Opened 14 months ago

Last modified 14 months ago

#15873 assigned defect

SEQCROW: index out of bounds showing orbitals

Reported by: mateuspaiao159@… Owned by: Tony Schaefer
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-6.8.0-40-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
não estou conseguindo ver os orbitais moleculares quando utilizo outra função de base, a partir de aruivo externo como é o site do basis set exchange (BSE)

Log:
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/mateus/ORCA_PLUS/orca504/teste/TRATANDO/ERRADO.out

Opened ERRADO.out as an ORCA output file  

> ui tool show "Orbital Viewer"

> close session

> open /home/mateus/ORCA_PLUS/orca504/teste/TRATANDO/CERTO.out

Opened CERTO.out as an ORCA output file  

> ui tool show "Orbital Viewer"

Opened MO alpha 21 as #1.1, grid size 62,61,38, pixel 0.203,0.203,0.203, shown
at level -0.025,0.025, step 1, values float64  

> close session

> open /home/mateus/ORCA_PLUS/orca504/teste/TRATANDO/ERRADO.out

Opened ERRADO.out as an ORCA output file  

> ui tool show "Orbital Viewer"

Traceback (most recent call last):  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/SEQCROW/tools/mo_viewer.py", line 799, in show_orbit  
val = orbits.mo_value(mo, coords, alpha=alpha, n_jobs=threads)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1693, in mo_value  
return sum([shells.result() for shells in out])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1693, in <listcomp>  
return sum([shells.result() for shells in out])  
^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/concurrent/futures/_base.py", line
449, in result  
return self.__get_result()  
^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/concurrent/futures/_base.py", line
401, in __get_result  
raise self._exception  
File "/usr/lib/ucsf-chimerax/lib/python3.11/concurrent/futures/thread.py",
line 58, in run  
result = self.fn(*self.args, **self.kwargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1628, in _get_value  
res = shell(  
^^^^^^  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1328, in d_shell  
if mo_coeffs[1] != 0:  
~~~~~~~~~^^^  
IndexError: index 1 is out of bounds for axis 0 with size 1  
  
IndexError: index 1 is out of bounds for axis 0 with size 1  
  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1328, in d_shell  
if mo_coeffs[1] != 0:  
~~~~~~~~~^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/SEQCROW/tools/mo_viewer.py", line 799, in show_orbit  
val = orbits.mo_value(mo, coords, alpha=alpha, n_jobs=threads)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1693, in mo_value  
return sum([shells.result() for shells in out])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1693, in <listcomp>  
return sum([shells.result() for shells in out])  
^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/concurrent/futures/_base.py", line
449, in result  
return self.__get_result()  
^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/concurrent/futures/_base.py", line
401, in __get_result  
raise self._exception  
File "/usr/lib/ucsf-chimerax/lib/python3.11/concurrent/futures/thread.py",
line 58, in run  
result = self.fn(*self.args, **self.kwargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1628, in _get_value  
res = shell(  
^^^^^^  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1328, in d_shell  
if mo_coeffs[1] != 0:  
~~~~~~~~~^^^  
IndexError: index 1 is out of bounds for axis 0 with size 1  
  
IndexError: index 1 is out of bounds for axis 0 with size 1  
  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1328, in d_shell  
if mo_coeffs[1] != 0:  
~~~~~~~~~^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/SEQCROW/tools/mo_viewer.py", line 799, in show_orbit  
val = orbits.mo_value(mo, coords, alpha=alpha, n_jobs=threads)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1693, in mo_value  
return sum([shells.result() for shells in out])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1693, in <listcomp>  
return sum([shells.result() for shells in out])  
^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/concurrent/futures/_base.py", line
449, in result  
return self.__get_result()  
^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/concurrent/futures/_base.py", line
401, in __get_result  
raise self._exception  
File "/usr/lib/ucsf-chimerax/lib/python3.11/concurrent/futures/thread.py",
line 58, in run  
result = self.fn(*self.args, **self.kwargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1628, in _get_value  
res = shell(  
^^^^^^  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1328, in d_shell  
if mo_coeffs[1] != 0:  
~~~~~~~~~^^^  
IndexError: index 1 is out of bounds for axis 0 with size 1  
  
IndexError: index 1 is out of bounds for axis 0 with size 1  
  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1328, in d_shell  
if mo_coeffs[1] != 0:  
~~~~~~~~~^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/SEQCROW/tools/mo_viewer.py", line 799, in show_orbit  
val = orbits.mo_value(mo, coords, alpha=alpha, n_jobs=threads)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1693, in mo_value  
return sum([shells.result() for shells in out])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1693, in <listcomp>  
return sum([shells.result() for shells in out])  
^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/concurrent/futures/_base.py", line
449, in result  
return self.__get_result()  
^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/concurrent/futures/_base.py", line
401, in __get_result  
raise self._exception  
File "/usr/lib/ucsf-chimerax/lib/python3.11/concurrent/futures/thread.py",
line 58, in run  
result = self.fn(*self.args, **self.kwargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1628, in _get_value  
res = shell(  
^^^^^^  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1328, in d_shell  
if mo_coeffs[1] != 0:  
~~~~~~~~~^^^  
IndexError: index 1 is out of bounds for axis 0 with size 1  
  
IndexError: index 1 is out of bounds for axis 0 with size 1  
  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1328, in d_shell  
if mo_coeffs[1] != 0:  
~~~~~~~~~^^^  
  
