ISOLDE: 'MDFFMgr' object has no attribute 'was_deleted'

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.9rc202411130312 (2024-11-13 03:12:11 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9rc202411130312 (2024-11-13)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open D:\\\316W_diss_3.cxs

restore_snapshot for "NXmapHandler" returned None  

restore_snapshot for "FastVolumeSurface" returned None  

Exception ignored in: <function Drawing.__del__ at 0x0000025DAAD3EFC0>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9rc202411130312\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1215, in __del__  
if not self.was_deleted:  
^^^^^^^^^^^^^^^^  
AttributeError: 'MDFFMgr' object has no attribute 'was_deleted'  

restore_snapshot for "MDFFMgr" returned None  

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9rc202411130312\bin\Lib\site-
packages\chimerax\core\session.py", line 854, in restore  
self.add_state_manager(name, data)  
File "C:\Program Files\ChimeraX 1.9rc202411130312\bin\Lib\site-
packages\chimerax\core\session.py", line 647, in add_state_manager  
raise ValueError(  
ValueError: container "Isolde Residue Stepper Manager" of type "<class
'NoneType'>" does not have snapshot methods and does not have clear method  
  
Log from Wed Nov 13 21:59:07 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "C:\Users\daniellem\Desktop\CryoEM workshop\Dissertation final 316W
> model\316W_diss_2.cxs" format session

Opened DeepEMhancer_Danielle_4_9.mrc as #1.1.1.1, grid size 128,128,128, pixel
1.66, shown at level 0.12, step 1, values float32  
Log from Wed Nov 13 21:10:41 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "C:\Users\daniellem\Desktop\CryoEM workshop\Dissertation final 316W
> model\Isolde_316W.cxs" format session

Opened DeepEMhancer_Danielle_4_9.mrc as #1, grid size 128,128,128, pixel 1.66,
shown at level 0.171, step 1, values float32  
Log from Wed Nov 13 16:05:25 2024 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> C:\\\Users\\\daniellem\\\Downloads\\\ChimeraX_ISOLDE-1.8-cp311-cp311-win_amd64.whl

Unrecognized file suffix '.whl'  

> open "C:/Users/daniellem/Desktop/CryoEM
> workshop/DeepEMhancer_Danielle_4_9.mrc"

Opened DeepEMhancer_Danielle_4_9.mrc as #1, grid size 128,128,128, pixel 1.66,
shown at level 0.171, step 1, values float32  

> open
> C:/Users/daniellem/Downloads/fold_202411_11_fresh/fold_202411_11_fresh_model_0.cif

Chain information for fold_202411_11_fresh_model_0.cif #2  
---  
Chain | Description  
A B C | .  
  

> fitmap #2 inMap #1

Fit molecule fold_202411_11_fresh_model_0.cif (#2) to map
DeepEMhancer_Danielle_4_9.mrc (#1) using 16827 atoms  
average map value = 0.07522, steps = 844  
shifted from previous position = 175  
rotated from previous position = 54.2 degrees  
atoms outside contour = 14504, contour level = 0.17065  
  
Position of fold_202411_11_fresh_model_0.cif (#2) relative to
DeepEMhancer_Danielle_4_9.mrc (#1) coordinates:  
Matrix rotation and translation  
0.64792760 -0.62354966 -0.43746502 96.82197592  
0.74386964 0.64153909 0.18731140 110.82058535  
0.16385295 -0.44678117 0.87951055 97.73764625  
Axis -0.39073889 -0.37054262 0.84262761  
Axis point -58.82632784 190.65888686 0.00000000  
Rotation angle (degrees) 54.23312860  
Shift along axis 3.46057824  
  

> select add #2

16827 atoms, 17253 bonds, 2103 residues, 1 model selected  

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.90908,-0.24195,0.33917,98.645,-0.23659,0.3703,0.89828,112.27,-0.34293,-0.89685,0.27939,96.701

> view matrix models
> #2,0.53124,-0.06761,0.84452,97.684,-0.82947,0.1615,0.5347,110.22,-0.17254,-0.98455,0.029713,96.843

> view matrix models
> #2,0.41491,-0.042433,0.90887,97.121,-0.90723,-0.095219,0.40971,113.02,0.069157,-0.99455,-0.078003,97.834

> view matrix models
> #2,0.75288,0.027834,0.65757,97.316,-0.63298,-0.24308,0.73502,119.44,0.1803,-0.96961,-0.16539,97.49

> ui mousemode right "move picked models"

