSGGNFCRSCPSKLHNYSTTVTGQNSGRQACIRCEACKKAGNLYDISEDNSLQELDQPAAPVAVTSNASTTKYPQSPTNSKAQKKNRNKLRRQHSYDTFVDLQKEEAALAPRSVSLKDKGRFMDGSPYAHMFEMSAGESTFANNKSSVPTAGHHHHNNPGGGYMLSKSLYPDRVTQNPFIPTFGDDQCLLHGSKSYFFRQPTVAGASKARPDFRALVTNKPVVSALHGAVPARFQKDICIGNQSNPCVPNNKNPRAFNGSSNGHVYEKLSSIESDV
s1:
..............................SPPSIGIAVILVGTSDEVAIKDAHEKDDFHHLSVVPRVELVAMNETDPKSIITRICDLMSDRKIQGVVFADDTDQEAIAQILDFISAQTLTPILGIHGGSSMIMADKDESSMFFQFGPSIEQQASVMLNIMEEYDWYIFSIVTTYFPGYQDFVNKIRSTIENSFVGWELEEVLLLDMSLDDGDSKIQNQLKKLQSPIILLYCTKEEATYIFEVANSVGLTGYGYTWIVPSLVAGDTDTVPAEFPTGLISVSYDEWDYGLPARVRDGIAIITTAASDMLSEHSFIPEPKSSCYNTHEKRIYQSNMLNRYLINVTFEGRDLSFSEDGYQMHPKLVIILLNKERKWERVGKWKDKSLQMKYYVWPRM..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
s2:
MKPRAECCSPKFWLVLAVLAVSGSRARSQKSPPSIGIAVILVGTSDEVAIKDAHEKDDFHHLSVVPRVELVAMNETDPKSIITRICDLMSDRKIQGVVFADDTDQEAIAQILDFISAQTLTPILGIHGGSSMIMADKDESSMFFQFGPSIEQQASVMLNIMEEYDWYIFSIVTTYFPGYQDFVNKIRSTIENSFVGWELEEVLLLDMSLDDGDSKIQNQLKKLQSPIILLYCTKEEATYIFEVANSVGLTGYGYTWIVPSLVAGDTDTVPAEFPTGLISVSYDEWDYGLPARVRDGIAIITTAASDMLSEHSFIPEPKSSCYNTHEKRIYQSNMLNRYLINVTFEGRNLSFSEDGYQMHPKLVIILLNKERKWERVGKWKDKSLQMKYYVWPRMCPETEEQEDDHLSIVTLEEAPFVIVESVDPLSGTCMRNTVPCQKRIVTENKTDEEPGYIKKCCKGFCIDILKKISKSVKFTYDLYLVTNGKHGKKINGTWNGMIGEVVMKRAYMAVGSLTINEERSEVVDFSVPFIETGISVMVSRSNGTVSPSAFLEPFSADVWVMMFVMLLIVSAVAVFVFEYFSPVGYNRCLADGREPGGPSFTIGKAIWLLWGLVFNNSVPVQNPKGTTSKIMVSVWAFFAVIFLASYTANLAAFMIQEEYVDQVSGLSDKKFQRPNDFSPPFRFGTVPNGSTERNIRNNYAEMHAYMGKFNQRGVDDALLSLKTGKLDAFIYDAAVLNYMAGRDEGCKLVTIGSGKVFASTGYGIAIQKDSGWKRQVDLAILQLFGDGEMEELEALWLTGICHNEKNEVMSSQLDIDNMAGVFYMLGAAMALSLITFICEHLFYWQFRHCFMGVCSGKPGMVFSISRGIYSCIHGVAIEERQSVMNSPTATMNNTHSNILRLLRTAKNMANLSGVNGSPQSALDFIRRESSVYDISEHRRSFTHSDCKSYNNPPCEENLFSDYISEVERTFGNLQLKDSNVYQDHYHHHHRPHSIGSASSIDGLYDCDNPPFTTQSRSISKKPLDIGLPSSKHSQLSDLYGKFSFKSDRYSGHDDLIRSDVSDISTHTVTYGNIEGNAAKRRKQQYKDSLKKRPASAKSRREFDEIELAYRRRPPRSPDHKRYFRDKEGLRDFYLDQFRTKENSPHWEHVDLTDIYKERSDDFKRDSVSGGGPCTNRSHIKHGTGDKHGVVSGVPAPWEKNLTNVEWEDRSGGNFCRSCPSKLHNYSTTVTGQNSGRQACIRCEACKKAGNLYDISEDNSLQELDQPAAPVAVTSNASTTKYPQSPTNSKAQKKNRNKLRRQHSYDTFVDLQKEEAALAPRSVSLKDKGRFMDGSPYAHMFEMSAGESTFANNKSSVPTAGHHHHNNPGGGYMLSKSLYPDRVTQNPFIPTFGDDQCLLHGSKSYFFRQPTVAGASKARPDFRALVTNKPVVSALHGAVPARFQKDICIGNQSNPCVPNNKNPRAFNGSSNGHVYEKLSSIESDV
> isolde restrain distances "#1.2/B" templateAtoms "#2.1/B" perChain false
> adjustForConfidence true useCoordinateAlignment false kappa 4.40 fallOff
> 2.50 groupName "Reference Distance Restraints"
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 23 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 213 residues in model #2.1 to IUPAC-IUB
standards.
