ISOLDE: various problems

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.dev202301240259 (2023-01-24 02:59:28 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.6.dev202301240259 (2023-01-24)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/krd822/Documents/Projects/Postdoc_Cobenhagen/Projects/Zor
> system/Zorya_I_E.coli_structures/ZorI_AB/ZorB_head_V4.pdb" format pdb

Chain information for ZorB_head_V4.pdb #1  
---  
Chain | Description  
A B | No description available  
  

> open "/Users/krd822/Documents/Projects/Postdoc_Cobenhagen/Projects/Zor
> system/Zorya_I_E.coli_structures/ZorI_AB/MapBox_37/ZorAb_head_box_out.ccp4"
> format ccp4

Opened ZorAb_head_box_out.ccp4 as #2, grid size 128,122,167, pixel 0.5, shown
at level 1.15, step 1, values float32  

> ui tool show ISOLDE

> set selectionWidth 4

Populating font family aliases took 230 ms. Replace uses of missing font
family "Carlito" with one that exists to avoid this cost.  

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 38 residues in model #1 to IUPAC-IUB
standards.  
Chain information for ZorB_head_V4.pdb  
---  
Chain | Description  
1.2/A 1.2/B | No description available  
  

> clipper associate #2 toModel #1

Opened ZorAb_head_box_out.ccp4 as #1.1.1.1, grid size 128,122,167, pixel 0.5,
shown at step 1, values float32  

> isolde sim start sel

Sim termination reason: None  
ISOLDE: stopped sim  

> isolde sim start sel

Sim termination reason: None  
ISOLDE: stopped sim  

> addh #1.2

Summary of feedback from adding hydrogens to ZorB_head_V4.pdb #1.2  
---  
notes | No usable SEQRES records for ZorB_head_V4.pdb (#1.2) chain A; guessing
termini instead  
No usable SEQRES records for ZorB_head_V4.pdb (#1.2) chain B; guessing termini
instead  
Chain-initial residues that are actual N termini: /A VAL 1, /B VAL 1  
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 LEU 207, /B LEU 207  
309 hydrogen bonds  
/A LEU 207 is not terminus, removing H atom from 'C'  
/B LEU 207 is not terminus, removing H atom from 'C'  
3304 hydrogens added  
  

> ui tool show "Ramachandran Plot"