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.87103,0.31614,0.37598,92.913,-0.28071,-0.30778,0.90911,123.97,0.40312,-0.8974,-0.17934,97.549

> view matrix models
> #2,0.91536,0.086966,0.39313,97.148,-0.39835,0.053566,0.91567,117.07,0.058573,-0.99477,0.083675,97.517

> view matrix models
> #2,0.69172,-0.58695,0.42073,107.25,-0.39031,0.18632,0.90163,114.71,-0.60761,-0.78789,-0.10021,89.196

> view matrix models
> #2,0.65444,-0.63502,0.41045,107.75,-0.39395,0.17697,0.90193,114.84,-0.64538,-0.75195,-0.13435,88.167

> view matrix models
> #2,0.74125,-0.50299,0.44446,106.36,-0.46474,0.093202,0.88053,115.65,-0.48433,-0.85925,-0.16467,90.397

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.74125,-0.50299,0.44446,122.67,-0.46474,0.093202,0.88053,118.02,-0.48433,-0.85925,-0.16467,90.501

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.83206,-0.25682,0.49165,119.4,-0.49196,0.067772,0.86798,118.23,-0.25624,-0.96408,-0.069956,93.922

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.83206,-0.25682,0.49165,110.78,-0.49196,0.067772,0.86798,107.87,-0.25624,-0.96408,-0.069956,93.209

> select subtract #2

Nothing selected  

> 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  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 277 residues in model #2 to IUPAC-IUB
standards.  
Chain information for fold_202411_11_fresh_model_0.cif  
---  
Chain | Description  
2.2/A 2.2/B 2.2/C | .  
  
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: created disulfide bonds between the following residues:  
B125-B137; A125-A137; B484-B590; A120-A176; B355-B428; C484-C590; C181-C416;
A208-A219; A276-A309; B198-B227; B120-B176; A113-A185; B181-B416; B208-B219;
A181-A416; C120-C176; C125-C137; C198-C227; A484-A590; A362-A401; B583-B589;
A583-A589; C362-C401; A48-A68; B113-B185; B276-B309; C113-C185; C208-C219;
B362-B401; B48-B68; C48-C68; C276-C309; A198-A227; A355-A428; C355-C428;
C583-C589  

> save "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
> model/Isolde_316W.cxs"

> select add #2

16827 atoms, 17289 bonds, 2103 residues, 14 models selected  

> select subtract #1

16827 atoms, 17289 bonds, 2103 residues, 12 models selected  

> select add #2

16827 atoms, 17289 bonds, 2103 residues, 12 models selected  

> select add #2

16827 atoms, 17289 bonds, 2103 residues, 12 models selected  

> select add #2

16827 atoms, 17289 bonds, 2103 residues, 12 models selected  

> select subtract #2.1

16827 atoms, 17289 bonds, 2103 residues, 11 models selected  

> select add #2

16827 atoms, 17289 bonds, 2103 residues, 12 models selected  

> save "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
> model/Isolde_316W.cxs"

——— End of log from Wed Nov 13 16:05:25 2024 ———

opened ChimeraX session  

> ui mousemode right "rotate selected models"

> ui mousemode right rotate

> select add #2

16827 atoms, 17289 bonds, 2103 residues, 15 models selected  

> select add #2

16827 atoms, 17289 bonds, 2103 residues, 15 models selected  

> select subtract #2.1

16827 atoms, 17289 bonds, 2103 residues, 14 models selected  

> select #2

16827 atoms, 17289 bonds, 2103 residues, 15 models selected  

> select subtract #2.1

16827 atoms, 17289 bonds, 2103 residues, 14 models selected  

> select subtract #2.3

16827 atoms, 17289 bonds, 2103 residues, 13 models selected  

> ui mousemode right "move picked models"

> ui mousemode right "rotate selected models"

> stop isolde

Expected fewer arguments  

> select add #2

16827 atoms, 17289 bonds, 2103 residues, 15 models selected  

> deselect all

Unknown command: deselect all  

> deselect

Unknown command: deselect  

> ~select

Nothing selected  

> select add #2

16827 atoms, 17289 bonds, 2103 residues, 15 models selected  

> view matrix models
> #2,0.99575,-0.015637,0.090722,-4.4839,0.0014031,0.98793,0.15488,-10.121,-0.092049,-0.1541,0.98376,27.255

> view matrix models
> #2,0.78145,0.090022,-0.61745,60.114,0.035975,0.98139,0.18861,-15.794,0.62294,-0.1696,0.76367,-35.953

