"Particle coordinate is NaN" error in ISOLDE 1.0b2

[dkreitle@…]

The following bug report has been submitted:
Platform:        Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.8 (2018-12-17)
Description
Running simulation in ISOLDE. Particle coordinate is nan error that stops simulation. (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  

> toolshed show ISOLDE

before.pdb title:  
Crystal structure of etub from clostridium kluyveri [more info...]  
  
Chain information for before.pdb #1  
---  
Chain | Description  
A | predicted microcompartment protein  
  
before.pdb title:  
Crystal structure of etub from clostridium kluyveri [more info...]  
  
Chain information for before.pdb  
---  
Chain | Description  
1.3/A | predicted microcompartment protein  
  

> toolshed show "File History"

> toolshed show "Side View"

> help help:user/tools/modelpanel.html

Exception ignored in: <bound method Texture.__del__ of
<chimerax.core.graphics.opengl.Texture object at 0x13792a240>>  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/graphics/opengl.py", line 2509, in __del__  
raise RuntimeError('OpenGL texture was not deleted before
core.graphics.Texture destroyed')  
RuntimeError: OpenGL texture was not deleted before core.graphics.Texture
destroyed  
Exception ignored in: <bound method Framebuffer.__del__ of
<chimerax.core.graphics.opengl.Framebuffer object at 0x137923940>>  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/graphics/opengl.py", line 1743, in __del__  
% self.name)  
RuntimeError: OpenGL framebuffer mask was not deleted before
core.graphics.Framebuffer destroyed  

> close session

> open
/Users/dkreitler/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30_ISOLDE.pdb

Chain information for NpsA_32_refine_30_ISOLDE.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open NpsA_32_refine_30_ISOLDE.mtz

File not found: NpsA_32_refine_30_ISOLDE.mtz  

> open NpsA_32_refine_30_ISOLDE.mtz structureModel #1

File not found: NpsA_32_refine_30_ISOLDE.mtz  

> open ~/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30_2mFo-
DFc.ccp4 structureModel #1

Opened NpsA_32_refine_30_2mFo-DFc.ccp4, grid size 80,87,114, pixel
0.934,0.915,0.921, shown at level 3.2, step 1, values float32  

> toolshed show ISOLDE

Chain information for NpsA_32_refine_30_ISOLDE.pdb  
---  
Chain | Description  
1.3/A | No description available  
  

> hide selAtoms ribbons

> open ~/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30_2mFo-
DFc.ccp4 structureModel #1

Opened NpsA_32_refine_30_2mFo-DFc.ccp4, grid size 80,87,114, pixel
0.934,0.915,0.921, shown at level 3.2, step 1, values float32  
Bad residue number: match  
Doing nothing  

> addh hbond true

No usable SEQRES records for NpsA_32_refine_30_ISOLDE.pdb (#1.3) chain A;
guessing termini instead  
Chain-initial residues that are actual N termini: /A GLN 9  
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: /A ALA 504  
402 hydrogen bonds  
/A ALA 504 is not terminus, removing H atom from 'C'  
3830 hydrogens added  

