ISOLDE session restore: 'AtomicStructure' object has no attribute 'session'

[michal.ponczek@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22000
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open T:/PhenixProjects/HK_hu_Prediction/MapJob149PredictionsIsolda2.cxs

Traceback (most recent call last):  
File "F:\ChimeraX 1.4\bin\lib\site-packages\chimerax\core\triggerset.py", line
134, in invoke  
return self._func(self._name, data)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\ui\restraints_tab\manage_restraints.py", line 203, in
_model_add_or_remove_cb  
self._expanded_cb()  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\ui\restraints_tab\manage_restraints.py", line 184, in
_expanded_cb  
tm = self.torsion_restraint_mgr  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\ui\restraints_tab\manage_restraints.py", line 281, in
torsion_restraint_mgr  
return sx.get_adaptive_dihedral_restraint_mgr(self.isolde.selected_model)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\session_extensions.py", line 62, in
get_adaptive_dihedral_restraint_mgr  
return AdaptiveDihedralRestraintMgr(model)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 4171, in __init__  
super().__init__(model, c_pointer=c_pointer,  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 3633, in __init__  
super().__init__(display_name, model, c_pointer)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 1805, in __init__  
session = model.session  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
Error processing trigger "remove models":  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 1805, in __init__  
session = model.session  
  
See log for complete Python traceback.  
  
Exception ignored in: <function Drawing.__del__ at 0x0000020062C34160>  
Traceback (most recent call last):  
File "F:\ChimeraX 1.4\bin\lib\site-packages\chimerax\graphics\drawing.py",
line 1187, in __del__  
if not self.was_deleted:  
AttributeError: 'AdaptiveDihedralRestraintMgr' object has no attribute
'was_deleted'  
Opened cryosparc_P2_J571_006_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 0.86, shown at level 0.16, step 1, values float32  
Traceback (most recent call last):  
File "F:\ChimeraX 1.4\bin\lib\site-packages\chimerax\core\triggerset.py", line
134, in invoke  
return self._func(self._name, data)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\ui\restraints_tab\manage_restraints.py", line 203, in
_model_add_or_remove_cb  
self._expanded_cb()  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\ui\restraints_tab\manage_restraints.py", line 184, in
_expanded_cb  
tm = self.torsion_restraint_mgr  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\ui\restraints_tab\manage_restraints.py", line 281, in
torsion_restraint_mgr  
return sx.get_adaptive_dihedral_restraint_mgr(self.isolde.selected_model)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\session_extensions.py", line 62, in
get_adaptive_dihedral_restraint_mgr  
return AdaptiveDihedralRestraintMgr(model)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 4171, in __init__  
super().__init__(model, c_pointer=c_pointer,  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 3633, in __init__  
super().__init__(display_name, model, c_pointer)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 1805, in __init__  
session = model.session  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
Error processing trigger "add models":  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 1805, in __init__  
session = model.session  
  
See log for complete Python traceback.  
  
Exception ignored in: <function Drawing.__del__ at 0x0000020062C34160>  
Traceback (most recent call last):  
File "F:\ChimeraX 1.4\bin\lib\site-packages\chimerax\graphics\drawing.py",
line 1187, in __del__  
if not self.was_deleted:  
AttributeError: 'AdaptiveDihedralRestraintMgr' object has no attribute
'was_deleted'  
Opened cryosparc_P2_J151_map_sharp.mrc as #3, grid size 256,256,256, pixel
0.86, shown at level 0.133, step 1, values float32  
Traceback (most recent call last):  
File "F:\ChimeraX 1.4\bin\lib\site-packages\chimerax\core\triggerset.py", line
134, in invoke  
return self._func(self._name, data)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\ui\restraints_tab\manage_restraints.py", line 203, in
_model_add_or_remove_cb  
self._expanded_cb()  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\ui\restraints_tab\manage_restraints.py", line 184, in
_expanded_cb  
tm = self.torsion_restraint_mgr  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\ui\restraints_tab\manage_restraints.py", line 281, in
torsion_restraint_mgr  
return sx.get_adaptive_dihedral_restraint_mgr(self.isolde.selected_model)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\session_extensions.py", line 62, in
get_adaptive_dihedral_restraint_mgr  
return AdaptiveDihedralRestraintMgr(model)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 4171, in __init__  
super().__init__(model, c_pointer=c_pointer,  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 3633, in __init__  
super().__init__(display_name, model, c_pointer)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 1805, in __init__  
session = model.session  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
Error processing trigger "add models":  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 1805, in __init__  
session = model.session  
  
See log for complete Python traceback.  
  
Exception ignored in: <function Drawing.__del__ at 0x0000020062C34160>  
Traceback (most recent call last):  
File "F:\ChimeraX 1.4\bin\lib\site-packages\chimerax\graphics\drawing.py",
line 1187, in __del__  
if not self.was_deleted:  
AttributeError: 'AdaptiveDihedralRestraintMgr' object has no attribute
'was_deleted'  
Traceback (most recent call last):  
File "F:\ChimeraX 1.4\bin\lib\site-packages\chimerax\core\triggerset.py", line
134, in invoke  
return self._func(self._name, data)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\ui\restraints_tab\manage_restraints.py", line 203, in
_model_add_or_remove_cb  
self._expanded_cb()  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\ui\restraints_tab\manage_restraints.py", line 184, in
_expanded_cb  
tm = self.torsion_restraint_mgr  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\ui\restraints_tab\manage_restraints.py", line 281, in
torsion_restraint_mgr  
return sx.get_adaptive_dihedral_restraint_mgr(self.isolde.selected_model)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\session_extensions.py", line 62, in
get_adaptive_dihedral_restraint_mgr  
return AdaptiveDihedralRestraintMgr(model)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 4171, in __init__  
super().__init__(model, c_pointer=c_pointer,  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 3633, in __init__  
super().__init__(display_name, model, c_pointer)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 1805, in __init__  
session = model.session  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
Error processing trigger "add models":  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 1805, in __init__  
session = model.session  
  
See log for complete Python traceback.  
  
Exception ignored in: <function Drawing.__del__ at 0x0000020062C34160>  
Traceback (most recent call last):  
File "F:\ChimeraX 1.4\bin\lib\site-packages\chimerax\graphics\drawing.py",
line 1187, in __del__  
if not self.was_deleted:  
AttributeError: 'AdaptiveDihedralRestraintMgr' object has no attribute
'was_deleted'  
Traceback (most recent call last):  
File "F:\ChimeraX 1.4\bin\lib\site-packages\chimerax\core\triggerset.py", line
134, in invoke  
return self._func(self._name, data)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\ui\restraints_tab\manage_restraints.py", line 203, in
_model_add_or_remove_cb  
self._expanded_cb()  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\ui\restraints_tab\manage_restraints.py", line 184, in
_expanded_cb  
tm = self.torsion_restraint_mgr  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\ui\restraints_tab\manage_restraints.py", line 281, in
torsion_restraint_mgr  
return sx.get_adaptive_dihedral_restraint_mgr(self.isolde.selected_model)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\session_extensions.py", line 62, in
get_adaptive_dihedral_restraint_mgr  
return AdaptiveDihedralRestraintMgr(model)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 4171, in __init__  
super().__init__(model, c_pointer=c_pointer,  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 3633, in __init__  
super().__init__(display_name, model, c_pointer)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 1805, in __init__  
session = model.session  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
Error processing trigger "add models":  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 1805, in __init__  
session = model.session  
  
See log for complete Python traceback.  
  
Exception ignored in: <function Drawing.__del__ at 0x0000020062C34160>  
Traceback (most recent call last):  
File "F:\ChimeraX 1.4\bin\lib\site-packages\chimerax\graphics\drawing.py",
line 1187, in __del__  
if not self.was_deleted:  
AttributeError: 'AdaptiveDihedralRestraintMgr' object has no attribute
'was_deleted'  
Traceback (most recent call last):  
File "F:\ChimeraX 1.4\bin\lib\site-packages\chimerax\core\triggerset.py", line
134, in invoke  
return self._func(self._name, data)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\ui\restraints_tab\manage_restraints.py", line 203, in
_model_add_or_remove_cb  
self._expanded_cb()  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\ui\restraints_tab\manage_restraints.py", line 184, in
_expanded_cb  
tm = self.torsion_restraint_mgr  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\ui\restraints_tab\manage_restraints.py", line 281, in
torsion_restraint_mgr  
return sx.get_adaptive_dihedral_restraint_mgr(self.isolde.selected_model)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\session_extensions.py", line 62, in
get_adaptive_dihedral_restraint_mgr  
return AdaptiveDihedralRestraintMgr(model)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 4171, in __init__  
super().__init__(model, c_pointer=c_pointer,  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 3633, in __init__  
super().__init__(display_name, model, c_pointer)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 1805, in __init__  
session = model.session  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
Error processing trigger "add models":  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 1805, in __init__  
session = model.session  
  
See log for complete Python traceback.  
  
Exception ignored in: <function Drawing.__del__ at 0x0000020062C34160>  
Traceback (most recent call last):  
File "F:\ChimeraX 1.4\bin\lib\site-packages\chimerax\graphics\drawing.py",
line 1187, in __del__  
if not self.was_deleted:  
AttributeError: 'AdaptiveDihedralRestraintMgr' object has no attribute
'was_deleted'  
Traceback (most recent call last):  
File "F:\ChimeraX 1.4\bin\lib\site-packages\chimerax\core\triggerset.py", line
134, in invoke  
return self._func(self._name, data)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\ui\restraints_tab\manage_restraints.py", line 203, in
_model_add_or_remove_cb  
self._expanded_cb()  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\ui\restraints_tab\manage_restraints.py", line 184, in
_expanded_cb  
tm = self.torsion_restraint_mgr  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\ui\restraints_tab\manage_restraints.py", line 281, in
torsion_restraint_mgr  
return sx.get_adaptive_dihedral_restraint_mgr(self.isolde.selected_model)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\session_extensions.py", line 62, in
get_adaptive_dihedral_restraint_mgr  
return AdaptiveDihedralRestraintMgr(model)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 4171, in __init__  
super().__init__(model, c_pointer=c_pointer,  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 3633, in __init__  
super().__init__(display_name, model, c_pointer)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 1805, in __init__  
session = model.session  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
Error processing trigger "add models":  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 1805, in __init__  
session = model.session  
  
See log for complete Python traceback.  
  
Exception ignored in: <function Drawing.__del__ at 0x0000020062C34160>  
Traceback (most recent call last):  
File "F:\ChimeraX 1.4\bin\lib\site-packages\chimerax\graphics\drawing.py",
line 1187, in __del__  
if not self.was_deleted:  
AttributeError: 'AdaptiveDihedralRestraintMgr' object has no attribute
'was_deleted'  
Traceback (most recent call last):  
File "F:\ChimeraX 1.4\bin\lib\site-packages\chimerax\core\triggerset.py", line
134, in invoke  
return self._func(self._name, data)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\ui\restraints_tab\manage_restraints.py", line 203, in
_model_add_or_remove_cb  
self._expanded_cb()  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\ui\restraints_tab\manage_restraints.py", line 184, in
_expanded_cb  
tm = self.torsion_restraint_mgr  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\ui\restraints_tab\manage_restraints.py", line 281, in
torsion_restraint_mgr  
return sx.get_adaptive_dihedral_restraint_mgr(self.isolde.selected_model)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\session_extensions.py", line 62, in
get_adaptive_dihedral_restraint_mgr  
return AdaptiveDihedralRestraintMgr(model)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 4171, in __init__  
super().__init__(model, c_pointer=c_pointer,  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 3633, in __init__  
super().__init__(display_name, model, c_pointer)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 1805, in __init__  
session = model.session  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
Error processing trigger "add models":  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 1805, in __init__  
session = model.session  
  
See log for complete Python traceback.  
  
Exception ignored in: <function Drawing.__del__ at 0x0000020062C34160>  
Traceback (most recent call last):  
File "F:\ChimeraX 1.4\bin\lib\site-packages\chimerax\graphics\drawing.py",
line 1187, in __del__  
if not self.was_deleted:  
AttributeError: 'AdaptiveDihedralRestraintMgr' object has no attribute
'was_deleted'  
Traceback (most recent call last):  
File "F:\ChimeraX 1.4\bin\lib\site-packages\chimerax\core\triggerset.py", line
134, in invoke  
return self._func(self._name, data)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\ui\restraints_tab\manage_restraints.py", line 203, in
_model_add_or_remove_cb  
self._expanded_cb()  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\ui\restraints_tab\manage_restraints.py", line 184, in
_expanded_cb  
tm = self.torsion_restraint_mgr  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\ui\restraints_tab\manage_restraints.py", line 281, in
torsion_restraint_mgr  
return sx.get_adaptive_dihedral_restraint_mgr(self.isolde.selected_model)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\session_extensions.py", line 62, in
get_adaptive_dihedral_restraint_mgr  
return AdaptiveDihedralRestraintMgr(model)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 4171, in __init__  
super().__init__(model, c_pointer=c_pointer,  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 3633, in __init__  
super().__init__(display_name, model, c_pointer)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 1805, in __init__  
session = model.session  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
Error processing trigger "add models":  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 1805, in __init__  
session = model.session  
  
See log for complete Python traceback.  
  
Exception ignored in: <function Drawing.__del__ at 0x0000020062C34160>  
Traceback (most recent call last):  
File "F:\ChimeraX 1.4\bin\lib\site-packages\chimerax\graphics\drawing.py",
line 1187, in __del__  
if not self.was_deleted:  
AttributeError: 'AdaptiveDihedralRestraintMgr' object has no attribute
'was_deleted'  
Opened cryosparc_P2_J149_005_volume_map_sharp.mrc as #7.1.1.1, grid size
256,256,256, pixel 0.86, shown at level 0.13, step 1, values float32  
Traceback (most recent call last):  
File "F:\ChimeraX 1.4\bin\lib\site-packages\chimerax\core\triggerset.py", line
134, in invoke  
return self._func(self._name, data)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\ui\restraints_tab\manage_restraints.py", line 203, in
_model_add_or_remove_cb  
self._expanded_cb()  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\ui\restraints_tab\manage_restraints.py", line 184, in
_expanded_cb  
tm = self.torsion_restraint_mgr  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\ui\restraints_tab\manage_restraints.py", line 281, in
torsion_restraint_mgr  
return sx.get_adaptive_dihedral_restraint_mgr(self.isolde.selected_model)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\session_extensions.py", line 62, in
get_adaptive_dihedral_restraint_mgr  
return AdaptiveDihedralRestraintMgr(model)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 4171, in __init__  
super().__init__(model, c_pointer=c_pointer,  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 3633, in __init__  
super().__init__(display_name, model, c_pointer)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 1805, in __init__  
session = model.session  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
Error processing trigger "add models":  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 1805, in __init__  
session = model.session  
  
See log for complete Python traceback.  
  
Exception ignored in: <function Drawing.__del__ at 0x0000020062C34160>  
Traceback (most recent call last):  
File "F:\ChimeraX 1.4\bin\lib\site-packages\chimerax\graphics\drawing.py",
line 1187, in __del__  
if not self.was_deleted:  
AttributeError: 'AdaptiveDihedralRestraintMgr' object has no attribute
'was_deleted'  
Traceback (most recent call last):  
File "F:\ChimeraX 1.4\bin\lib\site-packages\chimerax\core\triggerset.py", line
134, in invoke  
return self._func(self._name, data)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\ui\restraints_tab\manage_restraints.py", line 203, in
_model_add_or_remove_cb  
self._expanded_cb()  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\ui\restraints_tab\manage_restraints.py", line 184, in
_expanded_cb  
tm = self.torsion_restraint_mgr  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\ui\restraints_tab\manage_restraints.py", line 281, in
torsion_restraint_mgr  
return sx.get_adaptive_dihedral_restraint_mgr(self.isolde.selected_model)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\session_extensions.py", line 62, in
get_adaptive_dihedral_restraint_mgr  
return AdaptiveDihedralRestraintMgr(model)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 4171, in __init__  
super().__init__(model, c_pointer=c_pointer,  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 3633, in __init__  
super().__init__(display_name, model, c_pointer)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 1805, in __init__  
session = model.session  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
Error processing trigger "add models":  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 1805, in __init__  
session = model.session  
  
See log for complete Python traceback.  
  
