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#1833 closed defect (fixed)

Modeller: Item in 'polymeric_res_names' arg is not a string

Reported by:	Elaine Meng	Owned by:	Eric Pettersen
Priority:	normal	Milestone:
Component:	Sequence	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

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

nhase-modeling.cxs

Attachments (1)

nhase-modeling.cxs (191.1 KB ) - added by Elaine Meng 7 years ago.: Added by email2trac

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Change History (6)

by Elaine Meng, 7 years ago

Attachment:	nhase-modeling.cxs added

Added by email2trac

comment:1 by Elaine Meng, 7 years ago

Component:	Unassigned → Sequence
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned

comment:2 by Eric Pettersen, 7 years ago

Status:	assigned → accepted
Summary:	ChimeraX bug report submission → Modeller: Item in 'polymeric_res_names' arg is not a string

comment:3 by Eric Pettersen, 7 years ago

Okay, once this specific bug was fixed, it produced a different error which looked quite similar to the one reported in #1834

comment:4 by Eric Pettersen, 7 years ago

Okay, next bug was in the PDB-writing code; despite being requested to output the in-chain HETs as ATOM records (as required by Modeller), it was still using HETATM records.

Next problem is that 'fast' keyword isn't producing a single model.

comment:5 by Eric Pettersen, 7 years ago

Resolution:	→ fixed
Status:	accepted → closed

Okay, there is not _inherent_ restriction of the number of model when using "fast" mode. So, when fast mode gets checked, the tool changed the number-of-models field to '1' and disables it (until 'fast' gets unchecked).

This means that if you use the command directly instead of the tool, you are free to specify more than one model in fast mode if you want that for some reason.

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