> hide H

> hide #!2.1 models

> close #2

> close #1.3

> close #1.2

> close #1.1.1.1

> close #1

> open 2bbv

Summary of feedback from opening 2bbv fetched from pdb  
---  
notes | Fetching compressed mmCIF 2bbv from
http://files.rcsb.org/download/2bbv.cif  
Fetching CCD U from http://ligand-expo.rcsb.org/reports/U/U/U.cif  
Fetching CCD C from http://ligand-expo.rcsb.org/reports/C/C/C.cif  
Fetching CCD A from http://ligand-expo.rcsb.org/reports/A/A/A.cif  
Fetching CCD LEU from http://ligand-expo.rcsb.org/reports/L/LEU/LEU.cif  
Fetching CCD THR from http://ligand-expo.rcsb.org/reports/T/THR/THR.cif  
Fetching CCD ARG from http://ligand-expo.rcsb.org/reports/A/ARG/ARG.cif  
Fetching CCD SER from http://ligand-expo.rcsb.org/reports/S/SER/SER.cif  
Fetching CCD GLN from http://ligand-expo.rcsb.org/reports/G/GLN/GLN.cif  
Fetching CCD PRO from http://ligand-expo.rcsb.org/reports/P/PRO/PRO.cif  
Fetching CCD GLY from http://ligand-expo.rcsb.org/reports/G/GLY/GLY.cif  
Fetching CCD ALA from http://ligand-expo.rcsb.org/reports/A/ALA/ALA.cif  
Fetching CCD PHE from http://ligand-expo.rcsb.org/reports/P/PHE/PHE.cif  
Fetching CCD LYS from http://ligand-expo.rcsb.org/reports/L/LYS/LYS.cif  
Fetching CCD CYS from http://ligand-expo.rcsb.org/reports/C/CYS/CYS.cif  
Fetching CCD ASP from http://ligand-expo.rcsb.org/reports/A/ASP/ASP.cif  
Fetching CCD ASN from http://ligand-expo.rcsb.org/reports/A/ASN/ASN.cif  
Fetching CCD ILE from http://ligand-expo.rcsb.org/reports/I/ILE/ILE.cif  
Fetching CCD GLU from http://ligand-expo.rcsb.org/reports/G/GLU/GLU.cif  
Fetching CCD VAL from http://ligand-expo.rcsb.org/reports/V/VAL/VAL.cif  
Fetching CCD TYR from http://ligand-expo.rcsb.org/reports/T/TYR/TYR.cif  
Fetching CCD TRP from http://ligand-expo.rcsb.org/reports/T/TRP/TRP.cif  
Fetching CCD MET from http://ligand-expo.rcsb.org/reports/M/MET/MET.cif  
Fetching CCD HIS from http://ligand-expo.rcsb.org/reports/H/HIS/HIS.cif  
Fetching CCD CA from http://ligand-expo.rcsb.org/reports/C/CA/CA.cif  
Fetching CCD HOH from http://ligand-expo.rcsb.org/reports/H/HOH/HOH.cif  
  
2bbv title:  
The refined three-dimensional structure of an insect virus At 2.8 angstroms
resolution [more info...]  
  
Chain information for 2bbv #1  
---  
Chain | Description  
A B C | protein (black beetle virus capsid protein)  
D E F | protein (black beetle virus capsid protein)  
N | RNA (5'-R(*up*CP*up*up*ap*up*ap*up*CP*U)-3')  
  
Non-standard residues in 2bbv #1  
---  
CA — calcium ion  
  
2bbv mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
6| crystal asymmetric unit, crystal frame  
  
  

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide solvent

> show solvent

> hide solvent

could not retrieve bundle list from toolshed  

Unknown command: bgcolor black  

> set bgColor black

> show selAtoms ribbons

> hide selAtoms surfaces

> hide selAtoms

> hide selAtoms surfaces

> show selAtoms ribbons

> hide selAtoms ribbons

> show selAtoms surfaces

> hide selAtoms surfaces

> show selAtoms

> close #1

> open 1a0m fromDatabase eds

Summary of feedback from opening 1a0m fetched from eds  
---  
note | Fetching map 1a0m from
http://www.ebi.ac.uk/pdbe/coordinates/files/1a0m.ccp4  
  
Opened 1a0m.ccp4, grid size 97,101,88, pixel 0.37,0.37,0.367, shown at level
2.28, step 1, values float32  

> open 1a0m

Summary of feedback from opening 1a0m fetched from pdb  
---  
notes | Fetching compressed mmCIF 1a0m from
http://files.rcsb.org/download/1a0m.cif  
Fetching CCD NH2 from http://ligand-expo.rcsb.org/reports/N/NH2/NH2.cif  
  
1a0m title:  
1.1 angstrom crystal structure of A-conotoxin [TYR15]-epi [more info...]  
  