Exception ignored in: <function Drawing.__del__ at 0x0000020062C34160>  
Traceback (most recent call last):  
File "F:\ChimeraX 1.4\bin\lib\site-packages\chimerax\graphics\drawing.py",
line 1187, in __del__  
if not self.was_deleted:  
AttributeError: 'AdaptiveDihedralRestraintMgr' object has no attribute
'was_deleted'  
Traceback (most recent call last):  
File "F:\ChimeraX 1.4\bin\lib\site-packages\chimerax\core\triggerset.py", line
134, in invoke  
return self._func(self._name, data)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\ui\restraints_tab\manage_restraints.py", line 203, in
_model_add_or_remove_cb  
self._expanded_cb()  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\ui\restraints_tab\manage_restraints.py", line 184, in
_expanded_cb  
tm = self.torsion_restraint_mgr  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\ui\restraints_tab\manage_restraints.py", line 281, in
torsion_restraint_mgr  
return sx.get_adaptive_dihedral_restraint_mgr(self.isolde.selected_model)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\session_extensions.py", line 62, in
get_adaptive_dihedral_restraint_mgr  
return AdaptiveDihedralRestraintMgr(model)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 4171, in __init__  
super().__init__(model, c_pointer=c_pointer,  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 3633, in __init__  
super().__init__(display_name, model, c_pointer)  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 1805, in __init__  
session = model.session  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
Error processing trigger "add models":  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
File "C:\Users\michp\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\molobject.py", line 1805, in __init__  
session = model.session  
  
See log for complete Python traceback.  
  
Exception ignored in: <function Drawing.__del__ at 0x0000020062C34160>  
Traceback (most recent call last):  
File "F:\ChimeraX 1.4\bin\lib\site-packages\chimerax\graphics\drawing.py",
line 1187, in __del__  
if not self.was_deleted:  
AttributeError: 'AdaptiveDihedralRestraintMgr' object has no attribute
'was_deleted'  
Log from Thu Nov 24 16:47:36 2022UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open T:\PhenixProjects\HK_hu_Prediction\MapJom149Predictions.cxs format
> session

Opened cryosparc_P2_J571_006_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 0.86, shown at level 0.16, step 1, values float32  
Opened cryosparc_P2_J149_005_volume_map_sharp.mrc as #2, grid size
256,256,256, pixel 0.86, shown at level 0.146, step 1, values float32  
Opened cryosparc_P2_J151_map_sharp.mrc as #3, grid size 256,256,256, pixel
0.86, shown at level 0.133, step 1, values float32  
Log from Thu Nov 24 15:31:19 2022UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> T:\\\SOLARIS\\\CryoSparcJobsResults\\\P2\\\J583\\\cryosparc_P2_J583_006_volume_map_sharp.mrc

Opened cryosparc_P2_J583_006_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 0.86, shown at level 0.0667, step 1, values float32  

> volume #1 level 0.09256

> volume #1 level 0.1327

> volume #1 level 0.1858

> volume #1 level 0.1556

> volume #1 level 0.1929

> volume #1 level 0.1055

> volume #1 level 0.137

> volume #1 level 0.1628

> open
> F:/SOLARIS/HKnewModelBuild/FolditSesion0611.2022/HKsidechainbackbonesminim.pdb

Summary of feedback from opening
F:/SOLARIS/HKnewModelBuild/FolditSesion0611.2022/HKsidechainbackbonesminim.pdb  
---  
warnings | Ignored bad PDB record found on line 9600  
  
  
Ignored bad PDB record found on line 9601  
complete: res ss phi psi omega frag rama seq  
  
Ignored bad PDB record found on line 9602  
1 L 0.000 0.000 0.000 ---- 0.00 Q  
  
Ignored bad PDB record found on line 9603  
2 L 0.000 0.000 0.000 ---- 0.00 E  
  
Ignored bad PDB record found on line 9604  
3 L 0.000 0.000 0.000 ---- 0.00 S  
  
623 messages similar to the above omitted  
  
Chain information for HKsidechainbackbonesminim.pdb #2  
---  
Chain | Description  
A | No description available  
  

> select ::name="CYS"

180 atoms, 162 bonds, 18 residues, 1 model selected  

> show sel target ab

> select /A:65@SG

1 atom, 1 residue, 1 model selected  

> select /A:76@SG

1 atom, 1 residue, 1 model selected  

> select add /A:65@SG

2 atoms, 2 residues, 1 model selected  

> ui tool show "Build Structure"

> ui mousemode right "tape measure"

> marker segment #3 position 26.43,-24.16,34.85 toPosition 26.87,-22.19,34.96
> color yellow radius 0.1 label 2.027 labelHeight 0.2027 labelColor yellow

No bonds selected  

> bond sel

Created 1 bond  

> select #2/A:10@SG

1 atom, 1 residue, 1 model selected  

> select add #2/A:596@SG

2 atoms, 2 residues, 1 model selected  

> ui mousemode right "tape measure"

> marker segment #3 position 37.47,-2.375,29.46 toPosition 37.61,-2.269,27.45
> color yellow radius 0.1 label 2.019 labelHeight 0.2019 labelColor yellow

No bonds selected  

> bond sel

Created 1 bond  

> select #2/A:76@SG

1 atom, 1 residue, 1 model selected  

> select add #2/A:65@SG

2 atoms, 2 residues, 1 model selected  

> ~bond sel

> bond sel

Created 1 bond  

> marker segment #3 position 24.32,-25.11,33.21 toPosition 24.55,-24.64,34.52
> color yellow radius 0.1 label 1.413 labelHeight 0.2 labelColor yellow

> marker delete #3

> select /A:108@SG

1 atom, 1 residue, 1 model selected  

> select add /A:89@SG

2 atoms, 2 residues, 1 model selected  

> marker segment #3 position 21.93,-9.233,27.95 toPosition 20,-9.107,28.58
> color yellow radius 0.1 label 2.033 labelHeight 0.2033 labelColor yellow

No bonds selected  

> bond sel

Created 1 bond  

> select #2/A:127@SG

1 atom, 1 residue, 1 model selected  

> select add #2/A:124@SG

2 atoms, 2 residues, 1 model selected  

> marker delete #3

> marker segment #3 position 7.679,-35.41,3.926 toPosition 5.942,-35.63,4.945
> color yellow radius 0.1 label 2.026 labelHeight 0.2026 labelColor yellow

No bonds selected  

> bond sel

Created 1 bond  

> select #2/A:246@SG

1 atom, 1 residue, 1 model selected  

> select add #2/A:249@SG

2 atoms, 2 residues, 1 model selected  

> ui mousemode right "tape measure"

> marker segment #3 position -14.06,13.56,10.79 toPosition -14.63,14.81,9.299
> color yellow radius 0.1 label 2.026 labelHeight 0.2026 labelColor yellow

No bonds selected  

> bond sel

Created 1 bond  

> ui mousemode right "tape measure"

> marker delete #3

> marker segment #3 position 21.93,-9.233,27.95 toPosition 20,-9.107,28.58
> color yellow radius 0.1 label 2.033 labelHeight 0.2033 labelColor yellow

> select #2/A:89@SG

1 atom, 1 residue, 1 model selected  

> select add #2/A:108@SG

2 atoms, 2 residues, 1 model selected  

> ~bond sel

> bond sel

Created 1 bond  

> select #2/A:246@SG

1 atom, 1 residue, 1 model selected  

> select add #2/A:249@SG

2 atoms, 2 residues, 1 model selected  

> select #2/A:10@SG

1 atom, 1 residue, 1 model selected  

> select add #2/A:596@SG

2 atoms, 2 residues, 1 model selected  

> ui mousemode right "tape measure"

> marker segment #3 position 37.47,-2.375,29.46 toPosition 37.61,-2.269,27.45
> color yellow radius 0.1 label 2.019 labelHeight 0.2019 labelColor yellow

> ~bond sel

> bond sel

Created 1 bond  

> ui mousemode right "tape measure"

> marker segment #3 position 5.942,-35.63,4.945 toPosition 7.679,-35.41,3.926
> color yellow radius 0.1 label 2.026 labelHeight 0.2026 labelColor yellow

> select #2/A:127@SG

1 atom, 1 residue, 1 model selected  

> select add #2/A:124@SG

2 atoms, 2 residues, 1 model selected  

> select #2/A:89@SG

1 atom, 1 residue, 1 model selected  

> select add #2/A:108@SG

2 atoms, 2 residues, 1 model selected  

> select add #2/A:76@SG

3 atoms, 3 residues, 1 model selected  

> select add #2/A:65@SG

4 atoms, 4 residues, 1 model selected  

> marker segment #3 position 26.87,-22.19,34.96 toPosition 26.43,-24.16,34.85
> color yellow radius 0.1 label 2.027 labelHeight 0.2027 labelColor yellow

> select clear

> select #2/A:76@SG

1 atom, 1 residue, 1 model selected  

> select add #2/A:65@SG

2 atoms, 2 residues, 1 model selected  

> select #2/A:124@SG

1 atom, 1 residue, 1 model selected  

> select add #2/A:127@SG

2 atoms, 2 residues, 1 model selected  

> select add #2/A:246@SG

3 atoms, 3 residues, 1 model selected  

> select #2/A:249@SG

1 atom, 1 residue, 1 model selected  

> select add #2/A:246@SG

2 atoms, 2 residues, 1 model selected  

> ui mousemode right "tape measure"

> marker segment #3 position -14.06,13.56,10.79 toPosition -14.63,14.81,9.299
> color yellow radius 0.1 label 2.026 labelHeight 0.2026 labelColor yellow

> select #2/A:89@SG

1 atom, 1 residue, 1 model selected  

> select add #2/A:108@SG

2 atoms, 2 residues, 1 model selected  

> hide #!3 models

> show #!3 models

> hide #2 models

> show #2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #2 models

> show #2 models

> select #2/A:65@SG

1 atom, 1 residue, 1 model selected  

> select add #2/A:76@SG

2 atoms, 2 residues, 1 model selected  

> select add #2/A:596@SG

3 atoms, 3 residues, 1 model selected  

> select add #2/A:10@SG

4 atoms, 4 residues, 1 model selected  

> select clear

> select #2/A:596@SG

1 atom, 1 residue, 1 model selected  

> select add #2/A:10@SG

2 atoms, 2 residues, 1 model selected  

> select add #2/A:124@SG

3 atoms, 3 residues, 1 model selected  

> select add #2/A:127@SG

4 atoms, 4 residues, 1 model selected  

> select clear

> select #2/A:127@SG

1 atom, 1 residue, 1 model selected  

> select add #2/A:124@SG

2 atoms, 2 residues, 1 model selected  

> select clear

> select #2/A:249@SG

1 atom, 1 residue, 1 model selected  

> select add #2/A:246@SG

2 atoms, 2 residues, 1 model selected  

> select clear

> select add #2/A:200@SG

1 atom, 1 residue, 1 model selected  

> select add #2/A:188@SG

2 atoms, 2 residues, 1 model selected  

> marker segment #3 position -29.91,-12.96,-4.682 toPosition
> -28.68,-14.14,-5.789 color yellow radius 0.1 label 2.033 labelHeight 0.2033
> labelColor yellow

No bonds selected  

> bond sel

Created 1 bond  

> select clear

> marker segment #3 position -18.65,-21.77,6.137 toPosition -19.61,-23.4,6.889
> color yellow radius 0.1 label 2.03 labelHeight 0.203 labelColor yellow

> select #2/A:211@SG

1 atom, 1 residue, 1 model selected  

> select add #2/A:230@SG

2 atoms, 2 residues, 1 model selected  
No bonds selected  

> bond sel

Created 1 bond  

> marker segment #3 position -44.64,4.316,-20.01 toPosition
> -44.38,4.221,-18.02 color yellow radius 0.1 label 2.014 labelHeight 0.2014
> labelColor yellow

> select clear

> select #2/A:310@SG

1 atom, 1 residue, 1 model selected  

> marker delete #3

> select add /A:322@SG

2 atoms, 2 residues, 1 model selected  

> marker segment #3 position -44.64,4.316,-20.01 toPosition
> -44.38,4.221,-18.02 color yellow radius 0.1 label 2.014 labelHeight 0.2014
> labelColor yellow

No bonds selected  

> bond sel

Created 1 bond  

> marker segment #3 position -28.98,13.47,-15.88 toPosition
> -28.41,11.51,-15.83 color yellow radius 0.1 label 2.042 labelHeight 0.2042
> labelColor yellow

> select clear

> select #2/A:333@SG

1 atom, 1 residue, 1 model selected  

> select add #2/A:352@SG

2 atoms, 2 residues, 1 model selected  
No bonds selected  

> bond sel

Created 1 bond  

> marker segment #3 position 37.61,-2.269,27.45 toPosition 37.47,-2.375,29.46
> color yellow radius 0.1 label 2.019 labelHeight 0.2019 labelColor yellow

> select clear

> select #2/A:596@SG

1 atom, 1 residue, 1 model selected  

> select add #2/A:10@SG

2 atoms, 2 residues, 1 model selected  

> select clear

> select #2/A:89@SG

1 atom, 1 residue, 1 model selected  

> select add #2/A:108@SG

2 atoms, 2 residues, 1 model selected  

> marker segment #3 position 21.93,-9.233,27.95 toPosition 20,-9.107,28.58
> color yellow radius 0.1 label 2.033 labelHeight 0.2033 labelColor yellow

> select clear

> select #2/A:76@SG

1 atom, 1 residue, 1 model selected  

> select add #2/A:65@SG

2 atoms, 2 residues, 1 model selected  

> marker segment #3 position 26.87,-22.19,34.96 toPosition 26.43,-24.16,34.85
> color yellow radius 0.1 label 2.027 labelHeight 0.2027 labelColor yellow

> marker segment #3 position 7.679,-35.41,3.926 toPosition 5.942,-35.63,4.945
> color yellow radius 0.1 label 2.026 labelHeight 0.2026 labelColor yellow

> select #2/A:124@SG

1 atom, 1 residue, 1 model selected  

> marker delete #3

> select add /A:127@SG

2 atoms, 2 residues, 1 model selected  

> save
> F:/SOLARIS/HKnewModelBuild/FolditSesion0611.2022/HKsidechainbackbonesminimSS.pdb
> relModel #2

> close #2

> open
> F:/SOLARIS/HKnewModelBuild/FolditSesion0611.2022/HKsidechainbackbonesminimSS.pdb

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

> select ::name="CYS"

180 atoms, 171 bonds, 18 residues, 1 model selected  

> show sel target ab

> molmap #2 5.76

Opened HKsidechainbackbonesminimSS.pdb map 5.76 as #3, grid size 79,58,77,
pixel 1.92, shown at level 0.0703, step 1, values float32  

> volume #3 level 0.3469

> hide #2 models

> volume #3 level 0.4168

> volume #3 level 0.4806

> volume #3 level 0.5278

> hide #!3 models

> molmap #2 6.83

Opened HKsidechainbackbonesminimSS.pdb map 6.83 as #3, grid size 69,52,68,
pixel 2.28, shown at level 0.0609, step 1, values float32  

> volume #3 level 0.3697

> volume #3 level 0.4413

> volume #3 level 0.4697

> volume #3 level 0.5142

> volume #3 level 0.5352

> select add #2

9598 atoms, 9730 bonds, 626 residues, 1 model selected  

> select subtract #2

Nothing selected  

> hide #!3 models

> show #!1 models

> volume #3 level 0.08433

> volume #3 level 0.3882

> volume #1 level 0.09256

> volume #1 level 0.1513

> volume #3 level 0.2153

> molmap #1 6.83

No atoms specified  

> volume #3 level 0.3894

> volume #1 level 0.09973

> volume #1 level 0.06961

> volume #1 level 0.1184

> hide #!1 models

> hide #!3 models

> open
> F:/SOLARIS/HKnewModelBuild/FolditSesion0611.2022/HKsidechainbackbonesminimSS.pdb

