Opened 7 years ago

Closed 7 years ago

#1736 closed defect (fixed)

Morph: No coordset id 1

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Structure Comparison 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: 0.8 (2018-12-17)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | Traceback (most recent call last):  
File  
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-  
packages/chimerax/core/toolshed/__init__.py", line 338, in __init__  
self.init_available_from_cache(logger)  
File  
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-  
packages/chimerax/core/toolshed/__init__.py", line 445, in  
init_available_from_cache  
abc.load_from_cache()  
File  
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-  
packages/chimerax/core/toolshed/available.py", line 61, in load_from_cache  
b = _build_bundle(d)  
File  
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-  
packages/chimerax/core/toolshed/available.py", line 242, in _build_bundle  
keywords = _extract_extra_keywords(keywords)  
File  
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-  
packages/chimerax/core/toolshed/installed.py", line 270, in  
_extract_extra_keywords  
all_kwds = [k.strip() for k in kwds.split(',')]  
AttributeError: 'list' object has no attribute 'split'  
  
UCSF ChimeraX version: 0.8 (2018-12-17)  
How to cite UCSF ChimeraX  

> open 5go4 format mmCIF fromDatabase pdb

Summary of feedback from opening 5go4 fetched from pdb  
---  
notes | Fetching compressed mmCIF 5go4 from
http://files.rcsb.org/download/5go4.cif  
Fetching CCD PRO from http://ligand-expo.rcsb.org/reports/P/PRO/PRO.cif  
Fetching CCD VAL from http://ligand-expo.rcsb.org/reports/V/VAL/VAL.cif  
Fetching CCD SER from http://ligand-expo.rcsb.org/reports/S/SER/SER.cif  
Fetching CCD LEU from http://ligand-expo.rcsb.org/reports/L/LEU/LEU.cif  
Fetching CCD LYS from http://ligand-expo.rcsb.org/reports/L/LYS/LYS.cif  
Fetching CCD HIS from http://ligand-expo.rcsb.org/reports/H/HIS/HIS.cif  
Fetching CCD PHE from http://ligand-expo.rcsb.org/reports/P/PHE/PHE.cif  
Fetching CCD ALA from http://ligand-expo.rcsb.org/reports/A/ALA/ALA.cif  
Fetching CCD ILE from http://ligand-expo.rcsb.org/reports/I/ILE/ILE.cif  
Fetching CCD THR from http://ligand-expo.rcsb.org/reports/T/THR/THR.cif  
Fetching CCD ASP from http://ligand-expo.rcsb.org/reports/A/ASP/ASP.cif  
Fetching CCD GLN from http://ligand-expo.rcsb.org/reports/G/GLN/GLN.cif  
Fetching CCD GLU from http://ligand-expo.rcsb.org/reports/G/GLU/GLU.cif  
Fetching CCD GLY from http://ligand-expo.rcsb.org/reports/G/GLY/GLY.cif  
Fetching CCD TYR from http://ligand-expo.rcsb.org/reports/T/TYR/TYR.cif  
Fetching CCD ASN from http://ligand-expo.rcsb.org/reports/A/ASN/ASN.cif  
Fetching CCD ARG from http://ligand-expo.rcsb.org/reports/A/ARG/ARG.cif  
Fetching CCD MET from http://ligand-expo.rcsb.org/reports/M/MET/MET.cif  
Fetching CCD TRP from http://ligand-expo.rcsb.org/reports/T/TRP/TRP.cif  
Fetching CCD CYS from http://ligand-expo.rcsb.org/reports/C/CYS/CYS.cif  
Fetching CCD HOH from http://ligand-expo.rcsb.org/reports/H/HOH/HOH.cif  
  
5go4 title:  
Truncated mitofusin-1, nucleotide-free [more info...]  
  
Chain information for 5go4 #1  
---  
Chain | Description  
A | Mitofusin-1  
  
  

> set bgColor white

> lighting simple

> lighting shadows true

> lighting soft

> lighting full

> lighting flat

> view cofr false

> hide #!1.1 models

> show #!1.1 models

> open
/Users/mikolajmr/Documents/ProteinStructPrediction/I-TASSER/Mfn1/S421070_results/model2.pdb

File not found:
/Users/mikolajmr/Documents/ProteinStructPrediction/I-TASSER/Mfn1/S421070_results/model2.pdb  

File not found:
/Users/mikolajmr/Documents/ProteinStructPrediction/I-TASSER/Mfn1/S421070_results/model2.pdb  