> isolde restrain torsions #1.2/B templateResidues #2.1/B adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20
The "isolde restrain torsions" command only applies to protein chains. Other
residues have been ignored.
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain distances "#1.2/D" templateAtoms "#2.1/B" perChain false
> adjustForConfidence true useCoordinateAlignment false kappa 4.40 fallOff
> 2.50 groupName "Reference Distance Restraints"
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain torsions #1.2/D templateResidues #2.1/B adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20
The "isolde restrain torsions" command only applies to protein chains. Other
residues have been ignored.
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> matchmaker #2.3 to #1.2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5ewj, chain A (#1.2) with AlphaFold A0A6I8QSJ4_XENTR chain A, chain
A (#2.3), sequence alignment score = 1844.2
RMSD between 351 pruned atom pairs is 0.520 angstroms; (across all 357 pairs:
0.782)
> color #2.3 bychain
> color #2.3 byhetero
> color modify #2.3 hue + 50
ISOLDE: attempting to load PAE matrix for model #2.3 from the AlphaFold-EBI
database. If this fails or you wish to use a different PAE matrix, use the
"Load PAE matrix" button in ISOLDE's reference model restraints widget.
> alphafold pae #2.3 uniprotId A0A6I8QSJ4 plot false
Fetching compressed AlphaFold PAE A0A6I8QSJ4 from
https://alphafold.ebi.ac.uk/files/AF-A0A6I8QSJ4-F1-predicted_aligned_error_v4.json
s1:
......................DPKIVNIGAVLSTKKHEQIFREAVNQANKRHFTRKIQLQATSVTHRPNAIQMALSVCEDLISSQVYAILVSHPPAPTDHLTPTPISYTAGFYRIPVIGLTTRMSIYSDKSIHLSFLRTVPPYSHQALVWFEMMRLFNWNHVILIVSDDHEGRAAQKKLETLLEGKESKSKKRNYENLDQLSYDNKRGPKADKVLQFEPGTKNLTALLLEAKELEARVIILSASEDDATAVYKSAAMLDMTGAGYVWLVGEREISGSALRYAPDGIIGLQLINGKNESAHISDAVAVVAQAIHELFEMENITDPPRGCVGNTNIWKTGPLFKRVLMSSKYPDGVTGRIEFNEDGDRKFAQYSIMNLQNRKLVQVGIFNGSYIIQNDRKIIWPGGETELVPR.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
s2:
MGTMRLFLLAVLFLFSFARAGCDPKIVNIGAVLSTKKHEQIFREAVNQANKRHGTWKIQLNATSVTHRPNAIQMALSVCEDLISSQVYAILVSHPPAPTDHLTPTPISYTAGFYRIPVIGLTTRMSIYSDKSIHLSFLRTVPPYSHQALVWFEMMRLFNWNHVILIVSDDHEGRAAQKKLETLLEEKESKSKKRNYENLDQLSYDNKRGPKADKVLQFEPGTKNLTALLLEAKELEARVIILSASEDDATAVYKSAAMLDMTGAGYVWLVGEREISGSALRYAPDGIIGLQLINGKNESAHISDAVAVAAQAIHELFEMENITDPPRGCVGNTNIWKTGPLFKRVLMSSKYPDGVTGRIEFNEDGDRKFANYSIMNLQNRKLVQVGIFNGSHVIQNDRKIIWPGGETER.PQGYQMSTRLKIVTIHQEPFVYVKPTMTDGTCREEYTINGDPIKKVICNGPNETIPGRPTVPQCCYGFCIDLLIKLAREMNFTYEVHLVADGKFGTQERVNNSNKKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKEIPRSTLDSFMQPFQSTLWLLVGLSVHVVAVMLYLLDRFSPFGRFKVNSEEEEEDALTLSSAMWFSWGVLLNSGIGEGAPRSFSARILGMVWAGFAMIIVASYTANLAAFLVLDRPEERITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQNVSLNILKSHENGFMEELDKTWVRYQECDSRSNAPATLTFENMAGVFMLVAGGIVAGIFLIFIEIAYKRHKDARRKQMQLAFAAVNVWRKNLQQYHPTDITGQLNLSDPSVSTVV
s1:
......................SPPSIGIAVILVGTSDEVAIKDAHEKDDFHHLSVVPRVELVAMNET...DPKSIITRICDLMSDRKIQGVVFAD...DTDQEAIAQILDFISAQTLTPILGIHGGSSMIMADKDESSMFFQFGPSIEQQASVMLNIMEEYDW.YIFSIVTTYFPG...................YQDFVNKIRSTIENSFVGWELEEVLLLDMSLDDGDSKIQNQLKKLQSPIILLYCTKEEATYIFEVANSVGLTGYGYTWIVPSLVAGDTDTVPAEFPTGLISVSYDEWDYGLPARVRDGIAIITTAASDMLSEHSFIPEPKSSCYNTH.......EKRIYQSNMLNRYLINVTFEGRDLSFSEDGYQMHPKLVIILLNKERKWERVGKWKDKSLQM..KYYVWPRM...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
s2:
MGTMRLFLLAVLFLFSFARAGCDPKIVNIGAVLSTKKHEQIFREAVNQANKRHGTW..KIQLNATSVTHRPNAIQMALSVCEDLISSQVYAILVSHPPAPTD.HLTPTPISYTAGFYRIPVIGL.TTRMSIYSDKSIHLSFLRTVPPYSHQALVWFEMMRLFNWNHVILIVSDDHEGRAAQKKLETLLEEKESKSKKRNYENLDQLSYDNK.RGPKADKVLQFEPGTKN.LTALLLEAKELEARVIILSASEDDATAVYKSAAMLDMTGAGYVWLVGEREISGSALRYA..PDGIIGLQLIN.GKNESAHISDAVAVAAQAIHELFEMENITDPPRGCVGNTNIWKTGPLFKRVLMS...SKYPDGVT..GR.IEFNEDGDRKFANYSIMNLQ.NRKLVQVGIFNGSHVIQNDRKIIWPGGETERPQGYQMSTRLKIVTIHQEPFVYVKPTMTDGTCREEYTINGDPIKKVICNGPNETIPGRPTVPQCCYGFCIDLLIKLAREMNFTYEVHLVADGKFGTQERVNNSNKKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKEIPRSTLDSFMQPFQSTLWLLVGLSVHVVAVMLYLLDRFSPFGRFKVNSEEEEEDALTLSSAMWFSWGVLLNSGIGEGAPRSFSARILGMVWAGFAMIIVASYTANLAAFLVLDRPEERITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQNVSLNILKSHENGFMEELDKTWVRYQECDSRSNAPATLTFENMAGVFMLVAGGIVAGIFLIFIEIAYKRHKDARRKQMQLAFAAVNVWRKNLQQYHPTDITGQLNLSDPSVSTVV
s1:
......................DPKIVNIGAVLSTKKHEQIFREAVNQANKRHFTRKIQLQATSVTHRPNAIQMALSVCEDLISSQVYAILVSHPPAPTDHLTPTPISYTAGFYRIPVIGLTTRMSIYSDKSIHLSFLRTVPPYSHQALVWFEMMRLFNWNHVILIVSDDHEGRAAQKKLETLLEGKESKSKKRNYENLDQLSYDNKRGPKADKVLQFEPGTKNLTALLLEAKELEARVIILSASEDDATAVYKSAAMLDMTGAGYVWLVGEREISGSALRYAPDGIIGLQLINGKNESAHISDAVAVVAQAIHELFEMENITDPPRGCVGNTNIWKTGPLFKRVLMSSKYPDGVTGRIEFNEDGDRKFAQYSIMNLQNRKLVQVGIFNGSYIIQNDRKIIWPGGETELVPR.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
s2:
MGTMRLFLLAVLFLFSFARAGCDPKIVNIGAVLSTKKHEQIFREAVNQANKRHGTWKIQLNATSVTHRPNAIQMALSVCEDLISSQVYAILVSHPPAPTDHLTPTPISYTAGFYRIPVIGLTTRMSIYSDKSIHLSFLRTVPPYSHQALVWFEMMRLFNWNHVILIVSDDHEGRAAQKKLETLLEEKESKSKKRNYENLDQLSYDNKRGPKADKVLQFEPGTKNLTALLLEAKELEARVIILSASEDDATAVYKSAAMLDMTGAGYVWLVGEREISGSALRYAPDGIIGLQLINGKNESAHISDAVAVAAQAIHELFEMENITDPPRGCVGNTNIWKTGPLFKRVLMSSKYPDGVTGRIEFNEDGDRKFANYSIMNLQNRKLVQVGIFNGSHVIQNDRKIIWPGGETER.PQGYQMSTRLKIVTIHQEPFVYVKPTMTDGTCREEYTINGDPIKKVICNGPNETIPGRPTVPQCCYGFCIDLLIKLAREMNFTYEVHLVADGKFGTQERVNNSNKKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKEIPRSTLDSFMQPFQSTLWLLVGLSVHVVAVMLYLLDRFSPFGRFKVNSEEEEEDALTLSSAMWFSWGVLLNSGIGEGAPRSFSARILGMVWAGFAMIIVASYTANLAAFLVLDRPEERITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQNVSLNILKSHENGFMEELDKTWVRYQECDSRSNAPATLTFENMAGVFMLVAGGIVAGIFLIFIEIAYKRHKDARRKQMQLAFAAVNVWRKNLQQYHPTDITGQLNLSDPSVSTVV
s1:
......................SPPSIGIAVILVGTSDEVAIKDAHEKDDFHHLSVVPRVELVAMNET...DPKSIITRICDLMSDRKIQGVVFAD...DTDQEAIAQILDFISAQTLTPILGIHGGSSMIMADKDESSMFFQFGPSIEQQASVMLNIMEEYDW.YIFSIVTTYFPG...................YQDFVNKIRSTIENSFVGWELEEVLLLDMSLDDGDSKIQNQLKKLQSPIILLYCTKEEATYIFEVANSVGLTGYGYTWIVPSLVAGDTDTVPAEFPTGLISVSYDEWDYGLPARVRDGIAIITTAASDMLSEHSFIPEPKSSCYNTH.......EKRIYQSNMLNRYLINVTFEGRDLSFSEDGYQMHPKLVIILLNKERKWERVGKWKDKSLQM..KYYVWPRM...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
s2:
MGTMRLFLLAVLFLFSFARAGCDPKIVNIGAVLSTKKHEQIFREAVNQANKRHGTW..KIQLNATSVTHRPNAIQMALSVCEDLISSQVYAILVSHPPAPTD.HLTPTPISYTAGFYRIPVIGL.TTRMSIYSDKSIHLSFLRTVPPYSHQALVWFEMMRLFNWNHVILIVSDDHEGRAAQKKLETLLEEKESKSKKRNYENLDQLSYDNK.RGPKADKVLQFEPGTKN.LTALLLEAKELEARVIILSASEDDATAVYKSAAMLDMTGAGYVWLVGEREISGSALRYA..PDGIIGLQLIN.GKNESAHISDAVAVAAQAIHELFEMENITDPPRGCVGNTNIWKTGPLFKRVLMS...SKYPDGVT..GR.IEFNEDGDRKFANYSIMNLQ.NRKLVQVGIFNGSHVIQNDRKIIWPGGETERPQGYQMSTRLKIVTIHQEPFVYVKPTMTDGTCREEYTINGDPIKKVICNGPNETIPGRPTVPQCCYGFCIDLLIKLAREMNFTYEVHLVADGKFGTQERVNNSNKKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKEIPRSTLDSFMQPFQSTLWLLVGLSVHVVAVMLYLLDRFSPFGRFKVNSEEEEEDALTLSSAMWFSWGVLLNSGIGEGAPRSFSARILGMVWAGFAMIIVASYTANLAAFLVLDRPEERITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQNVSLNILKSHENGFMEELDKTWVRYQECDSRSNAPATLTFENMAGVFMLVAGGIVAGIFLIFIEIAYKRHKDARRKQMQLAFAAVNVWRKNLQQYHPTDITGQLNLSDPSVSTVV