Chain information for HKsidechainbackbonesminimSS.pdb #4  
---  
Chain | Description  
A | No description available  
  

> ui mousemode right "tape measure"

[Repeated 2 time(s)]

> marker segment #5 position 57.04,-13.88,45.94 toPosition -23.16,5.296,-43.34
> color yellow radius 0.1 label 121.5 labelHeight 12.15 labelColor yellow

> marker delete #5

> marker segment #5 position 38.85,14.91,-15.36 toPosition
> -15.15,-38.54,-3.374 color yellow radius 0.1 label 76.92 labelHeight 7.692
> labelColor yellow

> marker delete #5

> marker segment #5 position 50.87,14.34,0.679 toPosition -28.76,0.1625,16.13
> color yellow radius 0.1 label 82.34 labelHeight 8.234 labelColor yellow

> marker delete #5

> molmap #14 5

No atoms specified  

> molmap #4 5

Opened HKsidechainbackbonesminimSS.pdb map 5 as #5, grid size 88,64,86, pixel
1.67, shown at level 0.0789, step 1, values float32  

QWindowsWindow::setGeometry: Unable to set geometry 2560x1088+0+23 (frame:
2576x1127-8-8) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY6".
Resulting geometry: 2560x1057+0+23 (frame: 2576x1096-8-8) margins: 8, 31, 8, 8
minimum size: 467x1088 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0,
y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=483, y=1127)))  

> marker segment #6 position 63.85,-9.935,47.84 toPosition -52.42,16.38,-22.79
> color yellow radius 0.4167 label 138.6 labelHeight 13.86 labelColor yellow

> marker delete #6

> marker segment #6 position 37.68,13.26,-26.35 toPosition -31.65,-6.448,16.46
> color yellow radius 0.4167 label 83.83 labelHeight 8.383 labelColor yellow

> marker segment #6 position 62.89,-13.65,48.94 toPosition 14.51,-18.52,-69.6
> color yellow radius 0.4167 label 128.1 labelHeight 12.81 labelColor yellow

> marker delete #6

> ui mousemode right "tape measure"

> marker segment #6 position 63.01,-10.48,49.85 toPosition 29.95,3.495,44.71
> color yellow radius 0.4167 label 36.26 labelHeight 3.626 labelColor yellow

> ui mousemode right "tape measure"

> marker segment #6 position 63.66,-10.81,49.69 toPosition -53.91,30.88,-16.31
> color yellow radius 0.4167 label 141.1 labelHeight 14.11 labelColor yellow

> marker segment #6 position -34.22,-25.28,11.1 toPosition -2.643,-16.99,0.684
> color yellow radius 0.4167 label 34.27 labelHeight 3.427 labelColor yellow

> marker delete #6

> marker segment #6 position -34.87,-26.12,10.72 toPosition 24.59,21.06,-30.28
> color yellow radius 0.4167 label 86.27 labelHeight 8.627 labelColor yellow

> marker delete #6

> ui mousemode right "tape measure"

> marker segment #6 position 63.58,-9.607,49.03 toPosition -64.3,12.64,-29.51
> color yellow radius 0.4167 label 151.7 labelHeight 15.17 labelColor yellow

> marker delete #6

> marker segment #6 position -8.512,-32.68,11.07 toPosition 21.66,22.59,-30.14
> color yellow radius 0.4167 label 75.26 labelHeight 7.526 labelColor yellow

> open
> T:/SOLARIS/CryoSparcJobsResults/P2/J524/cryosparc_P2_J524_006_volume_map_sharp.mrc

Opened cryosparc_P2_J524_006_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 0.86, shown at level 0.0573, step 1, values float32  

QWindowsWindow::setGeometry: Unable to set geometry 2560x1103+0+23 (frame:
2576x1142-8-8) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY6".
Resulting geometry: 2560x1057+0+23 (frame: 2576x1096-8-8) margins: 8, 31, 8, 8
minimum size: 467x1103 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0,
y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=483, y=1142)))  

> hide #!7 models

> show #!7 models

> hide #!6 models

> hide #4 models

> open
> T:/SOLARIS/CryoSparcJobsResults/P2/J261/cryosparc_P2_J261_004_volume_map_sharp.cs

Unrecognized file suffix '.cs'  

> open
> T:/SOLARIS/CryoSparcJobsResults/P2/J261/cryosparc_P2_J261_004_volume_map_sharp.mrc

Opened cryosparc_P2_J261_004_volume_map_sharp.mrc as #8, grid size
256,256,256, pixel 0.86, shown at level 0.0358, step 1, values float32  

> volume #7 level 0.04637

> volume #8 level 0.01995

> volume #8 level 0.04411

> volume #8 level 0.07355

> volume #8 level 0.03505

> open
> T:/SOLARIS/CryoSparcJobsResults/P2/J252/cryosparc_P2_J252_005_volume_map_sharp.mrc

Opened cryosparc_P2_J252_005_volume_map_sharp.mrc as #9, grid size
256,256,256, pixel 0.86, shown at level 0.0881, step 1, values float32  

> volume #9 level 0.1145

> volume #9 level 0.1409

> open
> T:/SOLARIS/CryoSparcJobsResults/P2/J387/cryosparc_P2_J387_003_volume_map_sharp.mrc

Opened cryosparc_P2_J387_003_volume_map_sharp.mrc as #10, grid size
256,256,256, pixel 0.86, shown at level 0.0219, step 1, values float32  

> close session

> open
> T:/SOLARIS/CryoSparcJobsResults/P2/J571/cryosparc_P2_J571_006_volume_map_sharp.mrc

Opened cryosparc_P2_J571_006_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 0.86, shown at level 0.0787, step 1, values float32  

> open
> T:/SOLARIS/CryoSparcJobsResults/P2/J149/cryosparc_P2_J149_005_volume_map_sharp.mrc

Opened cryosparc_P2_J149_005_volume_map_sharp.mrc as #2, grid size
256,256,256, pixel 0.86, shown at level 0.0772, step 1, values float32  

> hide #!2 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!2 models

> open T:/SOLARIS/CryoSparcJobsResults/P2/J151/cryosparc_P2_J151_map_sharp.mrc

Opened cryosparc_P2_J151_map_sharp.mrc as #3, grid size 256,256,256, pixel
0.86, shown at level 0.0537, step 1, values float32  

> hide #!2 models

> open T:/newMD/HK/Human/HKsidechainbackbonesminimSSnoH.pdb

Chain information for HKsidechainbackbonesminimSSnoH.pdb #4  
---  
Chain | Description  
A | No description available  
  

> open
> T:/ConfSurfResults/Consurf_Outputs_1669132597_HKhu_seq/hhpred_model_With_Conservation_Scores.pdb

Chain information for hhpred_model_With_Conservation_Scores.pdb #5  
---  
Chain | Description  
? | No description available  
  

> select add #5

2772 atoms, 2827 bonds, 352 residues, 1 model selected  

> marker segment #6 position -37.96,-13.55,-33.15 toPosition
> -31.63,-14.8,-10.75 color yellow radius 0.4167 label 23.31 labelHeight 2.331
> labelColor yellow

> ui mousemode right "translate selected atoms"

> ui mousemode right "rotate selected models"

> view matrix models
> #5,-0.075539,-0.10364,0.99174,67.061,-0.10831,0.98955,0.095161,6.8233,-0.99124,-0.10023,-0.085974,91.629

> view matrix models
> #5,-0.011724,-0.0060869,0.99991,58.731,-0.072421,0.99736,0.0052222,5.2687,-0.99731,-0.072353,-0.012134,89.95

> ui mousemode right "translate selected atoms"

> select ::name="CYS"

210 atoms, 184 bonds, 35 residues, 2 models selected  

> show sel target ab

> select add #4

5017 atoms, 5132 bonds, 643 residues, 2 models selected  

> select subtract #4

102 atoms, 85 bonds, 17 residues, 1 model selected  

> select add #5

2772 atoms, 2827 bonds, 352 residues, 1 model selected  

> select subtract #5

Nothing selected  

> select add #5

2772 atoms, 2827 bonds, 352 residues, 1 model selected  

> select subtract #5

Nothing selected  

> hide #4 models

> hide #!3 models

> hide #!6 models

> select add #5

2772 atoms, 2827 bonds, 352 residues, 1 model selected  

> select subtract #5

Nothing selected  

> select sequence CPGR

28 atoms, 28 bonds, 4 residues, 1 model selected  

> colordef CONSGRAY 0.50 0.50 0.50

> color name CONSGRAY 0.50 0.50 0.50

Missing or invalid "color" argument: Color must be 3 or 4 comma-separated
numbers 0-100  

> colordef CONSGRAY 0.50 0.50 0.50

> color name CONSGRAY 0.50 0.50 0.50

Missing or invalid "color" argument: Color must be 3 or 4 comma-separated
numbers 0-100  

> colordef CONSGRAY 0.50, 0.50, 0.50

> color name CONSGRAY 0.50, 0.50, 0.50

Missing or invalid "color" argument: Color must be 3 or 4 comma-separated
numbers 0-100  

> colordef 0.50, 0.50, 0.50

> color name 0.50, 0.50, 0.50

Missing or invalid "color" argument: Color must be 3 or 4 comma-separated
numbers 0-100  

> color CONSGRAY,a C

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color CONSGRAY,a C

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> colordef CONSGRAY 0.50, 0.50, 0.50

> color name CONSGRAY 0.50, 0.50, 0.50

Missing or invalid "color" argument: Color must be 3 or 4 comma-separated
numbers 0-100  

> colordef 0.50, 0.50, 0.50

> color name 0.50, 0.50, 0.50

Missing or invalid "color" argument: Color must be 3 or 4 comma-separated
numbers 0-100  

> colordef CONSGRAY 0.50

> color name CONSGRAY 0.50

Missing or invalid "color" argument: Color must be 3 or 4 comma-separated
numbers 0-100  

> colordef CONSGRAY 50

> color name CONSGRAY 50

Missing or invalid "color" argument: Color must be 3 or 4 comma-separated
numbers 0-100  

> colordef CONSGRAY 50, 50, 50

> color name CONSGRAY 50, 50, 50

Missing or invalid "color" argument: Color must be 3 or 4 comma-separated
numbers 0-100  

> colordef CONSGRAY 50, 50, 50

> color name CONSGRAY 50, 50, 50

Missing or invalid "color" argument: Color must be 3 or 4 comma-separated
numbers 0-100  

> colordef 50, 50, 50

> color name 50, 50, 50

Missing or invalid "color" argument: Color must be 3 or 4 comma-separated
numbers 0-100  

> hide #5 models

> show #4 models

> select add #3

28 atoms, 28 bonds, 4 residues, 3 models selected  

> select add #4

4915 atoms, 5047 bonds, 626 residues, 3 models selected  

> select subtract #4

2 models selected  

> hide #4 models

> show #4 models

> select add #2

4 models selected  

> select subtract #2

2 models selected  

> show #!2 models

> volume #2 level 0.1206

> ui mousemode right "tape measure"

> marker segment #6 position 118.4,64.4,85.46 toPosition 105.5,105.3,107.7
> color yellow radius 0.215 label 48.24 labelHeight 4.824 labelColor yellow

> marker segment #6 position 117.9,64.03,85.54 toPosition 93.84,172.2,113.4
> color yellow radius 0.215 label 114.3 labelHeight 11.43 labelColor yellow

> ui mousemode right "tape measure"

> marker segment #6 position 118.2,64.04,85.46 toPosition 113,86.73,84.76
> color yellow radius 0.215 label 23.29 labelHeight 2.329 labelColor yellow

> marker segment #6 position 118.5,64.04,85.37 toPosition 105.4,155.2,135.5
> color yellow radius 0.215 label 104.9 labelHeight 10.49 labelColor yellow

> marker segment #6 position 133.8,119.8,17.47 toPosition 43.16,151.7,33.37
> color yellow radius 0.215 label 97.42 labelHeight 9.742 labelColor yellow

> ui mousemode right "tape measure"

> marker segment #6 position 117.4,64.62,85.92 toPosition 100.5,147.3,127.8
> color yellow radius 0.215 label 94.2 labelHeight 9.42 labelColor yellow

> marker delete #6

> ui mousemode right "tape measure"

> marker segment #6 position -49.44,10.41,-24.06 toPosition 50.46,-9.339,56.93
> color yellow radius 0.215 label 130.1 labelHeight 13.01 labelColor yellow

> marker segment #6 position 7.387,25.36,-54.13 toPosition 31.29,-35.42,27.69
> color yellow radius 0.215 label 104.7 labelHeight 10.47 labelColor yellow

> marker segment #6 position 56.67,123.2,102.9 toPosition 131.8,61.08,123.6
> color yellow radius 0.215 label 99.66 labelHeight 9.966 labelColor yellow

> marker delete #6

> marker segment #6 position 117.5,153.5,146.1 toPosition 110.3,81.96,125.7
> color yellow radius 0.215 label 74.7 labelHeight 7.47 labelColor yellow

> marker segment #6 position 109.4,75.92,125.8 toPosition 109.1,73.38,124.6
> color yellow radius 0.215 label 2.807 labelHeight 0.43 labelColor yellow

> marker segment #6 position 115.8,152.5,145.8 toPosition 118.1,73.48,73.64
> color yellow radius 0.215 label 107 labelHeight 10.7 labelColor yellow

> marker segment #6 position 110.3,167,132.7 toPosition 128.7,58.74,95.84
> color yellow radius 0.215 label 115.8 labelHeight 11.58 labelColor yellow

> marker delete #6

> show #!1 models

> hide #!2 models

> volume #1 level 0.1035

> marker segment #6 position 136.4,113.2,57.41 toPosition 84.8,81.59,147.9
> color yellow radius 0.215 label 108.9 labelHeight 10.89 labelColor yellow

> marker segment #6 position 81.27,78.66,90.01 toPosition 181.3,105.8,129.6
> color yellow radius 0.215 label 110.9 labelHeight 11.09 labelColor yellow

> marker segment #6 position 80.79,98.97,81.81 toPosition 173.3,107.1,134.2
> color yellow radius 0.215 label 106.7 labelHeight 10.67 labelColor yellow

> select add #4

4915 atoms, 5047 bonds, 626 residues, 3 models selected  

> marker delete #6

> ui mousemode right "translate selected atoms"

> ui mousemode right "tape measure"

> marker segment #6 position 163.9,96.84,158 toPosition 78.64,127,67.75 color
> yellow radius 0.215 label 127.8 labelHeight 12.78 labelColor yellow

> marker delete #6

> marker segment #6 position 163.9,96.84,158 toPosition 94.44,130.4,64.94
> color yellow radius 0.215 label 120.9 labelHeight 12.09 labelColor yellow

> marker delete #6

> marker segment #6 position 163.9,96.84,158 toPosition 71.77,70.01,85.38
> color yellow radius 0.215 label 120.4 labelHeight 12.04 labelColor yellow

> marker delete #6

> marker segment #6 position 129.1,81.92,148.2 toPosition 86.8,146.4,92.41
> color yellow radius 0.215 label 95.17 labelHeight 9.517 labelColor yellow

> select subtract #4

2 models selected  

> hide #4 models

> hide #!1 models

> show #4 models

> marker delete #6

> marker segment #6 position 163.9,96.84,158 toPosition 106.2,164.3,116.2
> color yellow radius 0.215 label 98.14 labelHeight 9.814 labelColor yellow

> marker segment #6 position 112.3,132.4,57.19 toPosition 160.3,97.39,159
> color yellow radius 0.215 label 117.9 labelHeight 11.79 labelColor yellow

> marker segment #6 position 60.89,121.6,84.57 toPosition 166.2,90.24,153.9
> color yellow radius 0.215 label 129.9 labelHeight 12.99 labelColor yellow

> show #!1 models

> marker segment #6 position 175.3,105.4,139.8 toPosition 90.82,143,86.39
> color yellow radius 0.215 label 106.8 labelHeight 10.68 labelColor yellow