> view matrix models
> #2,0.71305,0.10657,-0.69297,71.605,-0.27531,0.95155,-0.13695,45.9,0.6448,0.28843,0.70784,-81.031

> view matrix models
> #2,0.89446,0.22625,-0.38569,16.741,-0.28596,0.95254,-0.10439,44.648,0.34377,0.20366,0.9167,-53.518

> view matrix models
> #2,0.94709,0.31726,0.048693,-29.856,-0.31545,0.94804,-0.041416,43.885,-0.059302,0.023864,0.99795,4.4102

> ui mousemode right "move picked models"

> view matrix models
> #2.2,1,5.6986e-16,-2.4286e-16,-9.5814,8.4893e-16,1,1.9082e-16,0.6637,-9.7145e-17,3.1225e-17,1,-0.41905

> select add #2

16827 atoms, 17289 bonds, 2103 residues, 15 models selected  

> ~select

Nothing selected  

> select add #1

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.99565,0.0035698,-0.093147,8.6107,0.0040819,0.99664,0.081827,-7.5691,0.093126,-0.081851,0.99228,-0.9953

> view matrix models
> #1,0.99643,0.0065949,-0.084219,7.3734,0.0032596,0.9932,0.11634,-10.247,0.084414,-0.1162,0.98963,4.0265

> ui mousemode right rotate

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.98436,-0.16331,-0.066065,25.793,0.1716,0.97369,0.14993,-30.516,0.039841,-0.15892,0.98649,14.137

> select subtract #1

Nothing selected  

> ~select

Nothing selected  

> select add #2

16827 atoms, 17289 bonds, 2103 residues, 15 models selected  

> ui mousemode right select

> ~select

Nothing selected  

> ~select

Nothing selected  

> clipper associate #1 toModel #2

Opened DeepEMhancer_Danielle_4_9.mrc as #2.1.1.1, grid size 128,128,128, pixel
1.66, shown at step 1, values float32  

> clipper associate #1 toModel #2

> volume #2.1.1.1 level 0.01818

> volume #2.1.1.1 level 0.006197

> volume #2.1.1.1 level 0.01884

> volume #2.1.1.1 level 0.01019

> volume #2.1.1.1 level 0.0042

> fitmap #2.2 inMap #2.1.1.1

Fit molecule fold_202411_11_fresh_model_0.cif (#2.2) to map
DeepEMhancer_Danielle_4_9.mrc (#2.1.1.1) using 16827 atoms  
average map value = 0, steps = 24  
shifted from previous position = 0  
rotated from previous position = 0 degrees  
atoms outside contour = 16827, contour level = 0.0042003  
  
Position of fold_202411_11_fresh_model_0.cif (#2.2) relative to
DeepEMhancer_Danielle_4_9.mrc (#2.1.1.1) coordinates:  
Matrix rotation and translation  
1.00000000 0.00000000 0.00000000 0.00000000  
0.00000000 1.00000000 0.00000000 0.00000000  
0.00000000 0.00000000 1.00000000 0.00000000  
Axis 0.00000000 0.00000000 1.00000000  
Axis point 0.00000000 0.00000000 0.00000000  
Rotation angle (degrees) 0.00000000  
Shift along axis 0.00000000  
  

> volume #2.1.1.1 color #ff6f82

> volume #2.1.1.1 orthoplanes xyz positionPlanes 64,64,64 style image region
> all

> mousemode rightMode "move planes"

> volume #2.1.1.1 orthoplanes xyz positionPlanes 64,64,64 style image region
> all

> mousemode rightMode "move planes"

> volume #2.1.1.1 orthoplanes xyz positionPlanes 64,64,64 style image region
> all

> mousemode rightMode "move planes"

> volume #2.1.1.1 orthoplanes xyz positionPlanes 64,64,64 style image region
> all

> mousemode rightMode "move planes"

> volume planes z style image imageMode "full region"

> mousemode rightMode "move planes"

> volume style mesh

[Repeated 1 time(s)]

> volume #2.1.1.1 style image region all imageMode "tilted slab"
> tiltedSlabAxis 0,0,1 tiltedSlabOffset 106.1 tiltedSlabSpacing 1.658
> tiltedSlabPlaneCount 10

> mousemode rightMode "rotate slab"

> volume planes z style image imageMode "full region"

> mousemode rightMode "move planes"

> volume #2.1.1.1 style image region all imageMode "tilted slab"
> tiltedSlabAxis 0,0,1 tiltedSlabOffset 106.1 tiltedSlabSpacing 1.658
> tiltedSlabPlaneCount 10