> isolde restrain distances "#1.2/A" templateAtoms "#2.3/A" perChain false
> adjustForConfidence true useCoordinateAlignment false kappa 4.40 fallOff
> 2.50 groupName "Reference Distance Restraints"
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]ISOLDE: Corrected atom nomenclature of 140 residues in
model #2.3 to IUPAC-IUB standards.
> isolde restrain torsions #1.2/A templateResidues #2.3/A adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20
The "isolde restrain torsions" command only applies to protein chains. Other
residues have been ignored.
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain distances "#1.2/C" templateAtoms "#2.3/A" perChain false
> adjustForConfidence true useCoordinateAlignment false kappa 4.40 fallOff
> 2.50 groupName "Reference Distance Restraints"
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain torsions #1.2/C templateResidues #2.3/A adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20
The "isolde restrain torsions" command only applies to protein chains. Other
residues have been ignored.
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> hide #!2 models
> isolde sim resume
> select clear
> isolde sim pause
> show #!2 models
> hide #!2 models
> select #1
22199 atoms, 22453 bonds, 11 pseudobonds, 1436 residues, 40 models selected
> rd
> isolde sim resume
> select clear
[Repeated 2 time(s)]
> select #1
22199 atoms, 22453 bonds, 11 pseudobonds, 1436 residues, 40 models selected
> ra
> select clear
Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 26 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start #1.2/A:132
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select up
52 atoms, 54 bonds, 1 residue, 1 model selected
> isolde sim start #1.2/B:503
ISOLDE: started sim
> select clear
> isolde sim pause
> ui mousemode right "translate selected atoms"
> isolde sim resume
> isolde sim pause
> isolde sim resume
> ui mousemode right "isolde tug atom"
> isolde sim pause
> ui mousemode right "translate selected atoms"
> ui mousemode right "isolde tug atom"
> isolde sim resume
> isolde sim pause
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view /D:QEL
> select up
52 atoms, 54 bonds, 1 residue, 1 model selected
> show sel
> isolde sim start #1.2/D:503
ISOLDE: started sim
> ui mousemode right "translate selected atoms"
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view /B:QEL
> isolde sim start #1.2/B:110,503
ISOLDE: started sim
> select clear
[Repeated 1 time(s)]
> isolde sim pause
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> al FMT
Fetching CCD FMT from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/T/FMT/FMT.cif
Loading residue template for FMT from internal database
Deleted the following atoms from residue FMT A503: HO2
> isolde sim start #1.2/A:503
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view /C:364
> al FMT
Deleted the following atoms from residue FMT C503: HO2
> isolde sim start #1.2/C:503
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #1.2/C:136
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> open 5ewj
5ewj title:
Crystal structure of amino terminal domains of the NMDA receptor subunit GLUN1
and GLUN2B In complex with ifenprodil [more info...]