> marker delete #6

> marker segment #6 position 158.3,100.4,157.7 toPosition 69.06,105.9,105.7
> color yellow radius 0.215 label 103.4 labelHeight 10.34 labelColor yellow

> marker segment #6 position 174.2,109.8,128 toPosition 79.11,117.2,84.65
> color yellow radius 0.215 label 104.8 labelHeight 10.48 labelColor yellow

> marker delete #6

> hide #4 models

> volume #1 level 0.1599

> select subtract #3

Nothing selected  

> select add #2

2 models selected  

> show #!2 models

> select subtract #2

Nothing selected  

> hide #!2 models

> hide #!1 models

> show #!2 models

> volume #2 level 0.166

> hide #!2 models

> show #!1 models

> volume #1 level 0.1959

> hide #!1 models

> show #!2 models

> volume #2 level 0.166

> volume #2 level 0.1164

> volume #2 level 0.1433

> show #!3 models

> hide #!2 models

> volume #3 level 0.08226

> volume #3 level 0.1495

> show #!2 models

> hide #!2 models

> volume #3 level 0.1327

> show #!2 models

> hide #!3 models

> show #!1 models

> hide #!2 models

> volume #1 level 0.1824

> volume #1 level 0.1689

> volume #1 level 0.1599

> hide #!1 models

> show #!2 models

> volume #2 level 0.1721

> volume #2 level 0.1474

> volume #2 level 0.1185

> volume #2 level 0.199

> volume #2 level 0.1556

> volume #2 level 0.1164

> volume #2 level 0.1866

> show #4 models

> hide #4 models

> show #4 models

> hide #4 models

> show #4 models

> ui mousemode right "tape measure"

> marker segment #6 position 124.8,92.12,146.5 toPosition 138.3,113,111.5
> color yellow radius 0.215 label 43.01 labelHeight 4.301 labelColor yellow

> hide #4 models

> hide #!6 models

> marker segment #6 position 122.5,91.31,101.5 toPosition 132.9,103.5,97.43
> color yellow radius 0.215 label 16.56 labelHeight 1.656 labelColor yellow

> marker segment #6 position 134.6,110.2,93.4 toPosition 124.6,101.2,94.51
> color yellow radius 0.215 label 13.47 labelHeight 1.347 labelColor yellow

> marker segment #6 position 115.9,70.33,119.3 toPosition 123.6,107.7,86.4
> color yellow radius 0.215 label 50.39 labelHeight 5.039 labelColor yellow

> marker segment #6 position 139.7,105.8,89.05 toPosition 129.9,100.5,96.42
> color yellow radius 0.215 label 13.36 labelHeight 1.336 labelColor yellow

> marker segment #6 position 142.4,105.6,89.61 toPosition 134.1,102.3,96.54
> color yellow radius 0.215 label 11.32 labelHeight 1.132 labelColor yellow

> marker segment #6 position 133.9,109.6,89.27 toPosition 126.6,80.72,95.14
> color yellow radius 0.215 label 30.41 labelHeight 3.041 labelColor yellow

> marker segment #6 position 133.7,109.5,89.65 toPosition 116,69.67,107.4
> color yellow radius 0.215 label 47.06 labelHeight 4.706 labelColor yellow

> volume #2 level 0.1474

> show #5 models

> hide #5 models

> show #4 models

> select

7703 atoms, 7882 bonds, 994 residues, 10 models selected  

> hide #4 models

> hide #!2 models

> show #!2 models

> select subtract #2

7703 atoms, 7882 bonds, 994 residues, 8 models selected  

> select subtract #1

7703 atoms, 7882 bonds, 994 residues, 6 models selected  

> select subtract #3

7703 atoms, 7882 bonds, 994 residues, 4 models selected  

> select subtract #4

2788 atoms, 2835 bonds, 368 residues, 3 models selected  

> select subtract #5

16 atoms, 8 bonds, 16 residues, 2 models selected  

> select subtract #6

Nothing selected  

> select #4

4915 atoms, 5047 bonds, 626 residues, 1 model selected  

> show #4 models

> select subtract #4

Nothing selected  

> select #4

4915 atoms, 5047 bonds, 626 residues, 1 model selected  

> select subtract #4

Nothing selected  

> hide #4 models

> volume #2 level 0.1226

> volume #2 level 0.1495

> show #4 models

> hide #!2 models

> select #4 254 276

Expected a keyword  

> select #4 residues 254 276

Invalid "residues" argument: Expected true or false (or 1 or 0)  

> select #4: 254 276

Expected a keyword  

> select #4: 254 276

Expected a keyword  

> select #4: 254 276

Expected a keyword  

> show #!2 models

> hide #!2 models

> select #4: 254 276

Expected a keyword  

> select #4 isHelix

Expected a keyword  

> select #4 :/isHelix

Expected a keyword  

> select #4 :275

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #4 :258-275

143 atoms, 144 bonds, 18 residues, 1 model selected  

> select ~sel

7560 atoms, 7736 bonds, 976 residues, 10 models selected  

> delete atoms (#4 & sel)

> delete bonds (#4 & sel)

> undo

Undo failed, probably because structures have been modified.  

> open T:/newMD/HK/Human/HKsidechainbackbonesminimSSnoH.pdb

Chain information for HKsidechainbackbonesminimSSnoH.pdb #7  
---  
Chain | Description  
A | No description available  
  

> select add #7

7703 atoms, 7882 bonds, 994 residues, 10 models selected  

> select subtract #7

2788 atoms, 2835 bonds, 368 residues, 9 models selected  

> select add #7

7703 atoms, 7882 bonds, 994 residues, 10 models selected  

> select subtract #7

2788 atoms, 2835 bonds, 368 residues, 9 models selected  

> close #4

> close #7

> open T:/newMD/HK/Human/HKsidechainbackbonesminimSSnoH.pdb

Chain information for HKsidechainbackbonesminimSSnoH.pdb #4  
---  
Chain | Description  
A | No description available  
  

> select add #4

7703 atoms, 7882 bonds, 994 residues, 10 models selected  

> select #4 :258-275

143 atoms, 144 bonds, 18 residues, 1 model selected  

> show #!2 models

> hide #!2 models

> show #!2 models

> select ~sel

7560 atoms, 7736 bonds, 976 residues, 10 models selected  

> delete atoms (#4 & sel)

> delete bonds (#4 & sel)

> select clear

> ui mousemode right "translate selected atoms"

> select add #4

143 atoms, 144 bonds, 18 residues, 1 model selected  

> ui mousemode right "move picked models"

> volume #2 level 0.1453

> view matrix models #4,1,0,0,-9.8445,0,1,0,16.342,0,0,1,-23.681

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.5373,0.8331,-0.13137,19.487,-0.84337,0.52955,-0.091148,198.12,-0.0063707,0.15976,0.98713,-22.743

> volume #2 level 0.1783

> view matrix models
> #4,0.34769,0.93755,0.010547,25.465,-0.92732,0.34551,-0.14389,229.33,-0.13855,0.040248,0.98954,5.2751

> ui mousemode right "translate selected atoms"

> volume #2 level 0.1515

> ui tool show "Fit in Map"

> fitmap #4 inMap #2

Fit molecule HKsidechainbackbonesminimSSnoH.pdb (#4) to map
cryosparc_P2_J149_005_volume_map_sharp.mrc (#2) using 143 atoms  
average map value = 0.1068, steps = 100  
shifted from previous position = 2.86  
rotated from previous position = 19.2 degrees  
atoms outside contour = 104, contour level = 0.15151  
  
Position of HKsidechainbackbonesminimSSnoH.pdb (#4) relative to
cryosparc_P2_J149_005_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.57667373 0.79737997 -0.17785555 17.35251549  
-0.81685147 0.56653657 -0.10858174 198.15166131  
0.01418077 0.20789781 0.97804775 -24.64110461  
Axis 0.19109536 -0.11595457 -0.97469847  
Axis point 198.32099168 84.57019705 0.00000000  
Rotation angle (degrees) 55.90068969  
Shift along axis 4.35704188  
  

> volume #2 level 0.1534

> fitmap #4 inMap #2

Fit molecule HKsidechainbackbonesminimSSnoH.pdb (#4) to map
cryosparc_P2_J149_005_volume_map_sharp.mrc (#2) using 143 atoms  
average map value = 0.1069, steps = 64  
shifted from previous position = 0.00719  
rotated from previous position = 0.037 degrees  
atoms outside contour = 105, contour level = 0.1534  
  
Position of HKsidechainbackbonesminimSSnoH.pdb (#4) relative to
cryosparc_P2_J149_005_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.57708192 0.79702297 -0.17813154 17.34162314  
-0.81656280 0.56689493 -0.10888216 198.12027344  
0.01420029 0.20828951 0.97796412 -24.64963619  
Axis 0.19156678 -0.11616545 -0.97458081  
Axis point 198.39487745 84.55555678 0.00000000  
Rotation angle (degrees) 55.87706001  
Shift along axis 4.33041121  
  

> fitmap #4 inMap #2

Fit molecule HKsidechainbackbonesminimSSnoH.pdb (#4) to map
cryosparc_P2_J149_005_volume_map_sharp.mrc (#2) using 143 atoms  
average map value = 0.1069, steps = 72  
shifted from previous position = 2.49  
rotated from previous position = 0.0496 degrees  
atoms outside contour = 105, contour level = 0.1534  
  
Position of HKsidechainbackbonesminimSSnoH.pdb (#4) relative to
cryosparc_P2_J149_005_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.57705199 0.79706510 -0.17803998 14.87483390  
-0.81659678 0.56668528 -0.10971549 198.36196741  
0.01344225 0.20869841 0.97788766 -24.90415846  
Axis 0.19229219 -0.11563735 -0.97450075  
Axis point 197.31450046 87.05049602 0.00000000  
Rotation angle (degrees) 55.88799629  
Shift along axis 4.19138396  
  

> volume #2 level 0.1987

> fitmap #4 inMap #2

Fit molecule HKsidechainbackbonesminimSSnoH.pdb (#4) to map
cryosparc_P2_J149_005_volume_map_sharp.mrc (#2) using 143 atoms  
average map value = 0.1329, steps = 164  
shifted from previous position = 3.78  
rotated from previous position = 32.2 degrees  
atoms outside contour = 118, contour level = 0.19872  
  
Position of HKsidechainbackbonesminimSSnoH.pdb (#4) relative to
cryosparc_P2_J149_005_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.31347782 0.93286953 0.17744321 4.10864609  
-0.84008986 0.35955746 -0.40616186 246.68840877  
-0.44269705 -0.02174550 0.89640753 67.43780631  
Axis 0.20050710 0.32345795 -0.92475502  
Axis point 183.84223932 134.81319639 0.00000000  
Rotation angle (degrees) 73.45780376  
Shift along axis 18.25369045  
  

> volume #2 level 0.1421

> volume #2 level 0.1761

> isolde start

> set selectionWidth 4

Forcefield cache not found or out of date. Regenerating from ffXML files. This
is normal if running ISOLDE for the first time, or after upgrading OpenMM.  
Done loading forcefield  
Matplotlib is building the font cache; this may take a moment.  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #4 to IUPAC-IUB
standards.  
Chain information for HKsidechainbackbonesminimSSnoH.pdb  
---  
Chain | Description  
4.2/A | No description available  
  
Cached rota8000-val data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-leu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ile data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-pro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-phe data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-tyr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-trp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ser data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-thr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-cys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-met data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-lys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-his data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-arg data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asn data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-gln data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-glu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-cispro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-transpro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-gly-sym data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-prepro-noGP data not found. Regenerating from text file. This
is normal if running ISOLDE for the first time  
Cached rama8000-ileval-nopreP data not found. Regenerating from text file.
This is normal if running ISOLDE for the first time  
Cached rama8000-general-noGPIVpreP data not found. Regenerating from text
file. This is normal if running ISOLDE for the first time  

> isolde tutorial

> volume #2 level 0.1519

> select clear

[Repeated 3 time(s)]

> hide #4.1 models

> show #4.1 models

> hide #!4 models

> hide #!2 models

> show #!4 models

> show #!2 models

> select add #4

143 atoms, 144 bonds, 18 residues, 9 models selected  

> select add #4

143 atoms, 144 bonds, 18 residues, 9 models selected  

> select subtract #4.3

143 atoms, 144 bonds, 18 residues, 8 models selected  

> select add #4.2

143 atoms, 144 bonds, 18 residues, 8 models selected  

> select subtract #4.1

143 atoms, 144 bonds, 18 residues, 7 models selected  

> select add #4

143 atoms, 144 bonds, 18 residues, 9 models selected  

> select subtract #4.3

143 atoms, 144 bonds, 18 residues, 8 models selected  

> select add #4.2

143 atoms, 144 bonds, 18 residues, 8 models selected  

> select add #4.2

143 atoms, 144 bonds, 18 residues, 8 models selected  

> select subtract #4.1

143 atoms, 144 bonds, 18 residues, 7 models selected  

> select add #4.2

143 atoms, 144 bonds, 18 residues, 7 models selected  

> select add #4

143 atoms, 144 bonds, 18 residues, 9 models selected  

> select subtract #4.3

143 atoms, 144 bonds, 18 residues, 8 models selected  

> select add #4.2

143 atoms, 144 bonds, 18 residues, 8 models selected  

> select subtract #4.1

143 atoms, 144 bonds, 18 residues, 7 models selected  

> select add #4

143 atoms, 144 bonds, 18 residues, 9 models selected  

> select subtract #4.3

143 atoms, 144 bonds, 18 residues, 8 models selected  

> select add #4.2

143 atoms, 144 bonds, 18 residues, 8 models selected  

> select add #4.2

143 atoms, 144 bonds, 18 residues, 8 models selected  

> select add #4.2

143 atoms, 144 bonds, 18 residues, 8 models selected  

> select subtract #4.1

143 atoms, 144 bonds, 18 residues, 7 models selected  

> select add #4

143 atoms, 144 bonds, 18 residues, 9 models selected  

> select add #4.2

143 atoms, 144 bonds, 18 residues, 9 models selected  

> select add #4.2

143 atoms, 144 bonds, 18 residues, 9 models selected  

> select add #4.2

143 atoms, 144 bonds, 18 residues, 9 models selected  

> select clear

> hide #!2 models

> select add #4

143 atoms, 144 bonds, 18 residues, 9 models selected  

> select add #4

143 atoms, 144 bonds, 18 residues, 9 models selected  

> select clear

> show #!2 models

> ui mousemode right "translate selected atoms"

> hide #!2 models

> show #!2 models

> hide #!2 models

> select clear

> show #!2 models

> hide #!2 models

> select clear

[Repeated 6 time(s)]

> show #!2 models

> volume #2 level 0.1668

> volume #2 level 0.1444

> volume #2 level 0.1203

> show #!1 models

> hide #!2 models

> hide #!4.2 models

> show #!4.2 models

> hide #!4.2 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> show #!4.2 models

> hide #!4.2 models

> show #!4.2 models

> open T:/newMD/HK/Human/HKsidechainbackbonesminimSSnoH.pdb format pdb

Chain information for HKsidechainbackbonesminimSSnoH.pdb #7  
---  
Chain | Description  
A | No description available  
  

> ui tool show Matchmaker

> hide #!4.2 models

> show #!4.2 models

> hide #!4.2 models

> show #!4.2 models

> matchmaker #7 to #4.2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKsidechainbackbonesminimSSnoH.pdb, chain A (#4.2) with
HKsidechainbackbonesminimSSnoH.pdb, chain A (#7), sequence alignment score =
2417.2  
RMSD between 17 pruned atom pairs is 0.611 angstroms; (across all 18 pairs:
1.312)  
  