> open
/Users/mikolajmr/Documents/Data/ProteinStructPrediction/I-TASSER/Mfn1/model1.pdb

Chain information for model1.pdb #2  
---  
Chain | Description  
A | No description available  
  

> hide #!1 models

> show #!1 models

> hide #!1 models

> view cofr false

> lighting soft

> lighting shadows true intensity 0.5

> lighting simple

> lighting flat

> lighting full

> lighting soft

> roll

> stop

> version

UCSF ChimeraX version: 0.8 (2018-12-17)  

blastprotein

Missing or invalid "atoms" argument: empty atom specifier  

> hide #1 target m

> close #1

> select #2

11845 atoms, 11951 bonds selected  

> ~select #2

Nothing selected  

> show selAtoms surfaces

> roll

> stop

> hide selAtoms surfaces

> open
/Users/mikolajmr/Documents/Data/ProteinStructPrediction/I-TASSER/Mfn1/S421070_results/model2.pdb

Summary of feedback from opening
/Users/mikolajmr/Documents/Data/ProteinStructPrediction/I-TASSER/Mfn1/S421070_results/model2.pdb  
---  
warnings | Ignored bad PDB record found on line 2  
METHOD  
  
Ignored bad PDB record found on line 3  
METHOD The models are generated by I-TASSER which combines the  
  
Ignored bad PDB record found on line 4  
METHOD methods of threading, ab initio modeling and structural  
  
Ignored bad PDB record found on line 5  
METHOD refinement. The procedure is fully automated.  
  
Ignored bad PDB record found on line 6  
METHOD  
  
8 messages similar to the above omitted  
  
Chain information for model2.pdb #1  
---  
Chain | Description  
A | No description available  
  

> select #2.1

11845 atoms selected  

> close

> open
/Users/mikolajmr/Documents/Data/ProteinStructPrediction/I-TASSER/Mfn1/S421070_results/model2.pdb

Summary of feedback from opening
/Users/mikolajmr/Documents/Data/ProteinStructPrediction/I-TASSER/Mfn1/S421070_results/model2.pdb  
---  
warnings | Ignored bad PDB record found on line 2  
METHOD  
  
Ignored bad PDB record found on line 3  
METHOD The models are generated by I-TASSER which combines the  
  
Ignored bad PDB record found on line 4  
METHOD methods of threading, ab initio modeling and structural  
  
Ignored bad PDB record found on line 5  
METHOD refinement. The procedure is fully automated.  
  
Ignored bad PDB record found on line 6  
METHOD  
  
8 messages similar to the above omitted  
  
Chain information for model2.pdb #1  
---  
Chain | Description  
A | No description available  
  

> sequence chain #1/A

Alignment identifier is 1.A  

> close

> open 5yew format mmCIF fromDatabase pdb

Summary of feedback from opening 5yew fetched from pdb  
---  
notes | Fetching compressed mmCIF 5yew from
http://files.rcsb.org/download/5yew.cif  
Fetching CCD GDP from http://ligand-expo.rcsb.org/reports/G/GDP/GDP.cif  
Fetching CCD BEF from http://ligand-expo.rcsb.org/reports/B/BEF/BEF.cif  
Fetching CCD K from http://ligand-expo.rcsb.org/reports/K/K/K.cif  
Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif  
  
5yew title:  
Structural basis for GTP hydrolysis and conformational change of mitofusin 1
in mediating mitochondrial fusion [more info...]  
  
Chain information for 5yew #1  
---  
Chain | Description  
A | Mitofusin-1,Mitofusin-1 fusion protein  
B C | Mitofusin-1,Mitofusin-1 fusion protein  
  
Non-standard residues in 5yew #1  
---  
BEF — beryllium trifluoride ion  
MG — magnesium ion  
  
5yew mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
  

> sequence chain #1/C

Alignment identifier is 1.C  

> hide selAtoms ribbons

> hide selAtoms

> ui mousemode rightMode select

> ui mousemode rightMode select

> hide selAtoms

> ui mousemode rightMode select

> hide selAtoms

> ui mousemode rightMode select

> hide selAtoms

> view cofr false

> select #1

9431 atoms, 9587 bonds, 34 pseudobonds, 2 models selected  

> ~select #1

Nothing selected  

> sequence chain #1/A

Alignment identifier is 1.A  

> view cofr false

> ui mousemode rightMode zone

> ui mousemode rightMode tug

> ui mousemode rightMode tug

> ui mousemode rightMode label

> label #1/A:732

> label #1/A:703

> undo

> undo

> undo

> label delete #1/A:732

> label delete #1/A:703

> select #1

9431 atoms, 9587 bonds, 34 pseudobonds, 2 models selected  

> ~select #1

Nothing selected  

> select #1

9431 atoms, 9587 bonds, 34 pseudobonds, 2 models selected  

> ~select #1

Nothing selected  

> close

> open
/Users/mikolajmr/Documents/Data/ProteinStructPrediction/I-TASSER/Mfn1/S421070_results/model1.pdb