Chain information for 5ewj #3
---
Chain | Description | UniProt
A C | NMDA glutamate receptor subunit | Q91977_XENLA 23-408
B D | Glutamate receptor ionotropic, NMDA 2B | NMDE2_HUMAN 31-394
Non-standard residues in 5ewj #3
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NA — sodium ion
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
QEL — 4-[(1R,2S)-2-(4-benzylpiperidin-1-yl)-1-hydroxypropyl]phenol
(Ifenprodil)
5ewj mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> show #3
> hide #3
> hide #!3 models
> view /B:QEL
> st /A
Multiple residues selected! Going to the first...
> st
[Repeated 2 time(s)]
> aw
> isolde sim start #1.2/A:26,504
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 2 time(s)]
> isolde sim start #1.2/A:29
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 4 time(s)]
> isolde sim start #1.2/A:34
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #1.2/A:94,104
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]
> swapaa mousemode sel LYS
> isolde sim start #1.2/A:36
ISOLDE: started sim
> isolde sim pause
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ab 10
[Repeated 1 time(s)]
> swapaa mousemode sel LYS
> isolde sim start #1.2/A:37
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ab 20
> isolde sim start #1.2/A:299
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> show #!3 models
> show #3
> hide #!3 models
> st
[Repeated 3 time(s)]
> show #!3 models
> hide #!3 models
> isolde sim start #1.2/A:40
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 3 time(s)]
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> aw
> isolde sim start #1.2/A:44,505
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> delete sel
> st
[Repeated 1 time(s)]
> ui tool show Shell
0.00s - Debugger warning: It seems that frozen modules are being used, which
may
0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off
0.00s - to python to disable frozen modules.
0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to
disable this validation.
> label #1.2/A:23
> label #1.2/A:102
> label #1.2/A:178
> label #1.2/A:185
> label #1.2/A:211
> label #1.2/A:214
> label #1.2/A:234
> label #1.2/A:281
> label #1.2/A:337
> label #1.2/A:379
> label #1.2/A:381
> label #1.2/B:34
> label #1.2/B:46
> label #1.2/B:47
> label #1.2/B:48
> label #1.2/B:52
> label #1.2/B:63
> label #1.2/B:67
> label #1.2/B:93
> label #1.2/B:139
> label #1.2/B:151
> label #1.2/B:162
> label #1.2/B:198
> label #1.2/B:221
> label #1.2/B:222
> label #1.2/B:281
> label #1.2/B:323
> label #1.2/B:347
> label #1.2/B:369
> label #1.2/C:102
> label #1.2/C:178
> label #1.2/C:185
> label #1.2/C:211
> label #1.2/C:223
> label #1.2/C:230
> label #1.2/C:238
> label #1.2/C:258
> label #1.2/C:318
> label #1.2/C:320
> label #1.2/C:337
> label #1.2/C:363
> label #1.2/C:391
> label #1.2/C:392
> label #1.2/C:399
> label #1.2/D:47
> label #1.2/D:48
> label #1.2/D:60
> label #1.2/D:67
> label #1.2/D:93
> label #1.2/D:139
> label #1.2/D:162
> label #1.2/D:198
> label #1.2/D:222
> label #1.2/D:235
> label #1.2/D:281
> label #1.2/D:294
> label #1.2/D:328
> label #1.2/D:385
> st
> isolde sim start #1.2/A:47
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 3 time(s)]
> al NA
> isolde sim start #1.2/A:51,505
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aw
> isolde sim start #1.2/A:48-54,506
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> show #!3 models
> hide #!3 models
> al NA
> isolde sim start #1.2/A:507
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aw
> isolde sim start #1.2/A:508
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> delete sel
> st
[Repeated 1 time(s)]
> delete sel
> isolde sim start #1.2/A:53
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 2 time(s)]
> aw
> isolde sim start #1.2/A:56,508
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]
> isolde sim start #1.2/A:58
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]
> isolde sim start #1.2/A:29
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
[Repeated 1 time(s)]
> st
[Repeated 2 time(s)]
> isolde sim start #1.2/A:63
ISOLDE: started sim
> show #!3 models
> hide #!3 models
> show #!3 models
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> hide #!3 models
> st
[Repeated 4 time(s)]
> isolde sim start #1.2/A:68
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
[Repeated 11 time(s)]
> al FMT
Deleted the following atoms from residue FMT B504: HO2
> isolde sim start #1.2/A:80/B:504
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select up
4 atoms, 3 bonds, 1 residue, 1 model selected
> ab 10
> st
[Repeated 12 time(s)]
> isolde sim start #1.2/A:93,123
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> aw
> isolde sim start #1.2/A:509
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 3 time(s)]
> swapaa mousemode sel LEU
> isolde sim start #1.2/A:102
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ab 20
> st
[Repeated 5 time(s)]
> isolde sim start #1.2/A:108
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start #1.2/A:136
ISOLDE: started sim
> show #!3 models
> hide #!3 models
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> close
Deleting Crystallographic maps(5ewj-sf.cif)
Deleting (LIVE) 2mFo-DFc
Deleting (LIVE) mFo-DFc
Deleting (LIVE) 2mFo-DFc_sharp_21
Deleting (LIVE) MDFF potential
> open 5ewj
5ewj title:
Crystal structure of amino terminal domains of the NMDA receptor subunit GLUN1
and GLUN2B In complex with ifenprodil [more info...]