> mousemode rightMode "rotate slab"

> volume style mesh

> volume #2.1.1.1 change image level -0.0001408,0 level 0.1705,0.8 level
> 2.096,1

> volume #2.1.1.1 level 0.3019

> volume #2.1.1.1 orthoplanes xyz positionPlanes 64,64,64 style image region
> all

> mousemode rightMode "move planes"

> volume #2.1.1.1 orthoplanes xyz positionPlanes 64,64,64 style image region
> all

> mousemode rightMode "move planes"

> volume zone #2.1.1.1 nearAtoms #2.2 range 9.95

> volume region all imageMode "full region"

> volume unzone

> mousemode rightMode "crop volume"

> close #2.1.1.1

> select #1

Nothing selected  

> clipper associate #1 toModel #2

> close session

> open
> C:/Users/daniellem/Downloads/fold_202411_11_fresh/fold_202411_11_fresh_model_1.cif

Chain information for fold_202411_11_fresh_model_1.cif #1  
---  
Chain | Description  
A B C | .  
  

> open "C:/Users/daniellem/Desktop/CryoEM
> workshop/DeepEMhancer_Danielle_4_9.mrc"

Opened DeepEMhancer_Danielle_4_9.mrc as #2, grid size 128,128,128, pixel 1.66,
shown at level 0.171, step 1, values float32  

> clipper associate #2 toModel #1

Opened DeepEMhancer_Danielle_4_9.mrc as #1.1.1.1, grid size 128,128,128, pixel
1.66, shown at level 0, step 1, values float32  
Chain information for fold_202411_11_fresh_model_1.cif  
---  
Chain | Description  
1.2/A 1.2/B 1.2/C | .  
  

> zoom

Pixel size at center of rotation is 0.252  

> zoom

Pixel size at center of rotation is 0.252  

> volume #1.1.1.1 level 2.378e-07

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 286 residues in model #1.2 to IUPAC-IUB
standards.  
Done loading forcefield  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  

> volume #1.1.1.1 region 0,2,0,11,15,12

> set bgColor white

> set bgColor #ffffff00

> select add #1

16827 atoms, 17253 bonds, 2103 residues, 15 models selected  

> select add #1.2

16827 atoms, 17253 bonds, 2103 residues, 15 models selected  

> select add #1

16827 atoms, 17253 bonds, 2103 residues, 15 models selected  

> select add #1.2

16827 atoms, 17253 bonds, 2103 residues, 15 models selected  

> ~select

Nothing selected  

> view #1.1.1.1.2 clip false

No displayed objects specified.  

> view #1.1.1.1.2 clip false

No displayed objects specified.  

> view #1.1.1.1.2 clip false

No displayed objects specified.  

> show #1.1.1.1.2 target m

> hide #1.1.1.1.2 target m

> close #1.1.1.1.2

> hide target m

[Repeated 1 time(s)]

> close

> open
> C:\Users\daniellem\Downloads\fold_202411_11_fresh\fold_202411_11_fresh_model_1.cif
> format mmcif

Chain information for fold_202411_11_fresh_model_1.cif #1  
---  
Chain | Description  
A B C | .  
  

> open "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
> model/DeepEMhancer_Danielle_4_9.mrc"

Opened DeepEMhancer_Danielle_4_9.mrc as #2, grid size 128,128,128, pixel 1.66,
shown at level 0.171, step 1, values float32  

> volume #2 region 0,6,0,127,127,127

> select add #1

16827 atoms, 17253 bonds, 2103 residues, 1 model selected  

> volume #2 region 0,9,0,127,127,127

> volume #2 region 0,31,0,127,127,127

> volume #2 region 0,2,0,127,127,127

> volume #2 region 2,2,0,127,127,127

> volume #2 region 0,2,0,127,127,127

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.66525,-0.10274,0.73952,-3.3498,-0.70987,0.21988,0.66913,6.6393,-0.23135,-0.9701,0.073343,18.122

> view matrix models
> #1,0.66436,-0.098392,0.74091,-3.4057,-0.70806,0.23457,0.66606,6.4683,-0.23933,-0.96711,0.086172,18.055

> view matrix models
> #1,0.73489,-0.0012862,0.67819,-3.9016,-0.49398,0.68416,0.53657,1.0277,-0.46468,-0.72933,0.50214,14.374

> view matrix models
> #1,0.48401,-0.29693,0.82315,-0.71801,-0.38327,0.77371,0.50446,-0.064179,-0.78666,-0.55965,0.26068,14.723

