id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1833 Modeller: Item in 'polymeric_res_names' arg is not a string Elaine Meng Eric Pettersen "{{{ The following bug report has been submitted: Platform: Darwin-17.7.0-x86_64-i386-64bit ChimeraX Version: 0.9 (2019-04-05) Description TypeError: Item in 'polymeric_res_names' arg is not a string Tried to run modeller with two alignments for two subunits. session attached. Tried using fast/approx mode with 3 models output. Log: > open /Users/meng/Desktop/startup.cxc > alias reset view orient; view initial > open presets.cxc > alias cardef car style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20; car style ~(nucleic|strand) x round; car style (nucleic|strand) x rect > alias nospheres style (protein|nucleic|solvent) & @@draw_mode=0 stick > alias nucrib cardef; car style nucleic x round width 1.6 thick 1.6 > alias cylinders cardef; car style protein modeh tube rad 2 sides 24 thick 0.6 > alias licorice cardef; car style protein modeh default arrows f x round width 1 thick 1 > alias cartoon1 surf hide; nospheres; cartoon; cardef; nuc tube/slab shape box > alias cartoon2 surf hide; nospheres; cartoon; cylinders; car style nucleic x round width 1.6 thick 1.6; nuc stubs > alias cartoon3 surf hide; nospheres; cartoon; licorice; car style nucleic x round width 1.6 thick 1.6; nuc tube/slab shape ellipsoid > alias surfw nospheres; surface; color white targ s trans 80 > alias surfat nospheres; surface; color fromatoms targ s trans 70 > alias surfc nospheres; surface; color bychain targ s trans 0 > alias surfm nospheres; surface; color bymodel targ s trans 0 > alias pub set bgcolor white silhouettes t > alias unpub ~set bgcolor; set silhouettes f executed presets.cxc executed startup.cxc UCSF ChimeraX version: 0.9 (2019-04-05) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open chidata/PF13*slx Summary of feedback from opening chidata/PF13609_seed.slx --- note | Alignment identifier is PF13609_seed.slx Opened 115 sequences from PF13609_seed.slx > open 1mpf Summary of feedback from opening 1mpf fetched from pdb --- note | Fetching compressed mmCIF 1mpf from http://files.rcsb.org/download/1mpf.cif 1mpf title: Structural and functional alterations of A colicin resistant mutant of OMPF- porin from escherichia coli [more info...] Chain information for 1mpf #1 --- Chain | Description A | matrix porin outer membrane protein F Non-standard residues in 1mpf #1 --- C8E — (hydroxyethyloxy)tri(ethyloxy)octane 1mpf mmCIF Assemblies --- 1| author_and_software_defined_assembly > close > open 1pho 1pho title: Crystal structures explain functional properties of two E. Coli porins [more info...] Chain information for 1pho #1 --- Chain | Description A | phosphoporin 1pho mmCIF Assemblies --- 1| author_and_software_defined_assembly > close > open 3pox Summary of feedback from opening 3pox fetched from pdb --- notes | Fetching compressed mmCIF 3pox from http://files.rcsb.org/download/3pox.cif Fetching CCD OLC from http://ligand-expo.rcsb.org/reports/O/OLC/OLC.cif 3pox title: Crystal Structure of E.coli OmpF porin in lipidic cubic phase: space group P1 [more info...] Chain information for 3pox #1 --- Chain | Description A B C D E F | OmpF protein Non-standard residues in 3pox #1 --- OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol) SCN — thiocyanate ion 3pox mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > close > open 1muc 1muc title: Structure of muconate lactonizing enzyme At 1.85 angstroms resolution [more info...] Chain information for 1muc #1 --- Chain | Description A B | muconate lactonizing enzyme Non-standard residues in 1muc #1 --- MN — manganese (II) ion 1muc mmCIF Assemblies --- 1| author_and_software_defined_assembly > open chidata/super8.msf Summary of feedback from opening chidata/super8.msf --- note | Alignment identifier is super8.msf Opened 8 sequences from super8.msf > close > open 2mnr 2mnr title: Mechanism of the reaction catalyzed by mandelate racemase. 