> select #7

4915 atoms, 5047 bonds, 626 residues, 1 model selected  

> select #7 helix

Expected a keyword  

> select #7:helix

Nothing selected  

> select #7 :isHelix

Nothing selected  

> select #7 :/isHelix

Expected a keyword  

> select :isHelix

Nothing selected  

> select helix

1133 atoms, 1142 bonds, 140 residues, 3 models selected  

QAccessibleTable::child: Invalid index at: 7 0  

QAccessibleTable::child: Invalid index at: 7 1  

QAccessibleTable::child: Invalid index at: 7 2  

QAccessibleTable::child: Invalid index at: 7 3  

QAccessibleTable::child: Invalid index at: 8 0  

QAccessibleTable::child: Invalid index at: 8 1  

QAccessibleTable::child: Invalid index at: 8 2  

QAccessibleTable::child: Invalid index at: 8 3  

QAccessibleTable::child: Invalid index at: 9 0  

QAccessibleTable::child: Invalid index at: 9 1  

QAccessibleTable::child: Invalid index at: 9 2  

QAccessibleTable::child: Invalid index at: 9 3  

QAccessibleTable::child: Invalid index at: 10 0  

QAccessibleTable::child: Invalid index at: 10 1  

QAccessibleTable::child: Invalid index at: 10 2  

QAccessibleTable::child: Invalid index at: 10 3  

QAccessibleTable::child: Invalid index at: 11 0  

QAccessibleTable::child: Invalid index at: 11 1  

QAccessibleTable::child: Invalid index at: 11 2  

QAccessibleTable::child: Invalid index at: 11 3  

QAccessibleTable::child: Invalid index at: 12 0  

QAccessibleTable::child: Invalid index at: 12 1  

QAccessibleTable::child: Invalid index at: 12 2  

QAccessibleTable::child: Invalid index at: 12 3  

QAccessibleTable::child: Invalid index at: 13 0  

QAccessibleTable::child: Invalid index at: 13 1  

QAccessibleTable::child: Invalid index at: 13 2  

QAccessibleTable::child: Invalid index at: 13 3  

QAccessibleTable::child: Invalid index at: 14 0  

QAccessibleTable::child: Invalid index at: 14 1  

QAccessibleTable::child: Invalid index at: 14 2  

QAccessibleTable::child: Invalid index at: 14 3  

QAccessibleTable::child: Invalid index at: 15 0  

QAccessibleTable::child: Invalid index at: 15 1  

QAccessibleTable::child: Invalid index at: 15 2  

QAccessibleTable::child: Invalid index at: 15 3  

QAccessibleTable::child: Invalid index at: 16 0  

QAccessibleTable::child: Invalid index at: 16 1  

QAccessibleTable::child: Invalid index at: 16 2  

QAccessibleTable::child: Invalid index at: 16 3  

> save T:/PhenixProjects/HK_hu_Prediction/HKAlphaHelixonly.pdb models #7
> selectedOnly true

> open T:/PhenixProjects/HK_hu_Prediction/HKAlphaHelixonly.pdb

Summary of feedback from opening
T:/PhenixProjects/HK_hu_Prediction/HKAlphaHelixonly.pdb  
---  
warnings | Start residue of secondary structure not found: SHEET 1 1 1 SER A 5
GLU A 7 0  
Start residue of secondary structure not found: SHEET 2 2 1 PHE A 36 ILE A 41
0  
Start residue of secondary structure not found: SHEET 3 3 1 GLU A 43 VAL A 48
0  
Start residue of secondary structure not found: SHEET 4 4 1 THR A 52 GLU A 62
0  
Start residue of secondary structure not found: SHEET 5 5 1 THR A 86 LYS A 95
0  
12 messages similar to the above omitted  
Cannot find LINK/SSBOND residue CYS (10 )  
Cannot find LINK/SSBOND residue CYS (65 )  
Cannot find LINK/SSBOND residue CYS (89 )  
Cannot find LINK/SSBOND residue CYS (124 )  
Cannot find LINK/SSBOND residue CYS (188 )  
4 messages similar to the above omitted  
  
Chain information for HKAlphaHelixonly.pdb #8  
---  
Chain | Description  
A | No description available  
  

> close #8

> select add #4.2

1141 atoms, 1150 bonds, 141 residues, 8 models selected  

> select add #4

1141 atoms, 1150 bonds, 141 residues, 11 models selected  

> select add #4

1141 atoms, 1150 bonds, 141 residues, 11 models selected  

> select clear

> hide #!1 models

> hide #!4 models

> hide #4.1 models

> hide #7 models

> hide #4.3 models

> hide #!4.2 models

> show #7 models

> hide #7 models

> open T:/PhenixProjects/HK_hu_Prediction/HKAlphaHelixonly.pdb

Summary of feedback from opening
T:/PhenixProjects/HK_hu_Prediction/HKAlphaHelixonly.pdb  
---  
warnings | Start residue of secondary structure not found: SHEET 1 1 1 SER A 5
GLU A 7 0  
Start residue of secondary structure not found: SHEET 2 2 1 PHE A 36 ILE A 41
0  
Start residue of secondary structure not found: SHEET 3 3 1 GLU A 43 VAL A 48
0  
Start residue of secondary structure not found: SHEET 4 4 1 THR A 52 GLU A 62
0  
Start residue of secondary structure not found: SHEET 5 5 1 THR A 86 LYS A 95
0  
12 messages similar to the above omitted  
Cannot find LINK/SSBOND residue CYS (10 )  
Cannot find LINK/SSBOND residue CYS (65 )  
Cannot find LINK/SSBOND residue CYS (89 )  
Cannot find LINK/SSBOND residue CYS (124 )  
Cannot find LINK/SSBOND residue CYS (188 )  
4 messages similar to the above omitted  
  
Chain information for HKAlphaHelixonly.pdb #8  
---  
Chain | Description  
A | No description available  
  

> ui mousemode right select

Drag select of 19 residues, 2 pseudobonds  

> select clear

Drag select of 17 residues, 1 pseudobonds  
[Repeated 1 time(s)]

> select clear

Drag select of 17 residues  

> save T:/PhenixProjects/HK_hu_Prediction/HKD1Helix.pdb models #8 selectedOnly
> true

> open T:/PhenixProjects/HK_hu_Prediction/HKD1Helix.pdb

Summary of feedback from opening
T:/PhenixProjects/HK_hu_Prediction/HKD1Helix.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 2 2 VAL A 67
SER A 69 1 3  
Start residue of secondary structure not found: HELIX 3 3 TRP A 73 ASP A 75 1
3  
Start residue of secondary structure not found: HELIX 4 4 PRO A 136 LEU A 138
1 3  
Start residue of secondary structure not found: HELIX 5 5 GLU A 139 ASN A 152
1 14  
Start residue of secondary structure not found: HELIX 6 6 GLY A 235 ASP A 237
1 3  
5 messages similar to the above omitted  
  
Chain information for HKD1Helix.pdb #9  
---  
Chain | Description  
A | No description available  
  

> hide #9 models

> hide #!8 models

> show #9 models

> show #!8 models

> hide #9 models

Drag select of 17 residues, 1 pseudobonds  

> select clear

Drag select of 17 residues  

QAccessibleTable::child: Invalid index at: 4 0  

QAccessibleTable::child: Invalid index at: 4 1  

QAccessibleTable::child: Invalid index at: 4 2  

QAccessibleTable::child: Invalid index at: 4 3  

QAccessibleTable::child: Invalid index at: 5 0  

QAccessibleTable::child: Invalid index at: 5 1  

QAccessibleTable::child: Invalid index at: 5 2  

QAccessibleTable::child: Invalid index at: 5 3  

QAccessibleTable::child: Invalid index at: 6 0  

QAccessibleTable::child: Invalid index at: 6 1  

QAccessibleTable::child: Invalid index at: 6 2  

QAccessibleTable::child: Invalid index at: 6 3  

QAccessibleTable::child: Invalid index at: 7 0  

QAccessibleTable::child: Invalid index at: 7 1  

QAccessibleTable::child: Invalid index at: 7 2  

QAccessibleTable::child: Invalid index at: 7 3  

QAccessibleTable::child: Invalid index at: 8 0  

QAccessibleTable::child: Invalid index at: 8 1  

QAccessibleTable::child: Invalid index at: 8 2  

QAccessibleTable::child: Invalid index at: 8 3  

QAccessibleTable::child: Invalid index at: 9 0  

QAccessibleTable::child: Invalid index at: 9 1  

QAccessibleTable::child: Invalid index at: 9 2  

QAccessibleTable::child: Invalid index at: 9 3  

QAccessibleTable::child: Invalid index at: 10 0  

QAccessibleTable::child: Invalid index at: 10 1  

QAccessibleTable::child: Invalid index at: 10 2  

QAccessibleTable::child: Invalid index at: 10 3  

QAccessibleTable::child: Invalid index at: 11 0  

QAccessibleTable::child: Invalid index at: 11 1  

QAccessibleTable::child: Invalid index at: 11 2  

QAccessibleTable::child: Invalid index at: 11 3  

QAccessibleTable::child: Invalid index at: 12 0  

QAccessibleTable::child: Invalid index at: 12 1  

QAccessibleTable::child: Invalid index at: 12 2  

QAccessibleTable::child: Invalid index at: 12 3  

QAccessibleTable::child: Invalid index at: 13 0  

QAccessibleTable::child: Invalid index at: 13 1  

QAccessibleTable::child: Invalid index at: 13 2  

QAccessibleTable::child: Invalid index at: 13 3  

QAccessibleTable::child: Invalid index at: 14 0  

QAccessibleTable::child: Invalid index at: 14 1  

QAccessibleTable::child: Invalid index at: 14 2  

QAccessibleTable::child: Invalid index at: 14 3  

QAccessibleTable::child: Invalid index at: 15 0  

QAccessibleTable::child: Invalid index at: 15 1  

QAccessibleTable::child: Invalid index at: 15 2  

QAccessibleTable::child: Invalid index at: 15 3  

QAccessibleTable::child: Invalid index at: 16 0  

QAccessibleTable::child: Invalid index at: 16 1  

QAccessibleTable::child: Invalid index at: 16 2  

QAccessibleTable::child: Invalid index at: 16 3  

> save T:/PhenixProjects/HK_hu_Prediction/HKD2Helix.pdb models #8 selectedOnly
> true

> select clear

> open T:/PhenixProjects/HK_hu_Prediction/HKD2Helix.pdb

Summary of feedback from opening
T:/PhenixProjects/HK_hu_Prediction/HKD2Helix.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 LYS A 13
GLN A 29 1 17  
Start residue of secondary structure not found: HELIX 2 2 VAL A 67 SER A 69 1
3  
Start residue of secondary structure not found: HELIX 3 3 TRP A 73 ASP A 75 1
3  
Start residue of secondary structure not found: HELIX 6 6 GLY A 235 ASP A 237
1 3  
Start residue of secondary structure not found: HELIX 7 7 PRO A 258 LEU A 260
1 3  
4 messages similar to the above omitted  
  
Chain information for HKD2Helix.pdb #10  
---  
Chain | Description  
A | No description available  
  

> hide #10 models

> show #10 models

> hide #!8 models

> show #!8 models

> hide #10 models

Drag select of 18 residues, 1 pseudobonds  

> select clear

Drag select of 14 residues  
Drag select of 17 residues  

QAccessibleTable::child: Invalid index at: 5 0  

QAccessibleTable::child: Invalid index at: 5 1  

QAccessibleTable::child: Invalid index at: 5 2  

QAccessibleTable::child: Invalid index at: 5 3  

QAccessibleTable::child: Invalid index at: 6 0  

QAccessibleTable::child: Invalid index at: 6 1  

QAccessibleTable::child: Invalid index at: 6 2  

QAccessibleTable::child: Invalid index at: 6 3  

QAccessibleTable::child: Invalid index at: 7 0  

QAccessibleTable::child: Invalid index at: 7 1  

QAccessibleTable::child: Invalid index at: 7 2  

QAccessibleTable::child: Invalid index at: 7 3  

QAccessibleTable::child: Invalid index at: 8 0  

QAccessibleTable::child: Invalid index at: 8 1  

QAccessibleTable::child: Invalid index at: 8 2  

QAccessibleTable::child: Invalid index at: 8 3  

QAccessibleTable::child: Invalid index at: 9 0  

QAccessibleTable::child: Invalid index at: 9 1  

QAccessibleTable::child: Invalid index at: 9 2  

QAccessibleTable::child: Invalid index at: 9 3  

QAccessibleTable::child: Invalid index at: 10 0  

QAccessibleTable::child: Invalid index at: 10 1  

QAccessibleTable::child: Invalid index at: 10 2  

QAccessibleTable::child: Invalid index at: 10 3  

QAccessibleTable::child: Invalid index at: 11 0  

QAccessibleTable::child: Invalid index at: 11 1  

QAccessibleTable::child: Invalid index at: 11 2  

QAccessibleTable::child: Invalid index at: 11 3  

QAccessibleTable::child: Invalid index at: 12 0  

QAccessibleTable::child: Invalid index at: 12 1  

QAccessibleTable::child: Invalid index at: 12 2  

QAccessibleTable::child: Invalid index at: 12 3  

QAccessibleTable::child: Invalid index at: 13 0  

QAccessibleTable::child: Invalid index at: 13 1  

QAccessibleTable::child: Invalid index at: 13 2  

QAccessibleTable::child: Invalid index at: 13 3  

QAccessibleTable::child: Invalid index at: 14 0  

QAccessibleTable::child: Invalid index at: 14 1  

QAccessibleTable::child: Invalid index at: 14 2  

QAccessibleTable::child: Invalid index at: 14 3  

QAccessibleTable::child: Invalid index at: 15 0  

QAccessibleTable::child: Invalid index at: 15 1  

QAccessibleTable::child: Invalid index at: 15 2  

QAccessibleTable::child: Invalid index at: 15 3  

QAccessibleTable::child: Invalid index at: 16 0  

QAccessibleTable::child: Invalid index at: 16 1  

QAccessibleTable::child: Invalid index at: 16 2  

QAccessibleTable::child: Invalid index at: 16 3  

> save T:/PhenixProjects/HK_hu_Prediction/HKD3Helix.pdb models #8 selectedOnly
> true

> open T:/PhenixProjects/HK_hu_Prediction/HKD3Helix.pdb

Summary of feedback from opening
T:/PhenixProjects/HK_hu_Prediction/HKD3Helix.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 LYS A 13
GLN A 29 1 17  
Start residue of secondary structure not found: HELIX 2 2 VAL A 67 SER A 69 1
3  
Start residue of secondary structure not found: HELIX 3 3 TRP A 73 ASP A 75 1
3  
Start residue of secondary structure not found: HELIX 4 4 PRO A 136 LEU A 138
1 3  
Start residue of secondary structure not found: HELIX 5 5 GLU A 139 ASN A 152
1 14  
4 messages similar to the above omitted  
  
Chain information for HKD3Helix.pdb #11  
---  
Chain | Description  
A | No description available  
  

> hide #!8 models

> show #!8 models

> hide #!8 models

> close #8

> show #!2 models

> volume #2 level 0.1723

> show #!4.2 models

> hide #!4.2 models

> show #!4.2 models

> hide #!4.2 models

> show #!4.2 models

> hide #!4.2 models

> show #10 models

> hide #10 models

> show #10 models

> show #9 models

> save T:/PhenixProjects/HK_hu_Prediction/MapJom149Predictions.cxs

> hide #9 models

> show #9 models

> hide #10 models

> show #10 models

> hide #11 models

> show #11 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #10 models

> show #10 models

> hide #9 models

> show #9 models

> ui tool show Matchmaker

> show #!4.2 models

> hide #!4.2 models

> show #!4.2 models

> hide #!4.2 models

> show #4.1 models

> hide #4.1 models

> show #!4.2 models

> hide #!4.2 models

> matchmaker #9 to #4.2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKsidechainbackbonesminimSSnoH.pdb, chain A (#4.2) with
HKD1Helix.pdb, chain A (#9), sequence alignment score = 58.8  
Fewer than 3 residues aligned; cannot match
HKsidechainbackbonesminimSSnoH.pdb, chain A with HKD1Helix.pdb, chain A  

> hide #9 models

> hide #10 models

> show #10 models

> hide #10 models

> hide #11 models

> show #11 models

> matchmaker #9 to #11

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKD3Helix.pdb, chain A (#11) with HKD1Helix.pdb, chain A (#9),
sequence alignment score = 39.9  
RMSD between 15 pruned atom pairs is 0.442 angstroms; (across all 17 pairs:
1.133)  
  