> view matrix models
> #1,0.45881,-0.3301,0.82494,-0.27877,-0.38342,0.76399,0.51895,-0.033803,-0.80155,-0.5544,0.22396,14.879

> view matrix models
> #1,0.58787,-0.42542,0.68806,1.4842,-0.33441,0.64668,0.68555,-0.022276,-0.7366,-0.63311,0.2379,15.786

> ui mousemode right "move picked models"

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.58787,-0.42542,0.68806,89.581,-0.33441,0.64668,0.68555,125,-0.7366,-0.63311,0.2379,28.389

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.69323,-0.26637,0.66969,87.572,-0.39958,0.63127,0.6647,125.4,-0.59981,-0.72838,0.33118,28.789

> view matrix models
> #1,0.68673,-0.25861,0.67936,87.446,-0.37136,0.67861,0.63371,124.95,-0.6249,-0.68747,0.36998,28.176

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.68673,-0.25861,0.67936,89.311,-0.37136,0.67861,0.63371,114.2,-0.6249,-0.68747,0.36998,81.84

> ui mousemode right "move picked models"

> view matrix models #2,1,0,0,-3.1953,0,1,0,8.6026,0,0,1,-26.98

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.71675,0.27424,0.64114,83.225,-0.50588,0.8373,0.20739,115.63,-0.47996,-0.47299,0.73887,76.524

> view matrix models
> #1,-0.12708,0.40435,0.90573,81.28,-0.68048,0.62882,-0.3762,118.42,-0.72166,-0.66414,0.19524,82.162

> ui mousemode right "translate selected atoms"

> ui mousemode right "move picked models"

> view matrix models #2,1,0,0,74.792,0,1,0,-99.562,0,0,1,-42.19

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.064661,0.98545,0.15717,76.985,0.45325,0.16932,-0.87516,123.44,-0.88904,0.014648,-0.4576,79.166

> view matrix models
> #1,0.20735,0.96008,0.18775,76.042,0.080933,0.17443,-0.98134,125.61,-0.97491,0.21868,-0.041534,73.66

> view matrix models
> #1,0.52905,0.84743,0.044425,76.673,-0.40974,0.30094,-0.86113,125.75,-0.74312,0.43737,0.50644,66.766

> view matrix models
> #1,0.66252,0.74875,-0.021062,77.638,-0.32016,0.25765,-0.91165,126.14,-0.67717,0.61073,0.41042,64.875

> ui mousemode right "move picked models"

> select subtract #1

Nothing selected  

> select add #2

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.36714,-0.13671,-0.92007,246.56,-0.46121,0.83223,-0.3077,-0.0059004,0.80777,0.53731,0.24249,-124.99

> view matrix models
> #2,0.52398,-0.03222,-0.85112,210.75,-0.71814,0.52057,-0.46182,77.879,0.45795,0.85321,0.24963,-120.19

> view matrix models
> #2,0.30109,-0.16473,-0.93926,258.99,-0.83534,0.42952,-0.3431,90.528,0.45995,0.8879,-0.0082803,-100.69

> ui mousemode right "move picked models"

> view matrix models
> #2,0.30109,-0.16473,-0.93926,198.41,-0.83534,0.42952,-0.3431,218.9,0.45995,0.8879,-0.0082803,-85.192

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.18816,-0.14391,-0.97154,212.04,-0.86165,0.45054,-0.23362,209.62,0.47133,0.88108,-0.039224,-82.925

> view matrix models
> #2,0.18599,-0.16879,-0.96794,214.7,-0.86627,0.43672,-0.24261,212.49,0.46367,0.88362,-0.064991,-79.971

> view matrix models
> #2,0.1282,-0.10727,-0.98593,216.22,-0.87167,0.46198,-0.16361,203.12,0.47303,0.88038,-0.034277,-83.494

> select subtract #2

Nothing selected  

> fitmap map

Missing or invalid "atomsOrMap" argument: invalid objects specifier  

> fitmap

Missing or invalid "atomsOrMap" argument: empty atom specifier  

> fitmap

Missing or invalid "atomsOrMap" argument: empty atom specifier  

> ui mousemode right "move picked models"

> view matrix models
> #1,0.66252,0.74875,-0.021062,121.8,-0.32016,0.25765,-0.91165,144.36,-0.67717,0.61073,0.41042,58.518

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> roll

> stop

> ui mousemode right "translate selected models"

> undo

> redo

> ui mousemode right rotate

> ui mousemode right "move picked models"

> volume #2 level 0.2875

> volume #2 level 0.06889

> clipper associate #2 toModel #1

Opened DeepEMhancer_Danielle_4_9.mrc as #1.1.1.1, grid size 128,128,128, pixel
1.66, shown at level 0.0215, step 1, values float32  
Chain information for fold_202411_11_fresh_model_1.cif  
---  
Chain | Description  
1.2/A 1.2/B 1.2/C | .  
  