See log for complete Python traceback.  
  

> close session

> open /home/mateus/ORCA_PLUS/orca504/teste/TRATANDO/ERRADO.out

Opened ERRADO.out as an ORCA output file  

> ui tool show "Orbital Viewer"

Traceback (most recent call last):  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/SEQCROW/tools/mo_viewer.py", line 799, in show_orbit  
val = orbits.mo_value(mo, coords, alpha=alpha, n_jobs=threads)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1693, in mo_value  
return sum([shells.result() for shells in out])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1693, in <listcomp>  
return sum([shells.result() for shells in out])  
^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/concurrent/futures/_base.py", line
449, in result  
return self.__get_result()  
^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/concurrent/futures/_base.py", line
401, in __get_result  
raise self._exception  
File "/usr/lib/ucsf-chimerax/lib/python3.11/concurrent/futures/thread.py",
line 58, in run  
result = self.fn(*self.args, **self.kwargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1628, in _get_value  
res = shell(  
^^^^^^  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1328, in d_shell  
if mo_coeffs[1] != 0:  
~~~~~~~~~^^^  
IndexError: index 1 is out of bounds for axis 0 with size 1  
  
IndexError: index 1 is out of bounds for axis 0 with size 1  
  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1328, in d_shell  
if mo_coeffs[1] != 0:  
~~~~~~~~~^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/SEQCROW/tools/mo_viewer.py", line 799, in show_orbit  
val = orbits.mo_value(mo, coords, alpha=alpha, n_jobs=threads)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1693, in mo_value  
return sum([shells.result() for shells in out])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1693, in <listcomp>  
return sum([shells.result() for shells in out])  
^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/concurrent/futures/_base.py", line
449, in result  
return self.__get_result()  
^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/concurrent/futures/_base.py", line
401, in __get_result  
raise self._exception  
File "/usr/lib/ucsf-chimerax/lib/python3.11/concurrent/futures/thread.py",
line 58, in run  
result = self.fn(*self.args, **self.kwargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1628, in _get_value  
res = shell(  
^^^^^^  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1328, in d_shell  
if mo_coeffs[1] != 0:  
~~~~~~~~~^^^  
IndexError: index 1 is out of bounds for axis 0 with size 1  
  
IndexError: index 1 is out of bounds for axis 0 with size 1  
  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1328, in d_shell  
if mo_coeffs[1] != 0:  
~~~~~~~~~^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/SEQCROW/tools/mo_viewer.py", line 799, in show_orbit  
val = orbits.mo_value(mo, coords, alpha=alpha, n_jobs=threads)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1693, in mo_value  
return sum([shells.result() for shells in out])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1693, in <listcomp>  
return sum([shells.result() for shells in out])  
^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/concurrent/futures/_base.py", line
449, in result  
return self.__get_result()  
^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/concurrent/futures/_base.py", line
401, in __get_result  
raise self._exception  
File "/usr/lib/ucsf-chimerax/lib/python3.11/concurrent/futures/thread.py",
line 58, in run  
result = self.fn(*self.args, **self.kwargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1628, in _get_value  
res = shell(  
^^^^^^  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1328, in d_shell  
if mo_coeffs[1] != 0:  
~~~~~~~~~^^^  
IndexError: index 1 is out of bounds for axis 0 with size 1  
  
IndexError: index 1 is out of bounds for axis 0 with size 1  
  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1328, in d_shell  
if mo_coeffs[1] != 0:  
~~~~~~~~~^^^  
  
See log for complete Python traceback.  
  