> show #9 models

> show #10 models

> matchmaker #10 to #11

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKD3Helix.pdb, chain A (#11) with HKD2Helix.pdb, chain A (#10),
sequence alignment score = 43.2  
RMSD between 17 pruned atom pairs is 0.393 angstroms; (across all 17 pairs:
0.393)  
  

> show #7 models

> hide #7 models

> show #7 models

> matchmaker #7 to #9

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKD1Helix.pdb, chain A (#9) with
HKsidechainbackbonesminimSSnoH.pdb, chain A (#7), sequence alignment score =
82.2  
RMSD between 17 pruned atom pairs is 0.000 angstroms; (across all 17 pairs:
0.000)  
  

> matchmaker #7 to #10

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKD2Helix.pdb, chain A (#10) with
HKsidechainbackbonesminimSSnoH.pdb, chain A (#7), sequence alignment score =
83.4  
RMSD between 17 pruned atom pairs is 0.000 angstroms; (across all 17 pairs:
0.000)  
  

> matchmaker #7 to #11

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKD3Helix.pdb, chain A (#11) with
HKsidechainbackbonesminimSSnoH.pdb, chain A (#7), sequence alignment score =
83.6  
RMSD between 17 pruned atom pairs is 0.000 angstroms; (across all 17 pairs:
0.000)  
  

> hide #11 models

> hide #10 models

> hide #9 models

> hide #7 models

> show #!4.2 models

> select add #4.2

143 atoms, 144 bonds, 18 residues, 6 models selected  

> volume #2 level 0.1556

> ui mousemode right "rotate selected models"

> view matrix models
> #4.2,0.10627,-0.93936,-0.32606,229.13,-0.78018,-0.28207,0.55835,161.19,-0.61646,0.19505,-0.76284,228.89

> hide #!4 models

> show #!4 models

> hide #!4.2 models

> show #!4.2 models

> matchmaker #11 to #4.2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKsidechainbackbonesminimSSnoH.pdb, chain A (#4.2) with
HKD3Helix.pdb, chain A (#11), sequence alignment score = 83  
RMSD between 16 pruned atom pairs is 0.621 angstroms; (across all 17 pairs:
1.339)  
  

> show #11 models

> show #10 models

> show #9 models

> matchmaker #10 to #4.2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKsidechainbackbonesminimSSnoH.pdb, chain A (#4.2) with
HKD2Helix.pdb, chain A (#10), sequence alignment score = 67.2  
Fewer than 3 residues aligned; cannot match
HKsidechainbackbonesminimSSnoH.pdb, chain A with HKD2Helix.pdb, chain A  

> matchmaker #11 to #4.2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKsidechainbackbonesminimSSnoH.pdb, chain A (#4.2) with
HKD3Helix.pdb, chain A (#11), sequence alignment score = 83  
RMSD between 16 pruned atom pairs is 0.621 angstroms; (across all 17 pairs:
1.339)  
  

> matchmaker #9 to #11

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKD3Helix.pdb, chain A (#11) with HKD1Helix.pdb, chain A (#9),
sequence alignment score = 39.9  
RMSD between 15 pruned atom pairs is 0.442 angstroms; (across all 17 pairs:
1.133)  
  

> matchmaker #10 to #11

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKD3Helix.pdb, chain A (#11) with HKD2Helix.pdb, chain A (#10),
sequence alignment score = 43.2  
RMSD between 17 pruned atom pairs is 0.393 angstroms; (across all 17 pairs:
0.393)  
  

> select add #7

5058 atoms, 5191 bonds, 644 residues, 7 models selected  

> select subtract #7

143 atoms, 144 bonds, 18 residues, 6 models selected  

> show #7 models

> matchmaker #7 to #9

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKD1Helix.pdb, chain A (#9) with
HKsidechainbackbonesminimSSnoH.pdb, chain A (#7), sequence alignment score =
82.2  
RMSD between 17 pruned atom pairs is 0.000 angstroms; (across all 17 pairs:
0.000)  
  

> matchmaker #7 to #10

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKD2Helix.pdb, chain A (#10) with
HKsidechainbackbonesminimSSnoH.pdb, chain A (#7), sequence alignment score =
83.4  
RMSD between 17 pruned atom pairs is 0.000 angstroms; (across all 17 pairs:
0.000)  
  

> matchmaker #7 to #11

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKD3Helix.pdb, chain A (#11) with
HKsidechainbackbonesminimSSnoH.pdb, chain A (#7), sequence alignment score =
83.6  
RMSD between 17 pruned atom pairs is 0.000 angstroms; (across all 17 pairs:
0.000)  
  

> matchmaker #7 to #10

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKD2Helix.pdb, chain A (#10) with
HKsidechainbackbonesminimSSnoH.pdb, chain A (#7), sequence alignment score =
83.4  
RMSD between 17 pruned atom pairs is 0.000 angstroms; (across all 17 pairs:
0.000)  
  

> matchmaker #7 to #11

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKD3Helix.pdb, chain A (#11) with
HKsidechainbackbonesminimSSnoH.pdb, chain A (#7), sequence alignment score =
83.6  
RMSD between 17 pruned atom pairs is 0.000 angstroms; (across all 17 pairs:
0.000)  
  

> matchmaker #7 to #9

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKD1Helix.pdb, chain A (#9) with
HKsidechainbackbonesminimSSnoH.pdb, chain A (#7), sequence alignment score =
82.2  
RMSD between 17 pruned atom pairs is 0.000 angstroms; (across all 17 pairs:
0.000)  
  

> matchmaker #7 to #10

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKD2Helix.pdb, chain A (#10) with
HKsidechainbackbonesminimSSnoH.pdb, chain A (#7), sequence alignment score =
83.4  
RMSD between 17 pruned atom pairs is 0.000 angstroms; (across all 17 pairs:
0.000)  
  

> matchmaker #7 to #11

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKD3Helix.pdb, chain A (#11) with
HKsidechainbackbonesminimSSnoH.pdb, chain A (#7), sequence alignment score =
83.6  
RMSD between 17 pruned atom pairs is 0.000 angstroms; (across all 17 pairs:
0.000)  
  

> matchmaker #7 to #9

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKD1Helix.pdb, chain A (#9) with
HKsidechainbackbonesminimSSnoH.pdb, chain A (#7), sequence alignment score =
82.2  
RMSD between 17 pruned atom pairs is 0.000 angstroms; (across all 17 pairs:
0.000)  
  

> select add #4.2

143 atoms, 144 bonds, 18 residues, 6 models selected  

> select add #4

143 atoms, 144 bonds, 18 residues, 9 models selected  

> select add #4

143 atoms, 144 bonds, 18 residues, 9 models selected  

> select clear

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #11 models

> hide #10 models

> hide #9 models

> hide #7 models

> select add #4

143 atoms, 144 bonds, 18 residues, 9 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.54591,0.10139,-0.83168,127.43,0.53846,0.71805,0.44098,-83.586,0.6419,-0.68857,0.3374,47.513

> select add #11

278 atoms, 280 bonds, 35 residues, 10 models selected  

> select add #10

422 atoms, 428 bonds, 52 residues, 11 models selected  

> select add #9

558 atoms, 565 bonds, 69 residues, 12 models selected  

> select add #7

5473 atoms, 5612 bonds, 695 residues, 13 models selected  

> select subtract #11

5338 atoms, 5476 bonds, 678 residues, 12 models selected  

> select subtract #10

5194 atoms, 5328 bonds, 661 residues, 11 models selected  

> select subtract #9

5058 atoms, 5191 bonds, 644 residues, 10 models selected  

> select subtract #7

143 atoms, 144 bonds, 18 residues, 9 models selected  

> show #11 models

> show #10 models

> show #9 models

> show #7 models

> matchmaker #11 to #4.2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKsidechainbackbonesminimSSnoH.pdb, chain A (#4.2) with
HKD3Helix.pdb, chain A (#11), sequence alignment score = 83  
RMSD between 16 pruned atom pairs is 0.621 angstroms; (across all 17 pairs:
1.339)  
  

> matchmaker #9 to #11

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKD3Helix.pdb, chain A (#11) with HKD1Helix.pdb, chain A (#9),
sequence alignment score = 39.9  
RMSD between 15 pruned atom pairs is 0.442 angstroms; (across all 17 pairs:
1.133)  
  

> matchmaker #10 to #11

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKD3Helix.pdb, chain A (#11) with HKD2Helix.pdb, chain A (#10),
sequence alignment score = 43.2  
RMSD between 17 pruned atom pairs is 0.393 angstroms; (across all 17 pairs:
0.393)  
  

> matchmaker #7 to #9

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKD1Helix.pdb, chain A (#9) with
HKsidechainbackbonesminimSSnoH.pdb, chain A (#7), sequence alignment score =
82.2  
RMSD between 17 pruned atom pairs is 0.000 angstroms; (across all 17 pairs:
0.000)  
  

> matchmaker #7 to #10

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKD2Helix.pdb, chain A (#10) with
HKsidechainbackbonesminimSSnoH.pdb, chain A (#7), sequence alignment score =
83.4  
RMSD between 17 pruned atom pairs is 0.000 angstroms; (across all 17 pairs:
0.000)  
  

> matchmaker #7 to #11

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKD3Helix.pdb, chain A (#11) with
HKsidechainbackbonesminimSSnoH.pdb, chain A (#7), sequence alignment score =
83.6  
RMSD between 17 pruned atom pairs is 0.000 angstroms; (across all 17 pairs:
0.000)  
  

> matchmaker #7 to #10

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKD2Helix.pdb, chain A (#10) with
HKsidechainbackbonesminimSSnoH.pdb, chain A (#7), sequence alignment score =
83.4  
RMSD between 17 pruned atom pairs is 0.000 angstroms; (across all 17 pairs:
0.000)  
  

> volume #2 level 0.1556

QAccessibleTable::child: Invalid index at: 3 0  

QAccessibleTable::child: Invalid index at: 3 1  

QAccessibleTable::child: Invalid index at: 3 2  

QAccessibleTable::child: Invalid index at: 3 3  

QAccessibleTable::child: Invalid index at: 4 0  

QAccessibleTable::child: Invalid index at: 4 1  

QAccessibleTable::child: Invalid index at: 4 2  

QAccessibleTable::child: Invalid index at: 4 3  

QAccessibleTable::child: Invalid index at: 5 0  

QAccessibleTable::child: Invalid index at: 5 1  

QAccessibleTable::child: Invalid index at: 5 2  

QAccessibleTable::child: Invalid index at: 5 3  

QAccessibleTable::child: Invalid index at: 6 0  

QAccessibleTable::child: Invalid index at: 6 1  

QAccessibleTable::child: Invalid index at: 6 2  

QAccessibleTable::child: Invalid index at: 6 3  

QAccessibleTable::child: Invalid index at: 7 0  

QAccessibleTable::child: Invalid index at: 7 1  

QAccessibleTable::child: Invalid index at: 7 2  

QAccessibleTable::child: Invalid index at: 7 3  

QAccessibleTable::child: Invalid index at: 8 0  

QAccessibleTable::child: Invalid index at: 8 1  

QAccessibleTable::child: Invalid index at: 8 2  

QAccessibleTable::child: Invalid index at: 8 3  

QAccessibleTable::child: Invalid index at: 9 0  

QAccessibleTable::child: Invalid index at: 9 1  

QAccessibleTable::child: Invalid index at: 9 2  

QAccessibleTable::child: Invalid index at: 9 3  

QAccessibleTable::child: Invalid index at: 10 0  

QAccessibleTable::child: Invalid index at: 10 1  

QAccessibleTable::child: Invalid index at: 10 2  

QAccessibleTable::child: Invalid index at: 10 3  

QAccessibleTable::child: Invalid index at: 11 0  

QAccessibleTable::child: Invalid index at: 11 1  

QAccessibleTable::child: Invalid index at: 11 2  

QAccessibleTable::child: Invalid index at: 11 3  

QAccessibleTable::child: Invalid index at: 12 0  

QAccessibleTable::child: Invalid index at: 12 1  

QAccessibleTable::child: Invalid index at: 12 2  

QAccessibleTable::child: Invalid index at: 12 3  

QAccessibleTable::child: Invalid index at: 13 0  

QAccessibleTable::child: Invalid index at: 13 1  

QAccessibleTable::child: Invalid index at: 13 2  

QAccessibleTable::child: Invalid index at: 13 3  

QAccessibleTable::child: Invalid index at: 14 0  

QAccessibleTable::child: Invalid index at: 14 1  

QAccessibleTable::child: Invalid index at: 14 2  

QAccessibleTable::child: Invalid index at: 14 3  

QAccessibleTable::child: Invalid index at: 15 0  

QAccessibleTable::child: Invalid index at: 15 1  

QAccessibleTable::child: Invalid index at: 15 2  

QAccessibleTable::child: Invalid index at: 15 3  

QAccessibleTable::child: Invalid index at: 16 0  

QAccessibleTable::child: Invalid index at: 16 1  

QAccessibleTable::child: Invalid index at: 16 2  

QAccessibleTable::child: Invalid index at: 16 3  

> save T:/PhenixProjects/HK_hu_Prediction/MapJom149Predictions.cxs

> view matrix models
> #4,0.4156,0.15913,-0.89552,144.49,0.68953,0.58696,0.4243,-88.697,0.59315,-0.79383,0.13421,82.882

> matchmaker #11 to #4.2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKsidechainbackbonesminimSSnoH.pdb, chain A (#4.2) with
HKD3Helix.pdb, chain A (#11), sequence alignment score = 83  
RMSD between 16 pruned atom pairs is 0.621 angstroms; (across all 17 pairs:
1.339)  
  

> matchmaker #10 to #4.2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKsidechainbackbonesminimSSnoH.pdb, chain A (#4.2) with
HKD2Helix.pdb, chain A (#10), sequence alignment score = 67.2  
Fewer than 3 residues aligned; cannot match
HKsidechainbackbonesminimSSnoH.pdb, chain A with HKD2Helix.pdb, chain A  

> matchmaker #10 to #11

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKD3Helix.pdb, chain A (#11) with HKD2Helix.pdb, chain A (#10),
sequence alignment score = 43.2  
RMSD between 17 pruned atom pairs is 0.393 angstroms; (across all 17 pairs:
0.393)  
  

> matchmaker #9 to #11

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKD3Helix.pdb, chain A (#11) with HKD1Helix.pdb, chain A (#9),
sequence alignment score = 39.9  
RMSD between 15 pruned atom pairs is 0.442 angstroms; (across all 17 pairs:
1.133)  
  

> matchmaker #7 to #11

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKD3Helix.pdb, chain A (#11) with
HKsidechainbackbonesminimSSnoH.pdb, chain A (#7), sequence alignment score =
83.6  
RMSD between 17 pruned atom pairs is 0.000 angstroms; (across all 17 pairs:
0.000)  
  

> matchmaker #7 to #10

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKD2Helix.pdb, chain A (#10) with
HKsidechainbackbonesminimSSnoH.pdb, chain A (#7), sequence alignment score =
83.4  
RMSD between 17 pruned atom pairs is 0.000 angstroms; (across all 17 pairs:
0.000)  
  

> matchmaker #7 to #11

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKD3Helix.pdb, chain A (#11) with
HKsidechainbackbonesminimSSnoH.pdb, chain A (#7), sequence alignment score =
83.6  
RMSD between 17 pruned atom pairs is 0.000 angstroms; (across all 17 pairs:
0.000)  
  

> matchmaker #7 to #10

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKD2Helix.pdb, chain A (#10) with
HKsidechainbackbonesminimSSnoH.pdb, chain A (#7), sequence alignment score =
83.4  
RMSD between 17 pruned atom pairs is 0.000 angstroms; (across all 17 pairs:
0.000)  
  

> matchmaker #7 to #9

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKD1Helix.pdb, chain A (#9) with
HKsidechainbackbonesminimSSnoH.pdb, chain A (#7), sequence alignment score =
82.2  
RMSD between 17 pruned atom pairs is 0.000 angstroms; (across all 17 pairs:
0.000)  
  