Chain information for 1a0m #2  
---  
Chain | Description  
A B | α-conotoxin [TYR15]-epi  
  
Non-standard residues in 1a0m #2  
---  
NH2 — amino group  
  
  

> hide ribbons

> show atoms

Expected a keyword  

> volume #1 level 2.0 style mesh

> close

> open
/Users/dkreitler/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30.pdb

Summary of feedback from opening
/Users/dkreitler/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Date 2019-05-01 Time 15:14:02 EDT -0400 (1556738042.71 s)  
  
Ignored bad PDB record found on line 2  
REMARK PHENIX refinement  
  
Ignored bad PDB record found on line 4  
REMARK ****************** INPUT FILES AND LABELS
******************************  
  
Ignored bad PDB record found on line 5  
REMARK Reflections:  
  
Ignored bad PDB record found on line 6  
REMARK file name :
/Users/dkreitler/Xray/Projects/NpsA/NpsA_32/phenix/rosetta_refine_13/NpsA_32_refine_11_rosetta_phenix_001.mtz  
  
38 messages similar to the above omitted  
  
Chain information for NpsA_32_refine_30.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open
/Users/dkreitler/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30_ISOLDE.mtz

Must specify a structure model to associate with crystallographic data  

Must specify a structure model to associate with crystallographic data  

> open
~/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30_ISOLDE.mtz

Must specify a structure model to associate with crystallographic data  

> open
~/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30_ISOLDE.mtz
NpsA_32_refine_30

Must specify a structure model to associate with crystallographic data  

> open
~/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30_ISOLDE.mtz
NpsA_32_refine_30.pdb

Must specify a structure model to associate with crystallographic data  

> open
~/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30_ISOLDE.mtz
model #1

Must specify a structure model to associate with crystallographic data  

> open
/Users/dkreitler/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30_2mFo-
DFc.ccp4

Opened NpsA_32_refine_30_2mFo-DFc.ccp4, grid size 80,87,114, pixel
0.934,0.915,0.921, shown at level 3.2, step 1, values float32  

> close

> open
/Users/dkreitler/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30_ISOLDE.pdb

Chain information for NpsA_32_refine_30_ISOLDE.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open
/Users/dkreitler/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30_ISOLDE

Missing filename suffix
/Users/dkreitler/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30_ISOLDE  

Missing filename suffix
/Users/dkreitler/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30_ISOLDE  

> open
/Users/dkreitler/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30_ISOLDE.ccp4

Opened NpsA_32_refine_30_ISOLDE.ccp4, grid size 85,92,129, pixel
0.692,0.703,0.691, shown at level 3.21, step 1, values float32  

> toolshed show ISOLDE

Chain information for NpsA_32_refine_30_ISOLDE.pdb  
---  
Chain | Description  
1.3/A | No description available  
  

> set bgColor white

Bad residue number: match  
Doing nothing  

> addh hbond true

No usable SEQRES records for NpsA_32_refine_30_ISOLDE.pdb (#1.3) chain A;
guessing termini instead  
Chain-initial residues that are actual N termini: /A GLN 9  
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: /A ALA 504  
402 hydrogen bonds  
/A ALA 504 is not terminus, removing H atom from 'C'  
3830 hydrogens added  

> hide H

Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/delayed_reaction.py", line 65, in callback  
self.ff(*self.ff_args)  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1460, in
_update_coordinates_and_repeat  
self.atoms.coords = th.coords  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 294, in coords  
f(self._c_pointer, n, pointer(coords))  
RuntimeError: Particle coordinate is nan  
  
Error processing trigger "new frame": Particle coordinate is nan:  
RuntimeError: Particle coordinate is nan  
  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 294, in coords  
f(self._c_pointer, n, pointer(coords))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 2482, in _start_sim_or_toggle_pause  
self.pause_sim_toggle()  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 2680, in pause_sim_toggle  
self.sim_manager.toggle_pause()  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 678, in
toggle_pause  
self.pause = not self.pause  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 657, in pause  
self.sim_handler.pause = flag  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1555, in pause  
self._resume()  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1450, in _resume  
self._repeat_step()  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1441, in
_repeat_step  
th.thread_finished, self._update_coordinates_and_repeat, final_args)  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/delayed_reaction.py", line 56, in delayed_reaction  
initiator_func(*initiator_args)  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 186, in minimize  
f(self._c_pointer, tolerance, max_iterations)  
RuntimeError: Particle coordinate is nan  
  