Chain information for model1.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open
/Users/mikolajmr/Documents/Data/ProteinStructPrediction/I-TASSER/Mfn1/S421070_results/model2.pdb

Summary of feedback from opening
/Users/mikolajmr/Documents/Data/ProteinStructPrediction/I-TASSER/Mfn1/S421070_results/model2.pdb  
---  
warnings | Ignored bad PDB record found on line 2  
METHOD  
  
Ignored bad PDB record found on line 3  
METHOD The models are generated by I-TASSER which combines the  
  
Ignored bad PDB record found on line 4  
METHOD methods of threading, ab initio modeling and structural  
  
Ignored bad PDB record found on line 5  
METHOD refinement. The procedure is fully automated.  
  
Ignored bad PDB record found on line 6  
METHOD  
  
8 messages similar to the above omitted  
  
Chain information for model2.pdb #2  
---  
Chain | Description  
A | No description available  
  

> align #1 toAtoms #2

Unequal number of atoms to pair, 11848 and 11834  

> matchmaker #2 to #1

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 model1.pdb, chain A (#1) with model2.pdb, chain A (#2), sequence
alignment score = 3314.2  
RMSD between 231 pruned atom pairs is 0.726 angstroms; (across all 741 pairs:
9.241)  
  

> morph #2,1 same true

Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/cmd_line/tool.py", line 229, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2587, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/morph/morph.py", line 70, in morph  
color_segments = color_segments, color_core = color_core)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/morph/motion.py", line 39, in compute_morph  
traj.active_coordset_id = 1 # Start at initial trajectory frame.  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/graphics/drawing.py", line 228, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/molc.py", line 112, in set_prop  
cset(self._c_pointer_ref, 1, v_ref)  
IndexError: No coordset id 1  
  
IndexError: No coordset id 1  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/molc.py", line 112, in set_prop  
cset(self._c_pointer_ref, 1, v_ref)  
  
See log for complete Python traceback.  
  

> morph #2,1

Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/cmd_line/tool.py", line 229, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2587, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/morph/morph.py", line 70, in morph  
color_segments = color_segments, color_core = color_core)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/morph/motion.py", line 39, in compute_morph  
traj.active_coordset_id = 1 # Start at initial trajectory frame.  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/graphics/drawing.py", line 228, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/molc.py", line 112, in set_prop  
cset(self._c_pointer_ref, 1, v_ref)  
IndexError: No coordset id 1  
  
IndexError: No coordset id 1  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/molc.py", line 112, in set_prop  
cset(self._c_pointer_ref, 1, v_ref)  
  
See log for complete Python traceback.  
  

> morph #2,1 frames 40

Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/cmd_line/tool.py", line 229, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2587, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/morph/morph.py", line 70, in morph  
color_segments = color_segments, color_core = color_core)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/morph/motion.py", line 39, in compute_morph  
traj.active_coordset_id = 1 # Start at initial trajectory frame.  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/graphics/drawing.py", line 228, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/molc.py", line 112, in set_prop  
cset(self._c_pointer_ref, 1, v_ref)  
IndexError: No coordset id 1  
  
IndexError: No coordset id 1  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/molc.py", line 112, in set_prop  
cset(self._c_pointer_ref, 1, v_ref)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-1.68.21
OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Change History (3)

comment:1 by Eric Pettersen, 7 years ago

Component: Unassigned → Structure Comparison
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Morph: No coordset id 1

comment:2 by Tom Goddard, 7 years ago

Tried to morph from a model which must have had a "MODEL 2" line in the PDB file which will cause the coordset id 2 to be used. The morph code copies this starting molecule and assumes its coordinate set has id 1. Need to check and if the coordset id is not 1 then change it to 1 in the copy which will be the returned trajectory.

comment:3 by Tom Goddard, 7 years ago

Resolution: → fixed
Status: assigned → closed

Fixed.

Morph was making a copy of the first model and then adding coordinate sets to it to make the morph, but assumed the first model had just one coordinate set with id = 1. Those assumptions are no longer made, only the active coordset of the first model is used and its id is set to 1 in the resulting morph.

Note: See TracTickets for help on using tickets.