2. Crystal structure of mandelate racemase At 2.5 angstroms resolution: identification of the active site and possible catalytic residues [more info...] Chain information for 2mnr #1 --- Chain | Description A | mandelate racemase Non-standard residues in 2mnr #1 --- MN — manganese (II) ion SO4 — sulfate ion 2mnr mmCIF Assemblies --- 1| author_and_software_defined_assembly Associated 2mnr chain A to mr with 0 mismatches > close > open 1muc 1muc title: Structure of muconate lactonizing enzyme At 1.85 angstroms resolution [more info...] Chain information for 1muc #1 --- Chain | Description A B | muconate lactonizing enzyme Non-standard residues in 1muc #1 --- MN — manganese (II) ion 1muc mmCIF Assemblies --- 1| author_and_software_defined_assembly Associated 1muc chain A to mleipp with 5 mismatches Associated 1muc chain B to mleipp with 5 mismatches > open chidata/super8.msf Summary of feedback from opening chidata/super8.msf --- note | Alignment identifier is super8.msf Opened 8 sequences from super8.msf > close > open 2mnr 2mnr title: Mechanism of the reaction catalyzed by mandelate racemase. 2. Crystal structure of mandelate racemase At 2.5 angstroms resolution: identification of the active site and possible catalytic residues [more info...] Chain information for 2mnr #1 --- Chain | Description A | mandelate racemase Non-standard residues in 2mnr #1 --- MN — manganese (II) ion SO4 — sulfate ion 2mnr mmCIF Assemblies --- 1| author_and_software_defined_assembly Associated 2mnr chain A to mr with 0 mismatches > open 1muc 1muc title: Structure of muconate lactonizing enzyme At 1.85 angstroms resolution [more info...] Chain information for 1muc #2 --- Chain | Description A B | muconate lactonizing enzyme Non-standard residues in 1muc #2 --- MN — manganese (II) ion 1muc mmCIF Assemblies --- 1| author_and_software_defined_assembly Associated 1muc chain A to mleipp with 5 mismatches Associated 1muc chain B to mleipp with 5 mismatches > open 4enl 4enl title: Crystal structure of holoenzyme refined At 1.9 angstroms resolution: trigonal- bipyramidal geometry of the cation binding site [more info...] Chain information for 4enl #3 --- Chain | Description A | enolase Non-standard residues in 4enl #3 --- SO4 — sulfate ion ZN — zinc ion 4enl mmCIF Assemblies --- 1| author_defined_assembly Associated 4enl chain A to enolyeast with 0 mismatches > open chidata/super8.msf Summary of feedback from opening chidata/super8.msf --- note | Alignment identifier is super8.msf Opened 8 sequences from super8.msf > open 114d 114d title: Inosine-adenine base pairs In A B-DNA duplex [more info...] Chain information for 114d #4 --- Chain | Description A B | DNA (5'-D(*CP*GP*CP*ip*ap*ap*TP*TP*ap*GP*CP*G)-3') > hide #!1 models > hide #!2 models > color modify :i whiteness + 25 > color modify :di whiteness + 25 > color modify :di whiteness - 25 > close #4 > open 114d 114d title: Inosine-adenine base pairs In A B-DNA duplex [more info...] Chain information for 114d #4 --- Chain | Description A B | DNA (5'-D(*CP*GP*CP*ip*ap*ap*TP*TP*ap*GP*CP*G)-3') > color modify sel whiteness +25 > color modify :di whiteness +25 > color modify :di whiteness + 25 > color bynucleotide > color red > color modify whiteness + 25 > color bynucleotide > color modify :di lightness + 25 > color bynucleotide > color modify :di lightness + 10 > color bynucleotide > color bynucleotide > color modify :di whiteness + 10 > color bynucleotide > color modify :di whiteness + 25 > color bynucleotide > ~select Nothing selected > color modify :di lightness + 10 > close > open 1muc 1muc title: Structure of muconate lactonizing enzyme At 1.85 angstroms resolution [more info...] Chain information for 1muc #1 --- Chain | Description A B | muconate lactonizing enzyme Non-standard residues in 1muc #1 --- MN — manganese (II) ion 1muc mmCIF Assemblies --- 1| author_and_software_defined_assembly Associated 1muc chain A to mleipp