Chain information for 5ewj #1
---
Chain | Description | UniProt
A C | NMDA glutamate receptor subunit | Q91977_XENLA 23-408
B D | Glutamate receptor ionotropic, NMDA 2B | NMDE2_HUMAN 31-394
Non-standard residues in 5ewj #1
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NA — sodium ion
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
QEL — 4-[(1R,2S)-2-(4-benzylpiperidin-1-yl)-1-hydroxypropyl]phenol
(Ifenprodil)
5ewj mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> addh
Summary of feedback from adding hydrogens to 5ewj #1
---
warnings | Not adding hydrogens to /A ASP 23 CB because it is missing heavy-atom bond partners
Not adding hydrogens to /A LYS 36 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A LYS 37 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A LEU 102 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A LYS 178 CB because it is missing heavy-atom bond
partners
55 messages similar to the above omitted
notes | Termini for 5ewj (#1) chain A determined from SEQRES records
Termini for 5ewj (#1) chain B determined from SEQRES records
Termini for 5ewj (#1) chain C determined from SEQRES records
Termini for 5ewj (#1) chain D determined from SEQRES records
Chain-initial residues that are actual N termini: /A ASP 23, /C ASP 23
Chain-initial residues that are not actual N termini: /A LEU 102, /A GLY 209,
/B PRO 32, /B LEU 62, /C LEU 102, /C GLY 209, /D PRO 32, /D PHE 59, /D ASP 348
Chain-final residues that are actual C termini: /D MET 394
Chain-final residues that are not actual C termini: /A PRO 96, /A GLU 185, /A
THR 407, /B ASP 52, /B ARG 393, /C PRO 95, /C GLU 185, /C THR 407, /D ASP 52,
/D GLU 345
Missing OXT added to C-terminal residue /D MET 394
1885 hydrogen bonds
Adding 'H' to /A LEU 102
Adding 'H' to /A GLY 209
Adding 'H' to /B LEU 62
Adding 'H' to /C LEU 102
Adding 'H' to /C GLY 209
2 messages similar to the above omitted
/A THR 407 is not terminus, removing H atom from 'C'
/B ARG 393 is not terminus, removing H atom from 'C'
/C THR 407 is not terminus, removing H atom from 'C'
11680 hydrogens added
> close
> open 5ewj structureFactors true overSampling 2.5
Summary of feedback from opening 5ewj fetched from pdb
---
warning | WARNING: multiple experimental reflection datasets found:
F_meas_au, F_meas_sigma_au,
pdbx_HL_A_iso, pdbx_HL_B_iso, pdbx_HL_C_iso, pdbx_HL_D_iso,
phase_calc, fom
Automatically choosing "F_meas_au, F_meas_sigma_au".
notes | Resolution: 2.770004960798391
Launching live xmap mgr took 2.351980209350586 seconds.
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 70,48,50, pixel
0.537,0.537,0.537, shown at level 0.134, step 1, values float32
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 70,48,50, pixel
0.537,0.537,0.537, shown at level -0.0749,0.0749, step 1, values float32
Opened (LIVE) 2mFo-DFc_sharp_21 as #1.1.1.4, grid size 70,48,50, pixel
0.537,0.537,0.537, shown at level 0.431, step 1, values float32
Opened (STATIC) F_calc, phase_calc as #1.1.1.5, grid size 70,48,50, pixel
0.537,0.537,0.537, shown at level -0.381,0.381, step 1, values float32
5ewj title:
Crystal structure of amino terminal domains of the NMDA receptor subunit GLUN1
and GLUN2B In complex with ifenprodil [more info...]
Chain information for 5ewj
---
Chain | Description | UniProt
1.2/A 1.2/C | NMDA glutamate receptor subunit | Q91977_XENLA 23-408
1.2/B 1.2/D | Glutamate receptor ionotropic, NMDA 2B | NMDE2_HUMAN 31-394
Non-standard residues in 5ewj #1.2
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NA — sodium ion
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
QEL — 4-[(1R,2S)-2-(4-benzylpiperidin-1-yl)-1-hydroxypropyl]phenol
(Ifenprodil)
5ewj mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> addh
Summary of feedback from adding hydrogens to 5ewj #1.2
---
warnings | Not adding hydrogens to /A ASP 23 CB because it is missing heavy-atom bond partners
Not adding hydrogens to /A LYS 36 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A LYS 37 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A LEU 102 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A LYS 178 CB because it is missing heavy-atom bond
partners
55 messages similar to the above omitted
notes | Termini for 5ewj (#1.2) chain A determined from SEQRES records
Termini for 5ewj (#1.2) chain B determined from SEQRES records
Termini for 5ewj (#1.2) chain C determined from SEQRES records
Termini for 5ewj (#1.2) chain D determined from SEQRES records
Chain-initial residues that are actual N termini: /A ASP 23, /C ASP 23
Chain-initial residues that are not actual N termini: /A LEU 102, /A GLY 209,
/B PRO 32, /B LEU 62, /C LEU 102, /C GLY 209, /D PRO 32, /D PHE 59, /D ASP 348
Chain-final residues that are actual C termini: /D MET 394
Chain-final residues that are not actual C termini: /A PRO 96, /A GLU 185, /A
THR 407, /B ASP 52, /B ARG 393, /C PRO 95, /C GLU 185, /C THR 407, /D ASP 52,
/D GLU 345
Missing OXT added to C-terminal residue /D MET 394
1885 hydrogen bonds
Adding 'H' to /A LEU 102
Adding 'H' to /A GLY 209
Adding 'H' to /B LEU 62
Adding 'H' to /C LEU 102
Adding 'H' to /C GLY 209
2 messages similar to the above omitted
/A THR 407 is not terminus, removing H atom from 'C'
/B ARG 393 is not terminus, removing H atom from 'C'
/C THR 407 is not terminus, removing H atom from 'C'
11683 hydrogens added
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 82 residues in model #1.2 to IUPAC-IUB
standards.