> isolde sim start sel

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "/Users/krd822/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/__init__.py", line 183, in run_provider  
toolbar_command(session, name)  
File "/Users/krd822/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/toolbar.py", line 17, in toolbar_command  
run(session, 'isolde sim start sel')  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/Users/krd822/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/cmd/cmd.py", line 111, in isolde_sim  
isolde.start_sim()  
File "/Users/krd822/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/isolde.py", line 894, in start_sim  
sm.start_sim()  
File "/Users/krd822/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 398, in start_sim  
sh.start_sim()  
File "/Users/krd822/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1409, in start_sim  
self._prepare_sim()  
File "/Users/krd822/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1367, in
_prepare_sim  
s = self._simulation = app.Simulation(self.topology, self._system,  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/app/simulation.py", line 103, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2469, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
openmm.OpenMMException: Error compiling kernel: <program source>:35:6: error:
redeclaration of 'atom_add' must have the 'overloadable' attribute  
void atom_add(volatile __global unsigned long* p, long unsigned val) {  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:5761:21:
note: previous overload of function is here  
ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val);  
^  
<program source>:35:6: error: conflicting types for 'atom_add'  
void atom_add(volatile __global unsigned long* p, long unsigned val) {  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:5761:21:
note: previous declaration is here  
ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val);  
^  
<program source>:71:9: warning: 'make_short2' macro redefined  
#define make_short2(x...) ((short2) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3187:9:
note: previous definition is here  
#define make_short2(A,B) (short2)((A),(B))  
^  
<program source>:72:9: warning: 'make_short3' macro redefined  
#define make_short3(x...) ((short3) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3188:9:
note: previous definition is here  
#define make_short3(A,B,C) (short3)((A),(B),(C))  
^  
<program source>:73:9: warning: 'make_short4' macro redefined  
#define make_short4(x...) ((short4) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3189:9:
note: previous definition is here  
#define make_short4(A,B,C,D) (short4)((A),(B),(C),(D))  
^  
<program source>:74:9: warning: 'make_int2' macro redefined  
#define make_int2(x...) ((int2) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3199:9:
note: previous definition is here  
#define make_int2(A,B) (int2)((A),(B))  
^  
<program source>:75:9: warning: 'make_int3' macro redefined  
#define make_int3(x...) ((int3) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3200:9:
note: previous definition is here  
#define make_int3(A,B,C) (int3)((A),(B),(C))  
^  
<program source>:76:9: warning: 'make_int4' macro redefined  
#define make_int4(x...) ((int4) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3201:9:
note: previous definition is here  
#define make_int4(A,B,C,D) (int4)((A),(B),(C),(D))  
^  
<program source>:77:9: warning: 'make_float2' macro redefined  
#define make_float2(x...) ((float2) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3223:9:
note: previous definition is here  
#define make_float2(A,B) (float2)((A),(B))  
^  
<program source>:78:9: warning: 'make_float3' macro redefined  
#define make_float3(x...) ((float3) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3224:9:
note: previous definition is here  
#define make_float3(A,B,C) (float3)((A),(B),(C))  
^  
<program source>:79:9: warning: 'make_float4' macro redefined  
#define make_float4(x...) ((float4) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3226:9:
note: previous definition is here  
#define make_float4(A,B,C,D) (float4)((A),(B),(C),(D))  
^  
<program source>:80:9: warning: 'make_double2' macro redefined  
#define make_double2(x...) ((double2) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3230:9:
note: previous definition is here  
#define make_double2(A,B) (double2)((A),(B))  
^  
<program source>:81:9: warning: 'make_double3' macro redefined  
#define make_double3(x...) ((double3) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3231:9:
note: previous definition is here  
#define make_double3(A,B,C) (double3)((A),(B),(C))  
^  
<program source>:82:9: warning: 'make_double4' macro redefined  
#define make_double4(x...) ((double4) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3232:9:
note: previous definition is here  
#define make_double4(A,B,C,D) (double4)((A),(B),(C),(D))  
^  
<program source>:218:45: warning: comparison of integers of different signs:
'unsigned int' and 'int'  
for (unsigned int index = thread; index < bufferSize; index +=
get_local_size(0))  
~~~~~ ^ ~~~~~~~~~~  
<program source>:223:43: warning: comparison of integers of different signs:
'unsigned int' and 'int'  
if (thread%(i*2) == 0 && thread+i < workGroupSize)  
~~~~~~~~ ^ ~~~~~~~~~~~~~  
  