> matchmaker #7 to #10

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKD2Helix.pdb, chain A (#10) with
HKsidechainbackbonesminimSSnoH.pdb, chain A (#7), sequence alignment score =
83.4  
RMSD between 17 pruned atom pairs is 0.000 angstroms; (across all 17 pairs:
0.000)  
  

> ui tool show "Fit in Map"

> fitmap #4.2 inMap #2

Fit molecule HKsidechainbackbonesminimSSnoH.pdb (#4.2) to map
cryosparc_P2_J149_005_volume_map_sharp.mrc (#2) using 143 atoms  
average map value = 0.1189, steps = 96  
shifted from previous position = 2.38  
rotated from previous position = 12.5 degrees  
atoms outside contour = 109, contour level = 0.1556  
  
Position of HKsidechainbackbonesminimSSnoH.pdb (#4.2) relative to
cryosparc_P2_J149_005_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.25261883 -0.94716746 -0.19762977 196.77316911  
-0.71155852 -0.32026931 0.62538951 149.73225059  
-0.65564335 -0.01736002 -0.75487114 253.03448771  
Axis -0.78035831 0.55607150 0.28605139  
Axis point 0.00000000 179.82681983 142.07031379  
Rotation angle (degrees) 155.68017130  
Shift along axis 2.08912598  
  

> matchmaker #11 to #4.2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKsidechainbackbonesminimSSnoH.pdb, chain A (#4.2) with
HKD3Helix.pdb, chain A (#11), sequence alignment score = 83  
RMSD between 16 pruned atom pairs is 0.621 angstroms; (across all 17 pairs:
1.339)  
  

> matchmaker #9 to #11

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKD3Helix.pdb, chain A (#11) with HKD1Helix.pdb, chain A (#9),
sequence alignment score = 39.9  
RMSD between 15 pruned atom pairs is 0.442 angstroms; (across all 17 pairs:
1.133)  
  

> matchmaker #10 to #11

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKD3Helix.pdb, chain A (#11) with HKD2Helix.pdb, chain A (#10),
sequence alignment score = 43.2  
RMSD between 17 pruned atom pairs is 0.393 angstroms; (across all 17 pairs:
0.393)  
  

> matchmaker #7 to #10

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKD2Helix.pdb, chain A (#10) with
HKsidechainbackbonesminimSSnoH.pdb, chain A (#7), sequence alignment score =
83.4  
RMSD between 17 pruned atom pairs is 0.000 angstroms; (across all 17 pairs:
0.000)  
  

> volume #2 level 0.1389

> volume #2 level 0.1909

> volume #2 level 0.1593

> view matrix models
> #4,0.0065033,0.36509,-0.93095,178.83,-0.30086,0.88855,0.34636,11.827,0.95365,0.27783,0.11562,-57.969

> undo

> select clear

> hide #!4.2 models

> hide #!4 models

> hide #11 models

> hide #10 models

> hide #9 models

> hide #7 models

> show #!4.2 models

> volume #2 level 0.1519

> hide #!4.2 models

> volume #2 level 0.1645

> volume #2 level 0.1537

> volume #2 level 0.1392

> volume #2 level 0.1555

> volume #2 level 0.1736

> volume #2 level 0.1609

> show #!4.2 models

> hide #!1 models

[Repeated 1 time(s)]

> volume #2 level 0.1665

> volume #2 level 0.146

> show #11 models

> show #10 models

> show #9 models

> fitmap #9 inMap #2

Fit molecule HKD1Helix.pdb (#9) to map
cryosparc_P2_J149_005_volume_map_sharp.mrc (#2) using 136 atoms  
average map value = 0.1235, steps = 92  
shifted from previous position = 3.41  
rotated from previous position = 21.4 degrees  
atoms outside contour = 87, contour level = 0.14605  
  
Position of HKD1Helix.pdb (#9) relative to
cryosparc_P2_J149_005_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.60043282 0.12566255 0.78974005 -48.89759927  
0.78305492 -0.29269157 -0.54877741 52.97132657  
0.16218949 0.94791380 -0.27414231 86.14291325  
Axis 0.85475420 0.35839155 0.37543408  
Axis point 0.00000000 8.22759011 70.92148182  
Rotation angle (degrees) 118.89464309  
Shift along axis 9.53003287  
  

> fitmap #10 inMap #2

Fit molecule HKD2Helix.pdb (#10) to map
cryosparc_P2_J149_005_volume_map_sharp.mrc (#2) using 144 atoms  
average map value = 0.1259, steps = 88  
shifted from previous position = 2.98  
rotated from previous position = 19.6 degrees  
atoms outside contour = 101, contour level = 0.14605  
  
Position of HKD2Helix.pdb (#10) relative to
cryosparc_P2_J149_005_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.77116992 -0.40054614 -0.49483304 271.90626375  
0.63284799 -0.56690344 -0.52737454 117.26096245  
-0.06928472 -0.71984948 0.69066370 81.68192824  
Axis -0.16972535 -0.37525061 0.91125204  
Axis point 124.56173439 121.38023776 0.00000000  
Rotation angle (degrees) 145.45739993  
Shift along axis -15.71880985  
  

> fitmap #11 inMap #2

Fit molecule HKD3Helix.pdb (#11) to map
cryosparc_P2_J149_005_volume_map_sharp.mrc (#2) using 135 atoms  
average map value = 0.1206, steps = 104  
shifted from previous position = 3.25  
rotated from previous position = 26.8 degrees  
atoms outside contour = 95, contour level = 0.14605  
  
Position of HKD3Helix.pdb (#11) relative to
cryosparc_P2_J149_005_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.47562614 -0.12417566 0.87083878 -11.84361644  
-0.15542678 -0.98627322 -0.05574635 206.37520777  
0.86580731 -0.10883725 -0.48839755 46.38033769  
Axis -0.85892400 0.08140104 -0.50559216  
Axis point 0.00000000 103.05972161 24.82165690  
Rotation angle (degrees) 178.22896517  
Shift along axis 3.52238847  
  

> fitmap #4.2 inMap #2

Fit molecule HKsidechainbackbonesminimSSnoH.pdb (#4.2) to map
cryosparc_P2_J149_005_volume_map_sharp.mrc (#2) using 143 atoms  
average map value = 0.1189, steps = 28  
shifted from previous position = 0.0103  
rotated from previous position = 0.0965 degrees  
atoms outside contour = 99, contour level = 0.14605  
  
Position of HKsidechainbackbonesminimSSnoH.pdb (#4.2) relative to
cryosparc_P2_J149_005_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999882 -0.00069047 -0.00136899 0.19324542  
0.00069142 0.99999952 0.00069528 -0.15225599  
0.00136851 -0.00069622 0.99999882 -0.09632381  
Axis -0.41321911 -0.81292684 0.41036560  
Axis point 71.82567281 0.00000000 142.42316273  
Rotation angle (degrees) 0.09647074  
Shift along axis 0.00439231  
  

> select add #7

4915 atoms, 5047 bonds, 626 residues, 1 model selected  

> select subtract #7

Nothing selected  

> show #7 models

> matchmaker #7 to #9

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKD1Helix.pdb, chain A (#9) with
HKsidechainbackbonesminimSSnoH.pdb, chain A (#7), sequence alignment score =
82.2  
RMSD between 17 pruned atom pairs is 0.000 angstroms; (across all 17 pairs:
0.000)  
  

> matchmaker #7 to #10

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKD2Helix.pdb, chain A (#10) with
HKsidechainbackbonesminimSSnoH.pdb, chain A (#7), sequence alignment score =
83.4  
RMSD between 17 pruned atom pairs is 0.000 angstroms; (across all 17 pairs:
0.000)  
  

> matchmaker #7 to #11

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKD3Helix.pdb, chain A (#11) with
HKsidechainbackbonesminimSSnoH.pdb, chain A (#7), sequence alignment score =
83.6  
RMSD between 17 pruned atom pairs is 0.000 angstroms; (across all 17 pairs:
0.000)  
  

> matchmaker #7 to #10

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKD2Helix.pdb, chain A (#10) with
HKsidechainbackbonesminimSSnoH.pdb, chain A (#7), sequence alignment score =
83.4  
RMSD between 17 pruned atom pairs is 0.000 angstroms; (across all 17 pairs:
0.000)  
  

QAccessibleTable::child: Invalid index at: 3 0  

QAccessibleTable::child: Invalid index at: 3 1  

QAccessibleTable::child: Invalid index at: 3 2  

QAccessibleTable::child: Invalid index at: 3 3  

QAccessibleTable::child: Invalid index at: 4 0  

QAccessibleTable::child: Invalid index at: 4 1  

QAccessibleTable::child: Invalid index at: 4 2  

QAccessibleTable::child: Invalid index at: 4 3  

QAccessibleTable::child: Invalid index at: 5 0  

QAccessibleTable::child: Invalid index at: 5 1  

QAccessibleTable::child: Invalid index at: 5 2  

QAccessibleTable::child: Invalid index at: 5 3  

QAccessibleTable::child: Invalid index at: 6 0  

QAccessibleTable::child: Invalid index at: 6 1  

QAccessibleTable::child: Invalid index at: 6 2  

QAccessibleTable::child: Invalid index at: 6 3  

QAccessibleTable::child: Invalid index at: 7 0  

QAccessibleTable::child: Invalid index at: 7 1  

QAccessibleTable::child: Invalid index at: 7 2  

QAccessibleTable::child: Invalid index at: 7 3  

QAccessibleTable::child: Invalid index at: 8 0  

QAccessibleTable::child: Invalid index at: 8 1  

QAccessibleTable::child: Invalid index at: 8 2  

QAccessibleTable::child: Invalid index at: 8 3  

QAccessibleTable::child: Invalid index at: 9 0  

QAccessibleTable::child: Invalid index at: 9 1  

QAccessibleTable::child: Invalid index at: 9 2  

QAccessibleTable::child: Invalid index at: 9 3  

QAccessibleTable::child: Invalid index at: 10 0  

QAccessibleTable::child: Invalid index at: 10 1  

QAccessibleTable::child: Invalid index at: 10 2  

QAccessibleTable::child: Invalid index at: 10 3  

QAccessibleTable::child: Invalid index at: 11 0  

QAccessibleTable::child: Invalid index at: 11 1  

QAccessibleTable::child: Invalid index at: 11 2  

QAccessibleTable::child: Invalid index at: 11 3  

QAccessibleTable::child: Invalid index at: 12 0  

QAccessibleTable::child: Invalid index at: 12 1  

QAccessibleTable::child: Invalid index at: 12 2  

QAccessibleTable::child: Invalid index at: 12 3  

QAccessibleTable::child: Invalid index at: 13 0  

QAccessibleTable::child: Invalid index at: 13 1  

QAccessibleTable::child: Invalid index at: 13 2  

QAccessibleTable::child: Invalid index at: 13 3  

QAccessibleTable::child: Invalid index at: 14 0  

QAccessibleTable::child: Invalid index at: 14 1  

QAccessibleTable::child: Invalid index at: 14 2  

QAccessibleTable::child: Invalid index at: 14 3  

QAccessibleTable::child: Invalid index at: 15 0  

QAccessibleTable::child: Invalid index at: 15 1  

QAccessibleTable::child: Invalid index at: 15 2  

QAccessibleTable::child: Invalid index at: 15 3  

QAccessibleTable::child: Invalid index at: 16 0  

QAccessibleTable::child: Invalid index at: 16 1  

QAccessibleTable::child: Invalid index at: 16 2  

QAccessibleTable::child: Invalid index at: 16 3  

> save T:/PhenixProjects/HK_hu_Prediction/MapJom149Predictions.cxs

> select ::name="CYS"

210 atoms, 184 bonds, 35 residues, 2 models selected  

> show (#7 & sel) target ab

> select clear

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> select #7:239

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #7:239-361

968 atoms, 989 bonds, 123 residues, 1 model selected  

QAccessibleTable::child: Invalid index at: 3 0  

QAccessibleTable::child: Invalid index at: 3 1  

QAccessibleTable::child: Invalid index at: 3 2  

QAccessibleTable::child: Invalid index at: 3 3  

QAccessibleTable::child: Invalid index at: 4 0  

QAccessibleTable::child: Invalid index at: 4 1  

QAccessibleTable::child: Invalid index at: 4 2  

QAccessibleTable::child: Invalid index at: 4 3  

QAccessibleTable::child: Invalid index at: 5 0  

QAccessibleTable::child: Invalid index at: 5 1  

QAccessibleTable::child: Invalid index at: 5 2  

QAccessibleTable::child: Invalid index at: 5 3  

QAccessibleTable::child: Invalid index at: 6 0  

QAccessibleTable::child: Invalid index at: 6 1  

QAccessibleTable::child: Invalid index at: 6 2  

QAccessibleTable::child: Invalid index at: 6 3  

QAccessibleTable::child: Invalid index at: 7 0  

QAccessibleTable::child: Invalid index at: 7 1  

QAccessibleTable::child: Invalid index at: 7 2  

QAccessibleTable::child: Invalid index at: 7 3  

QAccessibleTable::child: Invalid index at: 8 0  

QAccessibleTable::child: Invalid index at: 8 1  

QAccessibleTable::child: Invalid index at: 8 2  

QAccessibleTable::child: Invalid index at: 8 3  

QAccessibleTable::child: Invalid index at: 9 0  

QAccessibleTable::child: Invalid index at: 9 1  

QAccessibleTable::child: Invalid index at: 9 2  

QAccessibleTable::child: Invalid index at: 9 3  

QAccessibleTable::child: Invalid index at: 10 0  

QAccessibleTable::child: Invalid index at: 10 1  

QAccessibleTable::child: Invalid index at: 10 2  

QAccessibleTable::child: Invalid index at: 10 3  

QAccessibleTable::child: Invalid index at: 11 0  

QAccessibleTable::child: Invalid index at: 11 1  

QAccessibleTable::child: Invalid index at: 11 2  

QAccessibleTable::child: Invalid index at: 11 3  

QAccessibleTable::child: Invalid index at: 12 0  

QAccessibleTable::child: Invalid index at: 12 1  

QAccessibleTable::child: Invalid index at: 12 2  

QAccessibleTable::child: Invalid index at: 12 3  

QAccessibleTable::child: Invalid index at: 13 0  

QAccessibleTable::child: Invalid index at: 13 1  

QAccessibleTable::child: Invalid index at: 13 2  

QAccessibleTable::child: Invalid index at: 13 3  

QAccessibleTable::child: Invalid index at: 14 0  

QAccessibleTable::child: Invalid index at: 14 1  

QAccessibleTable::child: Invalid index at: 14 2  

QAccessibleTable::child: Invalid index at: 14 3  

QAccessibleTable::child: Invalid index at: 15 0  

QAccessibleTable::child: Invalid index at: 15 1  

QAccessibleTable::child: Invalid index at: 15 2  

QAccessibleTable::child: Invalid index at: 15 3  

QAccessibleTable::child: Invalid index at: 16 0  

QAccessibleTable::child: Invalid index at: 16 1  

QAccessibleTable::child: Invalid index at: 16 2  

QAccessibleTable::child: Invalid index at: 16 3  

> save T:/PhenixProjects/HK_hu_Prediction/MapJom149Predictions.cxs

——— End of log from Thu Nov 24 15:31:19 2022 ———

opened ChimeraX session  

> show #!2 models

> select #7:238-592

2786 atoms, 2867 bonds, 355 residues, 1 model selected  

> ui mousemode right "translate selected atoms"

> select #7:244-592

2738 atoms, 2816 bonds, 349 residues, 1 model selected  

> select #7:238-592

2786 atoms, 2867 bonds, 355 residues, 1 model selected  

> select #7:241-592

2759 atoms, 2839 bonds, 352 residues, 1 model selected  

> select #7:241-357

922 atoms, 943 bonds, 117 residues, 1 model selected  

> select #7:358-574

1700 atoms, 1753 bonds, 217 residues, 1 model selected  

> select #7:358-504

1179 atoms, 1217 bonds, 147 residues, 1 model selected  

> ui tool show "Fit in Map"