RuntimeError: Particle coordinate is nan  
  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 186, in minimize  
f(self._c_pointer, tolerance, max_iterations)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 2482, in _start_sim_or_toggle_pause  
self.pause_sim_toggle()  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 2680, in pause_sim_toggle  
self.sim_manager.toggle_pause()  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 678, in
toggle_pause  
self.pause = not self.pause  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 657, in pause  
self.sim_handler.pause = flag  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1555, in pause  
self._resume()  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1450, in _resume  
self._repeat_step()  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1441, in
_repeat_step  
th.thread_finished, self._update_coordinates_and_repeat, final_args)  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/delayed_reaction.py", line 56, in delayed_reaction  
initiator_func(*initiator_args)  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 186, in minimize  
f(self._c_pointer, tolerance, max_iterations)  
RuntimeError: Particle coordinate is nan  
  
RuntimeError: Particle coordinate is nan  
  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 186, in minimize  
f(self._c_pointer, tolerance, max_iterations)  
  
See log for complete Python traceback.  
  

> close

> open
/Users/dkreitler/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30_ISOLDE.pdb

Chain information for NpsA_32_refine_30_ISOLDE.pdb #1  
---  
Chain | Description  
A | No description available  
  

> addh hbond true

No usable SEQRES records for NpsA_32_refine_30_ISOLDE.pdb (#1) chain A;
guessing termini instead  
Chain-initial residues that are actual N termini: /A GLN 9  
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: /A ALA 504  
402 hydrogen bonds  
/A ALA 504 is not terminus, removing H atom from 'C'  
3830 hydrogens added  

> addh hbond true

No usable SEQRES records for NpsA_32_refine_30_ISOLDE.pdb (#1) chain A;
guessing termini instead  
Chain-initial residues that are actual N termini: /A GLN 9  
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: /A ALA 504  
376 hydrogen bonds  
/A ALA 504 is not terminus, removing H atom from 'C'  
0 hydrogens added  

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide H

> show selAtoms ribbons

> open
/Users/dkreitler/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30_2mFo-
DFc.ccp4

Opened NpsA_32_refine_30_2mFo-DFc.ccp4, grid size 80,87,114, pixel
0.934,0.915,0.921, shown at level 3.2, step 1, values float32  

> toolshed show ISOLDE

Chain information for NpsA_32_refine_30_ISOLDE.pdb  
---  
Chain | Description  
1.3/A | No description available  
  

> hide selAtoms ribbons

Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/delayed_reaction.py", line 65, in callback  
self.ff(*self.ff_args)  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1460, in
_update_coordinates_and_repeat  
self.atoms.coords = th.coords  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 294, in coords  
f(self._c_pointer, n, pointer(coords))  
RuntimeError: Particle coordinate is nan  
  
Error processing trigger "new frame": Particle coordinate is nan:  
RuntimeError: Particle coordinate is nan  
  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 294, in coords  
f(self._c_pointer, n, pointer(coords))  
  
See log for complete Python traceback.  
  

> close

> open
/Users/dkreitler/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30_ISOLDE.pdb

Chain information for NpsA_32_refine_30_ISOLDE.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open
/Users/dkreitler/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30_2mFo-
DFc.ccp4

Opened NpsA_32_refine_30_2mFo-DFc.ccp4, grid size 80,87,114, pixel
0.934,0.915,0.921, shown at level 3.2, step 1, values float32  

> toolshed show ISOLDE

Chain information for NpsA_32_refine_30_ISOLDE.pdb  
---  
Chain | Description  
1.3/A | No description available  
  

> hide selAtoms ribbons

Bad residue number: match  
Doing nothing  

> addh hbond true

No usable SEQRES records for NpsA_32_refine_30_ISOLDE.pdb (#1.3) chain A;
guessing termini instead  
Chain-initial residues that are actual N termini: /A GLN 9  
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: /A ALA 504  
402 hydrogen bonds  
/A ALA 504 is not terminus, removing H atom from 'C'  
3830 hydrogens added  

> hide H

reverting to start  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/delayed_reaction.py", line 65, in callback  
self.ff(*self.ff_args)  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1460, in
_update_coordinates_and_repeat  
self.atoms.coords = th.coords  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 294, in coords  
f(self._c_pointer, n, pointer(coords))  
RuntimeError: Particle coordinate is nan  
  
Error processing trigger "new frame": Particle coordinate is nan:  
RuntimeError: Particle coordinate is nan  
  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 294, in coords  
f(self._c_pointer, n, pointer(coords))  
  
See log for complete Python traceback.  
  

