id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15937 Generated CRYST1 record mis-formatted Tristan Croll Eric Pettersen "{{{ 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 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 }}} [attachment:""5ewj_ab.pdb""] " defect closed normal Input/Output nonchimerax Tristan Croll all ChimeraX