Opened (LIVE) MDFF potential as #1.1.1.6, grid size 70,48,50, pixel
0.537,0.537,0.537, shown at level 0.391, step 1, values float32
> select clear
> view /B:QEL
> select clear
> select #1
23252 atoms, 23155 bonds, 15 pseudobonds, 1787 residues, 35 models selected
> isolde sim start /A-E
ISOLDE: started sim
> select clear
[Repeated 1 time(s)]
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 24 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select up
52 atoms, 54 bonds, 1 residue, 1 model selected
> show sel
> isolde sim start /B:503
ISOLDE: started sim
> ui mousemode right "translate selected atoms"
> isolde sim pause
> ui mousemode right "isolde tug atom"
> isolde sim resume
> isolde sim pause
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save 5ewj_working.cxs
> select #1/A<B
Expected an objects specifier or a keyword
> select #1/A,B
11739 atoms, 11626 bonds, 7 pseudobonds, 953 residues, 3 models selected
> save 5ewj_ab.pdb #1 selectedOnly true
> open 5ewj_ab.pdb
Summary of feedback from opening 5ewj_ab.pdb
---
warnings | Start residue of secondary structure not found: HELIX 26 26 THR C 35 PHE C 54 1 20
Start residue of secondary structure not found: HELIX 27 27 ASN C 70 LEU C 82
1 13
Start residue of secondary structure not found: HELIX 28 28 ILE C 83 SER C 85
1 3
Start residue of secondary structure not found: HELIX 29 29 PRO C 104 TYR C
114 1 11
Start residue of secondary structure not found: HELIX 30 30 MET C 125 ASP C
130 1 6
50 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (79 )
Cannot find LINK/SSBOND residue CYS (86 )
Cannot find LINK/SSBOND residue NAG (1 )
Cannot find LINK/SSBOND residue ASN (297 )
Cannot find LINK/SSBOND residue ASN (74 )
9 messages similar to the above omitted
Chain information for 5ewj_ab.pdb #2
---
Chain | Description
A | No description available
B | No description available
> hide #!1 models
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
Chain information for 5ewj_ab.pdb
---
Chain | Description
2.2/A | No description available
2.2/B | No description available
> isolde restrain distances #2
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> select clear
> select up
52 atoms, 54 bonds, 1 residue, 1 model selected
> isolde ignore sel
ISOLDE: currently ignoring 1 residues in model 2.2
> open C1CN(CCN1CCCN2C(=O)N3C=CC=CC3=N2)C4=CC(=CC=C4)Cl fromDatabase smiles
Translated SMILES to 3D structure via NCI web service (SMILES:
C1CN(CCN1CCCN2C(=O)N3C=CC=CC3=N2)C4=CC(=CC=C4)Cl)
> setattr #3 residues chain_id C
Assigning chain_id attribute to 1 item
> move cofr #3
> select #3
48 atoms, 51 bonds, 1 residue, 1 model selected
> addh #3
Summary of feedback from adding hydrogens to
smiles:C1CN(CCN1CCCN2C(=O)N3C=CC=CC3=N2)C4=CC(=CC=C4)Cl #3
---
notes | Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
1 hydrogens added
> select #3
49 atoms, 52 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.059083,0.80445,-0.59107,88.215,-0.69851,0.38969,0.60018,8.5839,0.71315,0.44833,0.5389,-30.813
> view matrix models
> #3,-0.76952,0.29132,-0.56831,85.314,-0.63843,-0.32892,0.69586,6.9527,0.015787,0.8983,0.43909,-31.921
> view matrix models
> #3,-0.71051,-0.37375,-0.59623,85.765,-0.70313,0.34314,0.62279,6.6921,-0.028176,0.86172,-0.50659,-31.509
> view matrix models
> #3,0.098488,-0.97418,0.20315,85.352,0.84252,0.19027,0.50394,6.2062,-0.52958,0.12153,0.83951,-31.1
> view matrix models
> #3,0.098488,-0.97418,0.20315,85.875,0.84252,0.19027,0.50394,6.5418,-0.52958,0.12153,0.83951,-31.496
> view matrix models
> #3,0.53395,-0.84505,-0.02812,85.87,0.81702,0.50712,0.27442,6.8952,-0.21764,-0.1695,0.9612,-31.289
> view matrix models
> #3,0.53395,-0.84505,-0.02812,85.874,0.81702,0.50712,0.27442,6.8493,-0.21764,-0.1695,0.9612,-31.306
> view matrix models
> #3,0.53395,-0.84505,-0.02812,85.914,0.81702,0.50712,0.27442,6.3019,-0.21764,-0.1695,0.9612,-31.461
> view matrix models
> #3,0.53395,-0.84505,-0.02812,85.968,0.81702,0.50712,0.27442,5.8558,-0.21764,-0.1695,0.9612,-31.872
> isolde restrain ligands #1
> isolde restrain ligands #2
ISOLDE: merge models
Merging models #3 into #2.2.