> close

> open /Users/dkreitler/Xray/Projects/NpsA-312AAA-Nterm/NpsA-
N_14/phenix/Refine_19/NpsA-N_14_refine_19.pdb

Summary of feedback from opening /Users/dkreitler/Xray/Projects/NpsA-312AAA-
Nterm/NpsA-N_14/phenix/Refine_19/NpsA-N_14_refine_19.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Date 2019-04-25 Time 12:39:44 EDT -0400 (1556210384.29 s)  
  
Ignored bad PDB record found on line 2  
REMARK PHENIX refinement  
  
Ignored bad PDB record found on line 4  
REMARK ****************** INPUT FILES AND LABELS
******************************  
  
Ignored bad PDB record found on line 5  
REMARK Reflections:  
  
Ignored bad PDB record found on line 6  
REMARK file name : /Users/dkreitler/Xray/Projects/NpsA-312AAA-Nterm/NpsA-
N_14/data/NpsA-N_14_2_truncate-unique.mtz  
  
31 messages similar to the above omitted  
  
Chain information for NpsA-N_14_refine_19.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open /Users/dkreitler/Xray/Projects/NpsA-312AAA-Nterm/NpsA-
N_14/phenix/Refine_19/NpsA-N_14_refine_19_2mFo-DFc.ccp4

Opened NpsA-N_14_refine_19_2mFo-DFc.ccp4, grid size 176,180,232, pixel
0.5,0.493,0.503, shown at level 3.56, step 1, values float32  

> toolshed show ISOLDE

Chain information for NpsA-N_14_refine_19.pdb  
---  
Chain | Description  
1.3/A | No description available  
1.3/B | No description available  
  

> addh hbond true

No usable SEQRES records for NpsA-N_14_refine_19.pdb (#1.3) chain A; guessing
termini instead  
No usable SEQRES records for NpsA-N_14_refine_19.pdb (#1.3) chain B; guessing
termini instead  
Chain-initial residues that are actual N termini: /A TYR 8, /B TYR 8  
Chain-initial residues that are not actual N termini: /A PRO 320  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A VAL 401, /A ALA 312, /B
VAL 401  
2386 hydrogen bonds  
/A VAL 401 is not terminus, removing H atom from 'C'  
/A ALA 312 is not terminus, removing H atom from 'C'  
/B VAL 401 is not terminus, removing H atom from 'C'  
7168 hydrogens added  

> hide H

> hide selAtoms ribbons

> hide selAtoms

> show selAtoms

> open /Users/dkreitler/Xray/Projects/NpsA-312AAA-Nterm/NpsA-
N_14/phenix/Refine_19/NpsA-N_14_refine_19_2mFo-DFc.ccp4

Opened NpsA-N_14_refine_19_2mFo-DFc.ccp4, grid size 176,180,232, pixel
0.5,0.493,0.503, shown at level 3.56, step 1, values float32  

> toolshed show ISOLDE

Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.  
Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/mouse_modes/mousemodes.py", line 448, in _wheel_event  
f.wheel(MouseEvent(event))  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/mousemodes.py", line 263, in wheel  
rep, levels = adjust_threshold_level(v, step, self.symmetrical)  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/mousemodes.py", line 277, in adjust_threshold_level  
new_levels[-1] = (max(l,1.01*ms.maximum),b)  
NameError: name 'ms' is not defined  
  
NameError: name 'ms' is not defined  
  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/mousemodes.py", line 277, in adjust_threshold_level  
new_levels[-1] = (max(l,1.01*ms.maximum),b)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/mouse_modes/mousemodes.py", line 448, in _wheel_event  
f.wheel(MouseEvent(event))  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/mousemodes.py", line 263, in wheel  
rep, levels = adjust_threshold_level(v, step, self.symmetrical)  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/mousemodes.py", line 277, in adjust_threshold_level  
new_levels[-1] = (max(l,1.01*ms.maximum),b)  
NameError: name 'ms' is not defined  
  
NameError: name 'ms' is not defined  
  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/mousemodes.py", line 277, in adjust_threshold_level  
new_levels[-1] = (max(l,1.01*ms.maximum),b)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/mouse_modes/mousemodes.py", line 448, in _wheel_event  
f.wheel(MouseEvent(event))  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/mousemodes.py", line 263, in wheel  
rep, levels = adjust_threshold_level(v, step, self.symmetrical)  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/mousemodes.py", line 277, in adjust_threshold_level  
new_levels[-1] = (max(l,1.01*ms.maximum),b)  
NameError: name 'ms' is not defined  
  