> close session

> open /home/mateus/ORCA_PLUS/orca504/teste/TRATANDO/CERTO.out

Opened CERTO.out as an ORCA output file  

> ui tool show "Orbital Viewer"

Opened MO alpha 21 as #1.1, grid size 62,61,38, pixel 0.203,0.203,0.203, shown
at level -0.025,0.025, step 1, values float64  

> close session

> open /home/mateus/ORCA_PLUS/orca504/teste/TRATANDO/ERRADO.out

Opened ERRADO.out as an ORCA output file  

> ui tool show "Orbital Viewer"

Traceback (most recent call last):  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/SEQCROW/tools/mo_viewer.py", line 799, in show_orbit  
val = orbits.mo_value(mo, coords, alpha=alpha, n_jobs=threads)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1693, in mo_value  
return sum([shells.result() for shells in out])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1693, in <listcomp>  
return sum([shells.result() for shells in out])  
^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/concurrent/futures/_base.py", line
449, in result  
return self.__get_result()  
^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/concurrent/futures/_base.py", line
401, in __get_result  
raise self._exception  
File "/usr/lib/ucsf-chimerax/lib/python3.11/concurrent/futures/thread.py",
line 58, in run  
result = self.fn(*self.args, **self.kwargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1628, in _get_value  
res = shell(  
^^^^^^  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1328, in d_shell  
if mo_coeffs[1] != 0:  
~~~~~~~~~^^^  
IndexError: index 1 is out of bounds for axis 0 with size 1  
  
IndexError: index 1 is out of bounds for axis 0 with size 1  
  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1328, in d_shell  
if mo_coeffs[1] != 0:  
~~~~~~~~~^^^  
  
See log for complete Python traceback.  
  

> close session

> open /home/mateus/ORCA_PLUS/orca504/teste/ERRADO.out

Summary of feedback from opening
/home/mateus/ORCA_PLUS/orca504/teste/ERRADO.out  
---  
note | ERRADO.out has 0 imaginary harmonic vibrational modes  
  
Opened ERRADO.out as an ORCA output file  

> ui tool show "Orbital Viewer"

> close session

> open /home/mateus/ORCA_PLUS/orca504/teste/TRATANDO/ERRADO.out

Opened ERRADO.out as an ORCA output file  

> ui tool show "Orbital Viewer"

Traceback (most recent call last):  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/SEQCROW/tools/mo_viewer.py", line 799, in show_orbit  
val = orbits.mo_value(mo, coords, alpha=alpha, n_jobs=threads)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1693, in mo_value  
return sum([shells.result() for shells in out])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1693, in <listcomp>  
return sum([shells.result() for shells in out])  
^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/concurrent/futures/_base.py", line
449, in result  
return self.__get_result()  
^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/concurrent/futures/_base.py", line
401, in __get_result  
raise self._exception  
File "/usr/lib/ucsf-chimerax/lib/python3.11/concurrent/futures/thread.py",
line 58, in run  
result = self.fn(*self.args, **self.kwargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1628, in _get_value  
res = shell(  
^^^^^^  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1328, in d_shell  
if mo_coeffs[1] != 0:  
~~~~~~~~~^^^  
IndexError: index 1 is out of bounds for axis 0 with size 1  
  
IndexError: index 1 is out of bounds for axis 0 with size 1  
  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1328, in d_shell  
if mo_coeffs[1] != 0:  
~~~~~~~~~^^^  
  
See log for complete Python traceback.  
  

> close session

> open /home/mateus/ORCA_PLUS/orca504/teste/TRATANDO/ERRADO.out

Opened ERRADO.out as an ORCA output file  

> ui tool show "Orbital Viewer"

Traceback (most recent call last):  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/SEQCROW/tools/mo_viewer.py", line 799, in show_orbit  
val = orbits.mo_value(mo, coords, alpha=alpha, n_jobs=threads)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1693, in mo_value  
return sum([shells.result() for shells in out])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1693, in <listcomp>  
return sum([shells.result() for shells in out])  
^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/concurrent/futures/_base.py", line
449, in result  
return self.__get_result()  
^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/concurrent/futures/_base.py", line
401, in __get_result  
raise self._exception  
File "/usr/lib/ucsf-chimerax/lib/python3.11/concurrent/futures/thread.py",
line 58, in run  
result = self.fn(*self.args, **self.kwargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1628, in _get_value  
res = shell(  
^^^^^^  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1328, in d_shell  
if mo_coeffs[1] != 0:  
~~~~~~~~~^^^  
IndexError: index 1 is out of bounds for axis 0 with size 1  
  
IndexError: index 1 is out of bounds for axis 0 with size 1  
  
File "/home/mateus/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 1328, in d_shell  
if mo_coeffs[1] != 0:  
~~~~~~~~~^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 535.183.01
OpenGL renderer: NVIDIA GeForce GTX 1650/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: pt_BR.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Micro-Star International Co., Ltd.
Model: MS-7C96
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 12 AMD Ryzen 5 4600G with Radeon Graphics
Cache Size: 512 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            27Gi       5.0Gi        17Gi       182Mi       4.9Gi        21Gi
	Swap:          2.0Gi          0B       2.0Gi

Graphics:
	10:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU116 [GeForce GTX 1650] [10de:2188] (rev a1)	
	Subsystem: NVIDIA Corporation TU116 [GeForce GTX 1650] [10de:145e]	
	Kernel driver in use: nvidia