> hide #3 models
> select up
49 atoms, 52 bonds, 1 residue, 1 model selected
> isolde parameterise sel
Running ANTECHAMBER command: C:/Program
Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\TRISTA~1\AppData\Local\Temp\tmp_hvm6a_x\ante.in.mol2 -fi mol2 -o
C:\Users\TRISTA~1\AppData\Local\Temp\tmp_hvm6a_x\ante.out.mol2 -fo mol2 -c bcc
-nc 1 -j 5 -s 2 -dr n
(UNL) ``
(UNL) `Welcome to antechamber 20.0: molecular input file processor.`
(UNL) ``
(UNL) `Info: Finished reading file
(C:\Users\TRISTA~1\AppData\Local\Temp\tmp_hvm6a_x\ante.in.mol2); atoms read
(49), bonds read (52).`
(UNL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(UNL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(UNL) `bash.exe: warning: could not find /tmp, please create!`
(UNL) ``
(UNL) ``
(UNL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(UNL) `bash.exe: warning: could not find /tmp, please create!`
(UNL) `Info: Total number of electrons: 196; net charge: 1`
(UNL) ``
(UNL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`
(UNL) `bash.exe: warning: could not find /tmp, please create!`
(UNL) ``
(UNL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/am1bcc" -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program
Files/ChimeraX/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`
(UNL) `bash.exe: warning: could not find /tmp, please create!`
(UNL) ``
(UNL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(UNL) `bash.exe: warning: could not find /tmp, please create!`
(UNL) ``
Charges for residue UNL determined
OpenMM ffXML file UNL written to the current working directory.
New template added to forcefield as USER_UNL. This ligand should now work in
all remaining simulations for this session. To use in future sessions, load
the ffXML file with ISOLDE's Load Residue MD Definition(s) button.
> select zone sel 5
Selected 677 atoms, 4 surfaces
> isolde sim start
> #1.2/A:75,108-115,130-135,335,623,636/B:77-79,82,107,110-112,114-115,174-177,179,231,233,236,503,610
> #2.2/A:75,108-115,130-135,335,623,636/B:77-79,82,107,110-112,114-115,174-177,179,231,233,236,503,610
> #3/C
ISOLDE: started sim
> hide #2.3 models
> show #2.3 models
> hide #2.3 models
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> delete sel
> select up
52 atoms, 54 bonds, 1 residue, 1 model selected
> ra
> select up
49 atoms, 52 bonds, 1 residue, 1 model selected
> isolde sim start #2.2/C
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select up
52 atoms, 54 bonds, 1 residue, 1 model selected
> delete sel
> select up
49 atoms, 52 bonds, 1 residue, 1 model selected
> show sel
> select zone sel 5
Selected 554 atoms, 4 surfaces
> isolde sim start
> #1.2/A:75,108-110,112-113,115,131-135,623,636/B:78,82,106-107,110-111,114-115,134,174-177,207,233,235-236,503,610,624
> #2.2/A:75,108-110,112-113,115,131-135,623,636/B:78,82,106-107,110-111,114-115,134,174-177,207,233,235-236
> #3/C
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> save 5ewj_ab_trazodone_docked.pdb #2
> show #2.3 models
> hide #!2 models
> show #!1 models
> ui tool show Shell
OpenGL version: 3.3.0 NVIDIA 556.12
OpenGL renderer: NVIDIA GeForce RTX 3070 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: en_GB.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: windows
Manufacturer: HP
Model: HP ZBook Studio 15.6 inch G8 Mobile Workstation PC
OS: Microsoft Windows 11 Pro (Build 22631)
Memory: 34,007,068,672
MaxProcessMemory: 137,438,953,344
CPU: 16 11th Gen Intel(R) Core(TM) i7-11800H @ 2.30GHz
OSLanguage: en-GB
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2024.6.2
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.23.1
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
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: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.8
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-QScore: 1.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.1
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 24.1
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pywin32: 306
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
Send2Trash: 1.8.3
SEQCROW: 1.8.8
setuptools: 69.5.1
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
WMI: 1.5.1
File attachment: 5ewj_ab.pdb
5ewj_ab.pdb
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