NameError: name 'ms' is not defined  
  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/mousemodes.py", line 277, in adjust_threshold_level  
new_levels[-1] = (max(l,1.01*ms.maximum),b)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/mouse_modes/mousemodes.py", line 448, in _wheel_event  
f.wheel(MouseEvent(event))  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/mousemodes.py", line 263, in wheel  
rep, levels = adjust_threshold_level(v, step, self.symmetrical)  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/mousemodes.py", line 277, in adjust_threshold_level  
new_levels[-1] = (max(l,1.01*ms.maximum),b)  
NameError: name 'ms' is not defined  
  
NameError: name 'ms' is not defined  
  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/mousemodes.py", line 277, in adjust_threshold_level  
new_levels[-1] = (max(l,1.01*ms.maximum),b)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/mouse_modes/mousemodes.py", line 448, in _wheel_event  
f.wheel(MouseEvent(event))  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/mousemodes.py", line 263, in wheel  
rep, levels = adjust_threshold_level(v, step, self.symmetrical)  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/mousemodes.py", line 277, in adjust_threshold_level  
new_levels[-1] = (max(l,1.01*ms.maximum),b)  
NameError: name 'ms' is not defined  
  
NameError: name 'ms' is not defined  
  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/mousemodes.py", line 277, in adjust_threshold_level  
new_levels[-1] = (max(l,1.01*ms.maximum),b)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/mouse_modes/mousemodes.py", line 448, in _wheel_event  
f.wheel(MouseEvent(event))  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/mousemodes.py", line 263, in wheel  
rep, levels = adjust_threshold_level(v, step, self.symmetrical)  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/mousemodes.py", line 277, in adjust_threshold_level  
new_levels[-1] = (max(l,1.01*ms.maximum),b)  
NameError: name 'ms' is not defined  
  
NameError: name 'ms' is not defined  
  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/mousemodes.py", line 277, in adjust_threshold_level  
new_levels[-1] = (max(l,1.01*ms.maximum),b)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/mouse_modes/mousemodes.py", line 448, in _wheel_event  
f.wheel(MouseEvent(event))  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/mousemodes.py", line 263, in wheel  
rep, levels = adjust_threshold_level(v, step, self.symmetrical)  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/mousemodes.py", line 277, in adjust_threshold_level  
new_levels[-1] = (max(l,1.01*ms.maximum),b)  
NameError: name 'ms' is not defined  
  
NameError: name 'ms' is not defined  
  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/clipper/mousemodes.py", line 277, in adjust_threshold_level  
new_levels[-1] = (max(l,1.01*ms.maximum),b)  
  
See log for complete Python traceback.  
  

> close

> open
/Users/dkreitler/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30_ISOLDE.pdb

Chain information for NpsA_32_refine_30_ISOLDE.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open
/Users/dkreitler/Xray/Projects/NpsA/NpsA_32/phenix/Refine_30/NpsA_32_refine_30_2mFo-
DFc.ccp4

Opened NpsA_32_refine_30_2mFo-DFc.ccp4, grid size 80,87,114, pixel
0.934,0.915,0.921, shown at level 3.2, step 1, values float32  

> toolshed show ISOLDE

Chain information for NpsA_32_refine_30_ISOLDE.pdb  
---  
Chain | Description  
1.3/A | No description available  
  
Bad residue number: match  
Adding hydrogens  
No usable SEQRES records for NpsA_32_refine_30_ISOLDE.pdb (#1.3) chain A;
guessing termini instead  
Chain-initial residues that are actual N termini: /A GLN 9  
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: /A ALA 504  
402 hydrogen bonds  
/A ALA 504 is not terminus, removing H atom from 'C'  
3830 hydrogens added  

> hide H

> hide H

> hide H

Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/delayed_reaction.py", line 65, in callback  
self.ff(*self.ff_args)  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1460, in
_update_coordinates_and_repeat  
self.atoms.coords = th.coords  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 294, in coords  
f(self._c_pointer, n, pointer(coords))  
RuntimeError: Particle coordinate is nan  
  