with 5 mismatches Associated 1muc chain B to mleipp with 5 mismatches > toolshed show '""Modeller Comparitive Modeling""' > open 114d 114d title: Inosine-adenine base pairs In A B-DNA duplex [more info...] Chain information for 114d #2 --- Chain | Description A B | DNA (5'-D(*CP*GP*CP*ip*ap*ap*TP*TP*ap*GP*CP*G)-3') > select #1 5760 atoms, 5525 bonds, 14 pseudobonds, 2 models selected > ~select #1 Nothing selected > hide #!1 models > color :di #006400 target a > help color > usage color color [objects] [color [what]] [target characters from 'abcfprs'] [transparency a number] [halfbond true or false] — color objects objects: an objects specifier or nothing color: a color or one of byatom, bychain, byelement, byhetero, bymodel, bynucleotide, bypolymer, fromatoms, or random what: a collection of one of All, atoms, bonds, cartoons, pseudobonds, ribbons, rings, or surfaces Subcommands are: * color bfactor * color byattribute * color cylindrical * color delete * color electrostatic * color gradient * color height * color list * color modify * color name * color radial * color sample * color sequential * color show * color zone > toolshed show Log > color /a:di #40a440 target a > color bynucleotide target a > color /a:di #006400 target a > color modify :di whiteness + 25 > color sel blue > color modify sel lightness + 25 > color nucleic-acid white > color modify nucleic-acid whiteness + 25 > color nucleic-acid #006400 > color modify nucleic-acid whiteness + 25 > color nucleic-acid #006400 > color nucleic-acid #406440 > color nucleic-acid #006400 > color modify nucleic-acid whiteness + 25 > color nucleic-acid #006400 > color modify nucleic-acid lightness + 25 > color nucleic-acid #006400 > color nucleic-acid #40a440 > color #1 bynucleotide > color #2 bynucleotide > color :di #40a440 > close > open chidata/NH*ali Summary of feedback from opening files --- notes | Alignment identifier is NHase_alpha.ali Alignment identifier is NHase_beta.ali Opened 2 sequences from NHase_alpha.ali Opened 2 sequences from NHase_beta.ali > open 1ire Summary of feedback from opening 1ire fetched from pdb --- notes | Fetching compressed mmCIF 1ire from http://files.rcsb.org/download/1ire.cif Fetching CCD CSD from http://ligand-expo.rcsb.org/reports/C/CSD/CSD.cif Fetching CCD CSO from http://ligand-expo.rcsb.org/reports/C/CSO/CSO.cif Fetching CCD CO from http://ligand-expo.rcsb.org/reports/C/CO/CO.cif 1ire title: Crystal Structure of Co-type nitrile hydratase from Pseudonocardia thermophila [more info...] Chain information for 1ire #1 --- Chain | Description A | Nitrile Hydratase B | Nitrile Hydratase Non-standard residues in 1ire #1 --- CO — cobalt (II) ion 1ire mmCIF Assemblies --- 1| author_and_software_defined_assembly Associated 1ire chain B to 1ireb with 0 mismatches > select /a 1749 atoms, 1651 bonds, 6 pseudobonds, 1 model selected > select /b 2044 atoms, 1914 bonds selected > rainbow chains > color modify whiteness + 25 > color modify whiteness + 10 > sequence chain /a Alignment identifier is 1.A > close > open 1ire 1ire title: Crystal Structure of Co-type nitrile hydratase from Pseudonocardia thermophila [more info...] Chain information for 1ire #1 --- Chain | Description A | Nitrile Hydratase B | Nitrile Hydratase Non-standard residues in 1ire #1 --- CO — cobalt (II) ion 1ire mmCIF Assemblies --- 1| author_and_software_defined_assembly Associated 1ire chain B to 1ireb with 0 mismatches > close > open 2ahj Summary of feedback from opening 2ahj fetched from pdb --- notes | Fetching compressed mmCIF 2ahj from http://files.rcsb.org/download/2ahj.cif Fetching CCD FE from http://ligand-expo.rcsb.org/reports/F/FE/FE.cif Fetching CCD NO from http://ligand-expo.rcsb.org/reports/N/NO/NO.cif Fetching CCD DIO from http://ligand-expo.rcsb.org/reports/D/DIO/DIO.cif 2ahj title: Nitrile hydratase complexed with nitric oxide [more info...] Chain information for 2ahj #1 --- Chain | Description A C | nitrile hydratase B D | nitrile hydratase Non-standard residues in 2ahj #1 --- DIO — 1,4-diethylene dioxide FE — Fe (III) ion NO — nitric oxide (Nitrogen monoxide) SO4 — sulfate ion ZN — zinc ion 2ahj mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| software_defined_assembly Associated 2ahj chain D to 2ahjb with 0 mismatches Associated 2ahj chain B to 2ahjb with 0 mismatches > rainbow chains > close > open 1ire 1ire title: Crystal Structure of Co-type nitrile hydratase from Pseudonocardia thermophila [more info...] Chain information for 1ire #1 --- Chain | Description A | Nitrile Hydratase B | Nitrile Hydratase Non-standard residues in 1ire #1 --- CO — cobalt (II) ion 1ire mmCIF Assemblies --- 1| author_and_software_defined_assembly > open 2ahj 2ahj title: Nitrile hydratase complexed with nitric oxide [more info...] Chain information for 2ahj #2 --- Chain | Description A C | nitrile hydratase B D | nitrile hydratase Non-standard residues in 2ahj #2 --- DIO — 1,4-diethylene dioxide FE — Fe (III) ion NO — nitric oxide (Nitrogen monoxide) SO4 — sulfate ion ZN — zinc ion 2ahj mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| software_defined_assembly > sequence chain /a > sequence chain #1/a Alignment identifier is 1.A > sequence chain /a > sequence chain #2/a Alignment identifier is 2.A > open chidata/NH_alpha-edited.ali > open /Users/meng/Desktop/chidata/NHase_alpha_edited.ali Traceback (most recent call last): File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cmd_line/tool.py"", line 253, in execute cmd.run(cmd_text) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2628, in run result = ci.function(session, **kw_args) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/open.py"", line 41, in open from_database=from_database, ignore_cache=ignore_cache, **kw)) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/open.py"", line 117, in open models = handle_unknown_kw(session.models.open, paths, format=format, name=name, **kw) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/open.py"", line 62, in handle_unknown_kw return f(*args, **kw) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/models.py"", line 598, in open session, filenames, format=format, name=name, **kw) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py"", line 467, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py"", line 423, in open_data models, status = open_func(*args, **kw) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seqalign/__init__.py"", line 52, in open_file alignment=alignment, ident=ident, auto_associate=auto_associate) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seqalign/parse.py"", line 35, in open_file raise ValueError(""No sequences found in %s file '%s'!"" % (format_name, fname)) ValueError: No sequences found in PIR file 'NHase_alpha_edited.ali'! ValueError: No sequences found in PIR file 'NHase_alpha_edited.ali'! File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seqalign/parse.py"", line 35, in open_file raise ValueError(""No sequences found in %s file '%s'!"" % (format_name, fname)) See log for complete Python traceback. > open chidata/NH_alpha_edited.ali > open chidata/NHase_alpha_edited.ali Summary of feedback from opening chidata/NHase_alpha_edited.ali --- note | Alignment identifier is NHase_alpha_edited.ali Opened 2 sequences from NHase_alpha_edited.ali > close > open 1ire 1ire title: Crystal Structure of Co-type nitrile hydratase from Pseudonocardia thermophila [more info...] Chain information for 1ire #1 --- Chain | Description A | Nitrile Hydratase B | Nitrile Hydratase Non-standard residues in 1ire #1 --- CO — cobalt (II) ion 1ire mmCIF Assemblies --- 1| author_and_software_defined_assembly Associated 1ire chain A to 1ire chain A with 0 mismatches > open chidata/NHase_beta.ali Summary of feedback from opening chidata/NHase_beta.ali --- note | Alignment identifier is NHase_beta.ali Opened 2 sequences from NHase_beta.ali > close > open 1ire 1ire title: Crystal Structure of Co-type nitrile hydratase from Pseudonocardia thermophila [more info...] Chain information for 1ire #1 --- Chain | Description A | Nitrile Hydratase B | Nitrile Hydratase Non-standard residues in 1ire #1 --- CO — cobalt (II) ion 1ire mmCIF Assemblies --- 1| author_and_software_defined_assembly Associated 1ire chain A to 1ire chain A with 0 mismatches Associated 1ire chain B to 1ireb with 0 mismatches > close > open 2ahj 2ahj title: Nitrile hydratase complexed with nitric oxide [more info...] Chain information for 2ahj #1 --- Chain | Description A C | nitrile hydratase B D | nitrile hydratase Non-standard residues in 2ahj #1 --- DIO — 1,4-diethylene dioxide FE — Fe (III) ion NO — nitric oxide (Nitrogen monoxide) SO4 — sulfate ion ZN — zinc ion 2ahj mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| software_defined_assembly Associated 2ahj chain C to 2ahj chain A with 0 mismatches Associated 2ahj chain A to 2ahj chain A with 0 mismatches Associated 2ahj chain D to 2ahjb with 0 mismatches Associated 2ahj chain B to 2ahjb with 0 mismatches > modeller comparitive NHase_alpha_edited.ali:2,NHase_beta.ali:2 combineTemplates true numModels 3 fast true hetPreserve false hydrogens false waterPreserve false Traceback (most recent call last): File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/modeller/tool.py"", line 140, in launch_modeller repr(settings.water_preserve).lower() File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2628, in run result = ci.function(session, **kw_args) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/modeller/cmd.py"", line 43, in sequence_model temp_path=temp_path, thorough_opt=thorough_opt, water_preserve=water_preserve) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/modeller/comparitive.py"", line 205, in model save_pdb(session, pdb_file_name, models=[structure], polymeric_res_names=ATOM_res_names) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/pdb/pdb.py"", line 113, in save_pdb (serial_numbering == ""h36""), polymeric_res_names) TypeError: Item in 'polymeric_res_names' arg is not a string TypeError: Item in 'polymeric_res_names' arg is not a string File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/pdb/pdb.py"", line 113, in save_pdb (serial_numbering == ""h36""), polymeric_res_names) See log for complete Python traceback. > modeller comparitive NHase_alpha_edited.ali:2,NHase_beta.ali:2 combineTemplates false numModels 3 fast true hetPreserve false hydrogens false waterPreserve false Traceback (most recent call last): File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/modeller/tool.py"", line 140, in launch_modeller repr(settings.water_preserve).lower() File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2628, in run result = ci.function(session, **kw_args) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/modeller/cmd.py"", line 43, in sequence_model temp_path=temp_path, thorough_opt=thorough_opt, water_preserve=water_preserve) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/modeller/comparitive.py"", line 205, in model save_pdb(session, pdb_file_name, models=[structure], polymeric_res_names=ATOM_res_names) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/pdb/pdb.py"", line 113, in save_pdb (serial_numbering == ""h36""), polymeric_res_names) TypeError: Item in 'polymeric_res_names' arg is not a string TypeError: Item in 'polymeric_res_names' arg is not a string File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/pdb/pdb.py"", line 113, in save_pdb (serial_numbering == ""h36""), polymeric_res_names) See log for complete Python traceback. > save session /Users/meng/Desktop/nhase-modeling.cxs OpenGL version: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102 OpenGL renderer: NVIDIA GeForce GTX 675MX OpenGL Engine OpenGL vendor: NVIDIA Corporation File attachment: nhase-modeling.cxs }}} [attachment:""nhase-modeling.cxs""] " defect closed normal Sequence fixed all ChimeraX