  
openmm.OpenMMException: Error compiling kernel: :35:6: error: redeclaration of
'atom_add' must have the 'overloadable' attribute  
void atom_add(volatile __global unsigned long* p, long unsigned val) {  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:5761:21:
note: previous overload of function is here  
ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val);  
^  
:35:6: error: conflicting types for 'atom_add'  
void atom_add(volatile __global unsigned long* p, long unsigned val) {  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:5761:21:
note: previous declaration is here  
ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val);  
^  
:71:9: warning: 'make_short2' macro redefined  
#define make_short2(x...) ((short2) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3187:9:
note: previous definition is here  
#define make_short2(A,B) (short2)((A),(B))  
^  
:72:9: warning: 'make_short3' macro redefined  
#define make_short3(x...) ((short3) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3188:9:
note: previous definition is here  
#define make_short3(A,B,C) (short3)((A),(B),(C))  
^  
:73:9: warning: 'make_short4' macro redefined  
#define make_short4(x...) ((short4) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3189:9:
note: previous definition is here  
#define make_short4(A,B,C,D) (short4)((A),(B),(C),(D))  
^  
:74:9: warning: 'make_int2' macro redefined  
#define make_int2(x...) ((int2) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3199:9:
note: previous definition is here  
#define make_int2(A,B) (int2)((A),(B))  
^  
:75:9: warning: 'make_int3' macro redefined  
#define make_int3(x...) ((int3) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3200:9:
note: previous definition is here  
#define make_int3(A,B,C) (int3)((A),(B),(C))  
^  
:76:9: warning: 'make_int4' macro redefined  
#define make_int4(x...) ((int4) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3201:9:
note: previous definition is here  
#define make_int4(A,B,C,D) (int4)((A),(B),(C),(D))  
^  
:77:9: warning: 'make_float2' macro redefined  
#define make_float2(x...) ((float2) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3223:9:
note: previous definition is here  
#define make_float2(A,B) (float2)((A),(B))  
^  
:78:9: warning: 'make_float3' macro redefined  
#define make_float3(x...) ((float3) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3224:9:
note: previous definition is here  
#define make_float3(A,B,C) (float3)((A),(B),(C))  
^  
:79:9: warning: 'make_float4' macro redefined  
#define make_float4(x...) ((float4) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3226:9:
note: previous definition is here  
#define make_float4(A,B,C,D) (float4)((A),(B),(C),(D))  
^  
:80:9: warning: 'make_double2' macro redefined  
#define make_double2(x...) ((double2) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3230:9:
note: previous definition is here  
#define make_double2(A,B) (double2)((A),(B))  
^  
:81:9: warning: 'make_double3' macro redefined  
#define make_double3(x...) ((double3) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3231:9:
note: previous definition is here  
#define make_double3(A,B,C) (double3)((A),(B),(C))  
^  
:82:9: warning: 'make_double4' macro redefined  
#define make_double4(x...) ((double4) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3232:9:
note: previous definition is here  
#define make_double4(A,B,C,D) (double4)((A),(B),(C),(D))  
^  
:218:45: warning: comparison of integers of different signs: 'unsigned int'
and 'int'  
for (unsigned int index = thread; index ~~~~~ ^ ~~~~~~~~~~  
:223:43: warning: comparison of integers of different signs: 'unsigned int'
and 'int'  
if (thread%(i*2) == 0 && thread+i ~~~~~~~~ ^ ~~~~~~~~~~~~~  
  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2469, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
  
See log for complete Python traceback.  
  