Error processing trigger "new frame": Particle coordinate is nan:  
RuntimeError: Particle coordinate is nan  
  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 294, in coords  
f(self._c_pointer, n, pointer(coords))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/delayed_reaction.py", line 65, in callback  
self.ff(*self.ff_args)  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1460, in
_update_coordinates_and_repeat  
self.atoms.coords = th.coords  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 294, in coords  
f(self._c_pointer, n, pointer(coords))  
RuntimeError: Particle coordinate is nan  
  
Error processing trigger "new frame": Particle coordinate is nan:  
RuntimeError: Particle coordinate is nan  
  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 294, in coords  
f(self._c_pointer, n, pointer(coords))  
  
See log for complete Python traceback.  
  
reverting to start  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/delayed_reaction.py", line 65, in callback  
self.ff(*self.ff_args)  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1460, in
_update_coordinates_and_repeat  
self.atoms.coords = th.coords  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 294, in coords  
f(self._c_pointer, n, pointer(coords))  
RuntimeError: Particle coordinate is nan  
  
Error processing trigger "new frame": Particle coordinate is nan:  
RuntimeError: Particle coordinate is nan  
  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 294, in coords  
f(self._c_pointer, n, pointer(coords))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/delayed_reaction.py", line 65, in callback  
self.ff(*self.ff_args)  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1460, in
_update_coordinates_and_repeat  
self.atoms.coords = th.coords  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 294, in coords  
f(self._c_pointer, n, pointer(coords))  
RuntimeError: Particle coordinate is nan  
  
Error processing trigger "new frame": Particle coordinate is nan:  
RuntimeError: Particle coordinate is nan  
  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 294, in coords  
f(self._c_pointer, n, pointer(coords))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 2482, in _start_sim_or_toggle_pause  
self.pause_sim_toggle()  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 2680, in pause_sim_toggle  
self.sim_manager.toggle_pause()  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 678, in
toggle_pause  
self.pause = not self.pause  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 657, in pause  
self.sim_handler.pause = flag  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1555, in pause  
self._resume()  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1450, in _resume  
self._repeat_step()  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1441, in
_repeat_step  
th.thread_finished, self._update_coordinates_and_repeat, final_args)  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/delayed_reaction.py", line 56, in delayed_reaction  
initiator_func(*initiator_args)  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 186, in minimize  
f(self._c_pointer, tolerance, max_iterations)  
RuntimeError: Particle coordinate is nan  
  
RuntimeError: Particle coordinate is nan  
  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 186, in minimize  
f(self._c_pointer, tolerance, max_iterations)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/delayed_reaction.py", line 65, in callback  
self.ff(*self.ff_args)  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1460, in
_update_coordinates_and_repeat  
self.atoms.coords = th.coords  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 294, in coords  
f(self._c_pointer, n, pointer(coords))  
RuntimeError: Particle coordinate is nan  
  
Error processing trigger "new frame": Particle coordinate is nan:  
RuntimeError: Particle coordinate is nan  
  
File "/Users/dkreitler/Library/Application Support/ChimeraX/0.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 294, in coords  
f(self._c_pointer, n, pointer(coords))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-1.68.20
OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[Tristan Croll]

This typically indicates the presence of a particularly severe clash in your starting coordinates. There's a bug in the 1.0b2 version of ISOLDE causing the energy minimiser to fail to do anything in such cases, so when dynamics starts the model flies apart. I'll be releasing a new version of ISOLDE for ChimeraX 0.9 next week, in which this bug is fixed.

[tic20@…]

Your log also indicates a separate bug in some almost-never-used code: 
the Clipper plugin wasn't really designed to work together with the 
'solid' ('image' in the latest ChimeraX versions) representation, and so 
I've never noticed that my contouring MouseMode was broken for that 
mode. I've corrected it, in any case - that fix will also be in next 
week's release.

On 2019-06-07 17:35, ChimeraX wrote:

[dkreitle@…]

Thanks, I have been able to run without any issues by using a starting model with a lower Clashscore.

[Tristan Croll]

Great! I'll go ahead and close this then. Keep an eye out for the new version next week - some cool new features alongside the bug fixes and performance enhancements.