> fitmap sel inMap #1

Fit molecule HKsidechainbackbonesminimSSnoH.pdb (#7) to map
cryosparc_P2_J571_006_volume_map_sharp.mrc (#1) using 1179 atoms  
average map value = 0.01251, steps = 64  
shifted from previous position = 1.8  
rotated from previous position = 8.81 degrees  
atoms outside contour = 1152, contour level = 0.15986  
  
Position of HKsidechainbackbonesminimSSnoH.pdb (#7) relative to
cryosparc_P2_J571_006_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.30930840 -0.88642878 -0.34434334 105.05269906  
0.94465907 0.32802789 0.00411690 116.35647967  
0.10930488 -0.32656045 0.93883477 88.64083059  
Axis -0.17265859 -0.23686612 0.95607712  
Axis point -27.82759349 147.80094425 0.00000000  
Rotation angle (degrees) 73.25662605  
Shift along axis 39.04831060  
  

> select #7:501-584

635 atoms, 654 bonds, 84 residues, 1 model selected  

> fitmap sel inMap #1

Fit molecule HKsidechainbackbonesminimSSnoH.pdb (#7) to map
cryosparc_P2_J571_006_volume_map_sharp.mrc (#1) using 635 atoms  
average map value = 0.02353, steps = 116  
shifted from previous position = 5.91  
rotated from previous position = 15.8 degrees  
atoms outside contour = 592, contour level = 0.15986  
  
Position of HKsidechainbackbonesminimSSnoH.pdb (#7) relative to
cryosparc_P2_J571_006_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.18712476 -0.89740797 -0.39955383 103.56233733  
0.91648883 0.30589663 -0.25782840 119.21087852  
0.35359943 -0.31794054 0.87970521 84.57309651  
Axis -0.03059202 -0.38329155 0.92312064  
Axis point -32.10902203 145.48185221 0.00000000  
Rotation angle (degrees) 79.25937404  
Shift along axis 29.21046752  
  

> ui mousemode right "move picked models"

> view matrix models
> #7,0.18712,-0.89741,-0.39955,104.55,0.91649,0.3059,-0.25783,119.61,0.3536,-0.31794,0.87971,84.879

> ui mousemode right "rotate selected models"

> view matrix models
> #7,0.20284,-0.87153,-0.44641,105.13,0.9253,0.31978,-0.20387,118.92,0.32044,-0.37171,0.87129,85.01

> ui mousemode right "translate selected atoms"

> select clear

> select #7:501-584

635 atoms, 654 bonds, 84 residues, 1 model selected  

> select clear

> select #7:501-584

635 atoms, 654 bonds, 84 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> ui mousemode right rotate

> ui mousemode right "rotate selected models"

> view matrix models
> #7,0.18291,-0.87645,-0.4454,105.13,0.92131,0.31092,-0.23349,119.31,0.34312,-0.36764,0.86435,85.077

> view matrix models
> #7,0.20265,-0.87672,-0.43622,105,0.92759,0.31464,-0.20143,118.89,0.31385,-0.36382,0.877,84.944

> view matrix models
> #7,0.20292,-0.89627,-0.39436,104.45,0.93565,0.29625,-0.19184,118.75,0.28877,-0.33005,0.89871,84.693

> view matrix models
> #7,0.16933,-0.88348,-0.43679,105.04,0.9211,0.29951,-0.24874,119.51,0.35058,-0.36021,0.86449,85.069

> view matrix models
> #7,0.21827,-0.81962,-0.5297,106.2,0.90784,0.36967,-0.19792,118.87,0.35804,-0.43768,0.82477,85.564

> ui tool show Matchmaker

> matchmaker #7 to #10

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKD2Helix.pdb, chain A (#10) with
HKsidechainbackbonesminimSSnoH.pdb, chain A (#7), sequence alignment score =
83.4  
RMSD between 17 pruned atom pairs is 0.000 angstroms; (across all 17 pairs:
0.000)  
  

> show #!2 models

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 51 residues in model #7 to IUPAC-IUB
standards.  

> clipper associate #2 toModel #7

Opened cryosparc_P2_J149_005_volume_map_sharp.mrc as #7.1.1.1, grid size
256,256,256, pixel 0.86, shown at step 1, values float32  

> select add #7.2

4915 atoms, 5047 bonds, 626 residues, 6 models selected  

> select add #7.2

4915 atoms, 5047 bonds, 626 residues, 6 models selected  

> select add #7.2

4915 atoms, 5047 bonds, 626 residues, 6 models selected  

> select add #7.2

4915 atoms, 5047 bonds, 626 residues, 6 models selected  

> select add #7.2

4915 atoms, 5047 bonds, 626 residues, 6 models selected  

> ui mousemode right minimize

> ui mousemode right "bond rotation"

> ui tool show "Ramachandran Plot"

> matchmaker #5,9,11#!4.2#!7.2 to #10

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HKD2Helix.pdb, chain A (#10) with
hhpred_model_With_Conservation_Scores.pdb, chain (blank) (#5), sequence
alignment score = 89.4  
RMSD between 17 pruned atom pairs is 1.019 angstroms; (across all 17 pairs:
1.019)  
  
Matchmaker HKD2Helix.pdb, chain A (#10) with HKD1Helix.pdb, chain A (#9),
sequence alignment score = 30.6  
RMSD between 17 pruned atom pairs is 0.978 angstroms; (across all 17 pairs:
0.978)  
  
Matchmaker HKD2Helix.pdb, chain A (#10) with HKD3Helix.pdb, chain A (#11),
sequence alignment score = 43.2  
RMSD between 17 pruned atom pairs is 0.393 angstroms; (across all 17 pairs:
0.393)  
  
Matchmaker HKD2Helix.pdb, chain A (#10) with
HKsidechainbackbonesminimSSnoH.pdb, chain A (#4.2), sequence alignment score =
67.2  
Fewer than 3 residues aligned; cannot match HKD2Helix.pdb, chain A with
HKsidechainbackbonesminimSSnoH.pdb, chain A  
Matchmaker HKD2Helix.pdb, chain A (#10) with
HKsidechainbackbonesminimSSnoH.pdb, chain A (#7.2), sequence alignment score =
83.4  
RMSD between 17 pruned atom pairs is 0.000 angstroms; (across all 17 pairs:
0.000)  
  

> select add #7.2

4915 atoms, 5047 bonds, 626 residues, 6 models selected  

> hide #!7.2 models

> show #!7.2 models

> hide #!7 models

> show #!7 models

> hide #7.3 models

> show #7.3 models

> hide #9 models

> show #9 models

> isolde tutorial

[Repeated 1 time(s)]

> sim start

Unknown command: sim start  

> isolde sim start

ISOLDE: stopped sim  

> addh #7.2

Summary of feedback from adding hydrogens to
HKsidechainbackbonesminimSSnoH.pdb #7.2  
---  
notes | No usable SEQRES records for HKsidechainbackbonesminimSSnoH.pdb (#7.2)
chain A; guessing termini instead  
Chain-initial residues that are actual N termini:
HKsidechainbackbonesminimSSnoH.pdb #7.2/A GLN 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:
HKsidechainbackbonesminimSSnoH.pdb #7.2/A SER 626  
Chain-final residues that are not actual C termini:  
417 hydrogen bonds  
4683 hydrogens added  
  

> isolde sim start

ISOLDE: started sim  

> isolde sim start

Simulation already running!  

> select add #7

9598 atoms, 9730 bonds, 626 residues, 18 models selected  

> select add #7

9598 atoms, 9730 bonds, 626 residues, 18 models selected  

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #7.3 models

> hide #!7.2 models

> hide #!7.1 models

> show #!7.1 models

> hide #!7.1 models

> show #!7.1 models

> hide #!7.1 models

> show #!7.1 models

QAccessibleTable::child: Invalid index at: 5 0  

QAccessibleTable::child: Invalid index at: 5 1  

QAccessibleTable::child: Invalid index at: 5 2  

QAccessibleTable::child: Invalid index at: 5 3  

QAccessibleTable::child: Invalid index at: 6 0  

QAccessibleTable::child: Invalid index at: 6 1  

QAccessibleTable::child: Invalid index at: 6 2  

QAccessibleTable::child: Invalid index at: 6 3  

QAccessibleTable::child: Invalid index at: 7 0  

QAccessibleTable::child: Invalid index at: 7 1  

QAccessibleTable::child: Invalid index at: 7 2  

QAccessibleTable::child: Invalid index at: 7 3  

QAccessibleTable::child: Invalid index at: 8 0  

QAccessibleTable::child: Invalid index at: 8 1  

QAccessibleTable::child: Invalid index at: 8 2  

QAccessibleTable::child: Invalid index at: 8 3  

QAccessibleTable::child: Invalid index at: 9 0  

QAccessibleTable::child: Invalid index at: 9 1  

QAccessibleTable::child: Invalid index at: 9 2  

QAccessibleTable::child: Invalid index at: 9 3  

QAccessibleTable::child: Invalid index at: 10 0  

QAccessibleTable::child: Invalid index at: 10 1  

QAccessibleTable::child: Invalid index at: 10 2  

QAccessibleTable::child: Invalid index at: 10 3  

QAccessibleTable::child: Invalid index at: 11 0  

QAccessibleTable::child: Invalid index at: 11 1  

QAccessibleTable::child: Invalid index at: 11 2  

QAccessibleTable::child: Invalid index at: 11 3  

QAccessibleTable::child: Invalid index at: 12 0  

QAccessibleTable::child: Invalid index at: 12 1  

QAccessibleTable::child: Invalid index at: 12 2  

QAccessibleTable::child: Invalid index at: 12 3  

QAccessibleTable::child: Invalid index at: 13 0  

QAccessibleTable::child: Invalid index at: 13 1  

QAccessibleTable::child: Invalid index at: 13 2  

QAccessibleTable::child: Invalid index at: 13 3  

QAccessibleTable::child: Invalid index at: 14 0  

QAccessibleTable::child: Invalid index at: 14 1  

QAccessibleTable::child: Invalid index at: 14 2  

QAccessibleTable::child: Invalid index at: 14 3  

QAccessibleTable::child: Invalid index at: 15 0  

QAccessibleTable::child: Invalid index at: 15 1  

QAccessibleTable::child: Invalid index at: 15 2  

QAccessibleTable::child: Invalid index at: 15 3  

QAccessibleTable::child: Invalid index at: 16 0  

QAccessibleTable::child: Invalid index at: 16 1  

QAccessibleTable::child: Invalid index at: 16 2  

QAccessibleTable::child: Invalid index at: 16 3  

> save T:/PhenixProjects/HK_hu_Prediction/MapJob149PredictionsIsolda.cxs

> hide #!7.1 models

> hide #11 models

> hide #10 models

> hide #9 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> show #4.1 models

> hide #4.1 models

> hide #!4 models

> show #!7.1 models

> show #!7.2 models

> hide #!7.1 models

> show #!7.1 models

> select add #7.2

9598 atoms, 9730 bonds, 626 residues, 18 models selected  

> select add #7.2

9598 atoms, 9730 bonds, 626 residues, 18 models selected  

> select add #7.2

9598 atoms, 9730 bonds, 626 residues, 18 models selected  

> select add #7.2

9598 atoms, 9730 bonds, 626 residues, 18 models selected  

> select add #7.2

9598 atoms, 9730 bonds, 626 residues, 18 models selected  

> select subtract #7.3

9598 atoms, 9730 bonds, 626 residues, 17 models selected  

> select add #7.3

9598 atoms, 9730 bonds, 626 residues, 18 models selected  

> select subtract #7.1

9598 atoms, 9730 bonds, 626 residues, 13 models selected  

> select add #7

9598 atoms, 9730 bonds, 626 residues, 18 models selected  

> select add #7

9598 atoms, 9730 bonds, 626 residues, 18 models selected  

> select subtract #7.1

9598 atoms, 9730 bonds, 626 residues, 13 models selected  

> select add #7.2

9598 atoms, 9730 bonds, 626 residues, 13 models selected  

> select add #7.2

9598 atoms, 9730 bonds, 626 residues, 13 models selected  

> select subtract #7.3

9598 atoms, 9730 bonds, 626 residues, 12 models selected  

> select add #7.1

9598 atoms, 9730 bonds, 626 residues, 17 models selected  

> select subtract #7.1

9598 atoms, 9730 bonds, 626 residues, 12 models selected  

> select clear

QAccessibleTable::child: Invalid index at: 6 0  

QAccessibleTable::child: Invalid index at: 6 1  

QAccessibleTable::child: Invalid index at: 6 2  

QAccessibleTable::child: Invalid index at: 6 3  

QAccessibleTable::child: Invalid index at: 7 0  

QAccessibleTable::child: Invalid index at: 7 1  

QAccessibleTable::child: Invalid index at: 7 2  

QAccessibleTable::child: Invalid index at: 7 3  

QAccessibleTable::child: Invalid index at: 8 0  

QAccessibleTable::child: Invalid index at: 8 1  

QAccessibleTable::child: Invalid index at: 8 2  

QAccessibleTable::child: Invalid index at: 8 3  

QAccessibleTable::child: Invalid index at: 9 0  

QAccessibleTable::child: Invalid index at: 9 1  

QAccessibleTable::child: Invalid index at: 9 2  

QAccessibleTable::child: Invalid index at: 9 3  

QAccessibleTable::child: Invalid index at: 10 0  

QAccessibleTable::child: Invalid index at: 10 1  

QAccessibleTable::child: Invalid index at: 10 2  

QAccessibleTable::child: Invalid index at: 10 3  

QAccessibleTable::child: Invalid index at: 11 0  

QAccessibleTable::child: Invalid index at: 11 1  

QAccessibleTable::child: Invalid index at: 11 2  

QAccessibleTable::child: Invalid index at: 11 3  

QAccessibleTable::child: Invalid index at: 12 0  

QAccessibleTable::child: Invalid index at: 12 1  

QAccessibleTable::child: Invalid index at: 12 2  

QAccessibleTable::child: Invalid index at: 12 3  

QAccessibleTable::child: Invalid index at: 13 0  

QAccessibleTable::child: Invalid index at: 13 1  

QAccessibleTable::child: Invalid index at: 13 2  

QAccessibleTable::child: Invalid index at: 13 3  

QAccessibleTable::child: Invalid index at: 14 0  

QAccessibleTable::child: Invalid index at: 14 1  

QAccessibleTable::child: Invalid index at: 14 2  

QAccessibleTable::child: Invalid index at: 14 3  

QAccessibleTable::child: Invalid index at: 15 0  

QAccessibleTable::child: Invalid index at: 15 1  

QAccessibleTable::child: Invalid index at: 15 2  

QAccessibleTable::child: Invalid index at: 15 3  

QAccessibleTable::child: Invalid index at: 16 0  

QAccessibleTable::child: Invalid index at: 16 1  

QAccessibleTable::child: Invalid index at: 16 2  

QAccessibleTable::child: Invalid index at: 16 3  

> save T:/PhenixProjects/HK_hu_Prediction/MapJob149PredictionsIsolda2.cxs

——— End of log from Thu Nov 24 16:47:36 2022 ———

opened ChimeraX session  




OpenGL version: 3.3.0 NVIDIA 526.86
OpenGL renderer: NVIDIA GeForce GTX 1060 6GB/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: pl_PL.cp1250
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: windows

Manufacturer: ATComputers
Model: OPTIMUS 
OS: Microsoft Windows 11 Home (Build 22000)
Memory: 34,296,348,672
MaxProcessMemory: 137,438,953,344
CPU: 6 Intel(R) Core(TM) i5-8400 CPU @ 2.80GHz
OSLanguage: pl-PL

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2022.5.18.1
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.18.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.4
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StarMap: 1.1.70
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    pyqtgraph: 0.13.1
    python-dateutil: 2.8.2
    pytz: 2022.1
    pywin32: 303
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    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
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0
    WMI: 1.5.1

[Tristan Croll]

Loading the new session deleted the existing model while a simulation was actively running. I've finally gotten around to making sure ISOLDE handles that scenario gracefully - will be in the next release.