> isolde sim start sel

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "/Users/krd822/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/__init__.py", line 183, in run_provider  
toolbar_command(session, name)  
File "/Users/krd822/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/toolbar.py", line 17, in toolbar_command  
run(session, 'isolde sim start sel')  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/Users/krd822/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/cmd/cmd.py", line 111, in isolde_sim  
isolde.start_sim()  
File "/Users/krd822/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/isolde.py", line 894, in start_sim  
sm.start_sim()  
File "/Users/krd822/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 398, in start_sim  
sh.start_sim()  
File "/Users/krd822/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1409, in start_sim  
self._prepare_sim()  
File "/Users/krd822/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1367, in
_prepare_sim  
s = self._simulation = app.Simulation(self.topology, self._system,  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/app/simulation.py", line 103, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2469, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
openmm.OpenMMException: Error compiling kernel: <program source>:35:6: error:
redeclaration of 'atom_add' must have the 'overloadable' attribute  
void atom_add(volatile __global unsigned long* p, long unsigned val) {  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:5761:21:
note: previous overload of function is here  
ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val);  
^  
<program source>:35:6: error: conflicting types for 'atom_add'  
void atom_add(volatile __global unsigned long* p, long unsigned val) {  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:5761:21:
note: previous declaration is here  
ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val);  
^  
<program source>:71:9: warning: 'make_short2' macro redefined  
#define make_short2(x...) ((short2) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3187:9:
note: previous definition is here  
#define make_short2(A,B) (short2)((A),(B))  
^  
<program source>:72:9: warning: 'make_short3' macro redefined  
#define make_short3(x...) ((short3) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3188:9:
note: previous definition is here  
#define make_short3(A,B,C) (short3)((A),(B),(C))  
^  
<program source>:73:9: warning: 'make_short4' macro redefined  
#define make_short4(x...) ((short4) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3189:9:
note: previous definition is here  
#define make_short4(A,B,C,D) (short4)((A),(B),(C),(D))  
^  
<program source>:74:9: warning: 'make_int2' macro redefined  
#define make_int2(x...) ((int2) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3199:9:
note: previous definition is here  
#define make_int2(A,B) (int2)((A),(B))  
^  
<program source>:75:9: warning: 'make_int3' macro redefined  
#define make_int3(x...) ((int3) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3200:9:
note: previous definition is here  
#define make_int3(A,B,C) (int3)((A),(B),(C))  
^  
<program source>:76:9: warning: 'make_int4' macro redefined  
#define make_int4(x...) ((int4) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3201:9:
note: previous definition is here  
#define make_int4(A,B,C,D) (int4)((A),(B),(C),(D))  
^  
<program source>:77:9: warning: 'make_float2' macro redefined  
#define make_float2(x...) ((float2) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3223:9:
note: previous definition is here  
#define make_float2(A,B) (float2)((A),(B))  
^  
<program source>:78:9: warning: 'make_float3' macro redefined  
#define make_float3(x...) ((float3) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3224:9:
note: previous definition is here  
#define make_float3(A,B,C) (float3)((A),(B),(C))  
^  
<program source>:79:9: warning: 'make_float4' macro redefined  
#define make_float4(x...) ((float4) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3226:9:
note: previous definition is here  
#define make_float4(A,B,C,D) (float4)((A),(B),(C),(D))  
^  
<program source>:80:9: warning: 'make_double2' macro redefined  
#define make_double2(x...) ((double2) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3230:9:
note: previous definition is here  
#define make_double2(A,B) (double2)((A),(B))  
^  
<program source>:81:9: warning: 'make_double3' macro redefined  
#define make_double3(x...) ((double3) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3231:9:
note: previous definition is here  
#define make_double3(A,B,C) (double3)((A),(B),(C))  
^  
<program source>:82:9: warning: 'make_double4' macro redefined  
#define make_double4(x...) ((double4) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3232:9:
note: previous definition is here  
#define make_double4(A,B,C,D) (double4)((A),(B),(C),(D))  
^  
<program source>:218:45: warning: comparison of integers of different signs:
'unsigned int' and 'int'  
for (unsigned int index = thread; index < bufferSize; index +=
get_local_size(0))  
~~~~~ ^ ~~~~~~~~~~  
<program source>:223:43: warning: comparison of integers of different signs:
'unsigned int' and 'int'  
if (thread%(i*2) == 0 && thread+i < workGroupSize)  
~~~~~~~~ ^ ~~~~~~~~~~~~~  
  
