Modeller backend failure

[Elaine Meng]

The following bug report has been submitted:
Platform:        Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-04-05)
Description
KeyError: 'ok_models.dat'

Tried to run Modeller fast/approx output 3 models combineTemplates false when I had alignment associated with one monomer and one dimer.  Trying to understand combinTemplates option, but stymied by other errors. Session attached.

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/super8.msf

Summary of feedback from opening chidata/super8.msf  
---  
note | Alignment identifier is super8.msf  
  
Opened 8 sequences from super8.msf  

> 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 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 #2  
---  
Chain | Description  
A | mandelate racemase  
  
Non-standard residues in 2mnr #2  
---  
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  
  

> toolshed show '"Modeller Comparitive Modeling"'

> modeller comparitive super8.msf:8 combineTemplates false numModels 3 fast
true hetPreserve false hydrogens false waterPreserve false

Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v9.18) for
protein structure modeling  
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service  
Opal job id: appModeller9v8Service15547596250601167351092  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appModeller9v8Service15547596250601167351092  
stdout.txt = standard output  
stderr.txt = standard error  
Modeller job ID appModeller9v8Service15547596250601167351092 finished  
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/comparitive.py", line 332, in on_finish  
model_info = self.get_file("ok_models.dat")  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/webservices/opal_job.py", line 254, in get_file  
url = self._outputs[filename]  
KeyError: 'ok_models.dat'  
  
During handling of the above exception, another exception occurred:  
  
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/ui/gui.py", line 536, in customEvent  
func(*args, **kw)  
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 334, in on_finish  
raise RuntimeError("No output models from Modeller")  
RuntimeError: No output models from Modeller  
  
RuntimeError: No output models from Modeller  
  
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 334, in on_finish  
raise RuntimeError("No output models from Modeller")  
  
See log for complete Python traceback.  
  

> save dimer-monomer-super.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: dimer-monomer-super.cxs

dimer-monomer-super.cxs​

[Elaine Meng]

Added by email2trac

[pett]

Code assumed that chain associations started at the beginning of the chain, which was wrong.