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    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
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    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
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    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
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    ChimeraX-RenderByAttr: 1.4.1
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    ChimeraX-RotamerLibMgr: 4.0
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    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
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    ChimeraX-Segger: 1.0
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    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    distro: 1.9.0
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
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    jedi: 0.19.1
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    jupyter-client: 8.6.0
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File attachment: ERRADO.out

ERRADO.out​

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ERRADO.out​ (137.1 KB ) - added by mateuspaiao159@… 14 months ago.
Added by email2trac
ERRADO-1.out​ (137.1 KB ) - added by mateuspaiao159@… 14 months ago.
Added by email2trac
CERTO.out​ (256.2 KB ) - added by mateuspaiao159@… 14 months ago.
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Change History (8)

by mateuspaiao159@…, 14 months ago

Attachment: ERRADO.out​ added

Added by email2trac

comment:1 by pett, 14 months ago

Component: Unassigned → Third Party
Owner: set to Tony Schaefer
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → SEQCROW: index out of bounds showing orbitals

Google says the text translates to: "I am unable to see the molecular orbitals when I use another basis function, from an external file such as the basis set exchange website"

Reported by Mateus Batista Paiao

comment:2 by Tony Schaefer, 14 months ago 

 Mateus,

To see orbitals from ORCA files, you must include both ! PrintBasis and !
PrintMOs or equivalent in the input file. Your file has print[p_mos] 1 in
the "output" block, which is only equivalent to ! PrintMOs.

Best,

Tony

On Tue, Sep 3, 2024 at 2:35 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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comment:3 by mateuspaiao159@…, 14 months ago 

Boa noite, Tony,

Estou enfrentando um problema ao utilizar funções de bases externas (como
as fornecidas pelo Basis Set Exchange <https://www.basissetexchange.org/>).
O ChimeraX não consegue ler e plotar os orbitais quando utilizo essas
funções de bases externas. No entanto, quando uso funções de bases já
incluídas no programa, o ChimeraX consegue exibir os orbitais corretamente.

Enviei dois arquivos de saída de cálculos realizados com o benzeno: um em
que o ChimeraX consegue plotar os orbitais e outro em que não consegue.
Esse problema parece ocorrer especificamente quando utilizo funções de
bases externas, independentemente da molécula em questão.

Estou tentando manipular os arquivos de saída para que o ChimeraX possa
lê-los corretamente, mas até o momento, não obtive sucesso.

Agradeço qualquer orientação que você possa oferecer.

Atenciosamente,
Mateus

Em ter., 3 de set. de 2024 às 17:26, ChimeraX <
ChimeraX-bugs-admin@cgl.ucsf.edu> escreveu:

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ERRADO-1.out​

CERTO.out​

by mateuspaiao159@…, 14 months ago

Attachment: ERRADO-1.out​ added

Added by email2trac

by mateuspaiao159@…, 14 months ago

Attachment: CERTO.out​ added

Added by email2trac

comment:4 by Tony Schaefer, 14 months ago 

 Mateus,

In order to draw the orbitals, we need the molecular orbital coefficients
and the contraction coefficients and exponents of the basis functions. For
printing the molecular orbital coefficients, you have "print[p_mos] 1" in
the "output" block of your input file. For printing the contraction
coefficients and exponents, you need to include "! PrintBasis" or some
other equivalent. The file with the built-in 6-31G** basis set has "!
PrintBasis" in the input, whereas the one using the external 4-31G basis
set does not.

From the file you sent:

NAME = benzeno.inp
|  1> !  NumFreq  B3LYP
|  2>  %pal
|  3>         nprocs 12
|  4>  end
|  5> *! **PrintBasis* 6-31G**
|  6> %output
|  7>      print[p_mos] 1
|  8>  end #output
|  9> * xyzfile 0   1 benzeno.xyz

compared to the other file without "! PrintBasis". You could include
"PrintBasis" on the same line as "!  NumFreq  B3LYP/G" in the input file.
If you do not want to run the entire computation again, you can run a
shorter computation using "! PrintBasis" with the external 4-31G basis and
paste the section called "BASIS SET IN INPUT FORMAT" from that output file
into your existing output files. The short computation doesn't need to be
the same molecule, but it does need to have the same elements.

Best wishes,

Tony

On Tue, Sep 3, 2024 at 7:32 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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comment:5 by mateuspaiao159@…, 14 months ago 

Boa tarde Tony, agora eu consegui vizualizar aplicando a orientação que me
passou, obrigado!!!

Em qua., 4 de set. de 2024 às 03:47, ChimeraX <
ChimeraX-bugs-admin@cgl.ucsf.edu> escreveu:

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