  
openmm.OpenMMException: Error compiling kernel: :35:6: error: redeclaration of
'atom_add' must have the 'overloadable' attribute  
void atom_add(volatile __global unsigned long* p, long unsigned val) {  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:5761:21:
note: previous overload of function is here  
ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val);  
^  
:35:6: error: conflicting types for 'atom_add'  
void atom_add(volatile __global unsigned long* p, long unsigned val) {  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:5761:21:
note: previous declaration is here  
ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val);  
^  
:71:9: warning: 'make_short2' macro redefined  
#define make_short2(x...) ((short2) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3187:9:
note: previous definition is here  
#define make_short2(A,B) (short2)((A),(B))  
^  
:72:9: warning: 'make_short3' macro redefined  
#define make_short3(x...) ((short3) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3188:9:
note: previous definition is here  
#define make_short3(A,B,C) (short3)((A),(B),(C))  
^  
:73:9: warning: 'make_short4' macro redefined  
#define make_short4(x...) ((short4) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3189:9:
note: previous definition is here  
#define make_short4(A,B,C,D) (short4)((A),(B),(C),(D))  
^  
:74:9: warning: 'make_int2' macro redefined  
#define make_int2(x...) ((int2) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3199:9:
note: previous definition is here  
#define make_int2(A,B) (int2)((A),(B))  
^  
:75:9: warning: 'make_int3' macro redefined  
#define make_int3(x...) ((int3) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3200:9:
note: previous definition is here  
#define make_int3(A,B,C) (int3)((A),(B),(C))  
^  
:76:9: warning: 'make_int4' macro redefined  
#define make_int4(x...) ((int4) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3201:9:
note: previous definition is here  
#define make_int4(A,B,C,D) (int4)((A),(B),(C),(D))  
^  
:77:9: warning: 'make_float2' macro redefined  
#define make_float2(x...) ((float2) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3223:9:
note: previous definition is here  
#define make_float2(A,B) (float2)((A),(B))  
^  
:78:9: warning: 'make_float3' macro redefined  
#define make_float3(x...) ((float3) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3224:9:
note: previous definition is here  
#define make_float3(A,B,C) (float3)((A),(B),(C))  
^  
:79:9: warning: 'make_float4' macro redefined  
#define make_float4(x...) ((float4) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3226:9:
note: previous definition is here  
#define make_float4(A,B,C,D) (float4)((A),(B),(C),(D))  
^  
:80:9: warning: 'make_double2' macro redefined  
#define make_double2(x...) ((double2) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3230:9:
note: previous definition is here  
#define make_double2(A,B) (double2)((A),(B))  
^  
:81:9: warning: 'make_double3' macro redefined  
#define make_double3(x...) ((double3) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3231:9:
note: previous definition is here  
#define make_double3(A,B,C) (double3)((A),(B),(C))  
^  
:82:9: warning: 'make_double4' macro redefined  
#define make_double4(x...) ((double4) (x))  
^  
/System/Library/Frameworks/OpenCL.framework/Versions/A/lib/clang/3.2/include/cl_kernel.h:3232:9:
note: previous definition is here  
#define make_double4(A,B,C,D) (double4)((A),(B),(C),(D))  
^  
:218:45: warning: comparison of integers of different signs: 'unsigned int'
and 'int'  
for (unsigned int index = thread; index ~~~~~ ^ ~~~~~~~~~~  
:223:43: warning: comparison of integers of different signs: 'unsigned int'
and 'int'  
if (thread%(i*2) == 0 && thread+i ~~~~~~~~ ^ ~~~~~~~~~~~~~  
  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2469, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/Users/krd822/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 906, in
_dihe_r_changed_cb  
self.sim_handler.update_dihedral_restraints(all_changeds)  
File "/Users/krd822/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1793, in
update_dihedral_restraints  
force.update_targets(restraints.sim_indices,  
File "/Users/krd822/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/custom_forces.py", line 1301, in
update_targets  
_openmm_force_ext.customtorsionforce_update_torsion_parameters(int(self.this),
indices, params)  
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range  
  
Error processing trigger "changes":  
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range  
  
File "/Users/krd822/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/custom_forces.py", line 1301, in
update_targets  
_openmm_force_ext.customtorsionforce_update_torsion_parameters(int(self.this),
indices, params)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-4.12.7
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.0, Qt 6.4.0
Qt runtime version: 6.4.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2,4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 1968.120.12.0.0 (iBridge: 20.16.5058.0.0,0)
      OS Loader Version: 577~170

Software:

    System Software Overview:

      System Version: macOS 13.4 (22F66)
      Kernel Version: Darwin 22.5.0
      Time since boot: 2 days, 2 hours, 29 minutes

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3

    AMD Radeon Pro 5500M:

      Chipset Model: AMD Radeon Pro 5500M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0040
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32206U1-020
      Option ROM Version: 113-D32206U1-020
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL U2719D:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 6XF45R2     
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: DVI or HDMI
          Adapter Firmware Version:  2.4a


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.5.8
    ChimeraX-AddH: 2.2.3
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.8
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.5
    ChimeraX-AtomicLibrary: 10.0.2
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.20.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.dev202301240259
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3.2
    ChimeraX-DockPrep: 1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.6.dev0
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.11
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.11
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.8
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10
    ChimeraX-PDB: 2.6.12
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.1
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.26
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.6
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    comm: 0.1.2
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.6
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.0.0
    ipykernel: 6.19.2
    ipython: 8.7.0
    ipython-genutils: 0.2.0
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 7.4.8
    jupyter-core: 5.1.4
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.8
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.6.2
    prompt-toolkit: 3.0.36
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.4.0
    PyQt6-Qt6: 6.4.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.2
    python-dateutil: 2.8.2
    pytz: 2022.7.1
    pyzmq: 25.0.0
    qtconsole: 5.4.0
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.3
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.8.0
    typing-extensions: 4.4.0
    urllib3: 1.26.14
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.11.0

[Tristan Croll]

Fixed in the 1.6 release. The OpenMM 8.0.0beta used in the dev builds was failing on Intel Macs.