> volume #1.1.1.1 level 0.02788

> color #1.1.1.1 #1dffd9ff models

> set bgColor black

> set bgColor transparent

> save "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
> model/316W_diss_1.cxs"

> select add #1

16827 atoms, 17253 bonds, 2103 residues, 7 models selected  

> select subtract #1

Nothing selected  

> select add #1.2

16827 atoms, 17253 bonds, 2103 residues, 1 model selected  

> select subtract #1.2

Nothing selected  

> select add #1.2

16827 atoms, 17253 bonds, 2103 residues, 1 model selected  

> select subtract #1.2

Nothing selected  

> close #1

> open
> C:/Users/daniellem/Downloads/fold_202411_11_fresh/fold_202411_11_fresh_model_0.cif

Chain information for fold_202411_11_fresh_model_0.cif #1  
---  
Chain | Description  
A B C | .  
  

> open "C:/Users/daniellem/Desktop/CryoEM
> workshop/DeepEMhancer_Danielle_4_9.mrc"

Opened DeepEMhancer_Danielle_4_9.mrc as #2, grid size 128,128,128, pixel 1.66,
shown at level 0.171, step 1, values float32  

> fitmap #1 inMap #2

Fit molecule fold_202411_11_fresh_model_0.cif (#1) to map
DeepEMhancer_Danielle_4_9.mrc (#2) using 16827 atoms  
average map value = 0.07522, steps = 844  
shifted from previous position = 175  
rotated from previous position = 54.2 degrees  
atoms outside contour = 14504, contour level = 0.17065  
  
Position of fold_202411_11_fresh_model_0.cif (#1) relative to
DeepEMhancer_Danielle_4_9.mrc (#2) coordinates:  
Matrix rotation and translation  
0.64792760 -0.62354966 -0.43746502 96.82197592  
0.74386964 0.64153909 0.18731140 110.82058535  
0.16385295 -0.44678117 0.87951055 97.73764625  
Axis -0.39073889 -0.37054262 0.84262761  
Axis point -58.82632784 190.65888686 0.00000000  
Rotation angle (degrees) 54.23312860  
Shift along axis 3.46057824  
  

> select add #1

16827 atoms, 17253 bonds, 2103 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.99713,0.047993,-0.058537,89.39,0.058353,0.0052358,0.99828,118.88,0.048217,-0.99883,0.0024202,98.244

> view matrix models
> #1,0.8632,-0.0503,0.50236,89.98,-0.50441,-0.12817,0.8539,116.49,0.021437,-0.99048,-0.13601,96.623

> ui mousemode right "move picked models"

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.8632,-0.0503,0.50236,89.369,-0.50441,-0.12817,0.8539,114.78,0.021437,-0.99048,-0.13601,96.141

> view matrix models
> #1,0.8632,-0.0503,0.50236,51.119,-0.50441,-0.12817,0.8539,133.03,0.021437,-0.99048,-0.13601,97.843

> view matrix models
> #1,0.8632,-0.0503,0.50236,11.287,-0.50441,-0.12817,0.8539,109.46,0.021437,-0.99048,-0.13601,101.2

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.8632,-0.0503,0.50236,73.284,-0.50441,-0.12817,0.8539,117.42,0.021437,-0.99048,-0.13601,99.791

> view matrix models
> #1,0.8632,-0.0503,0.50236,70.626,-0.50441,-0.12817,0.8539,117.88,0.021437,-0.99048,-0.13601,99.742

> view matrix models
> #1,0.8632,-0.0503,0.50236,121.46,-0.50441,-0.12817,0.8539,114.41,0.021437,-0.99048,-0.13601,99.952

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.8253,-0.28919,0.48503,125.06,-0.54795,-0.20249,0.81163,115.12,-0.1365,-0.93561,-0.32557,97.173

> view matrix models
> #1,0.8233,-0.30662,0.47766,125.28,-0.55534,-0.26109,0.78958,115.9,-0.11739,-0.91532,-0.38523,96.754

> view matrix models
> #1,0.69075,0.22823,0.68613,117.35,-0.64306,-0.24003,0.72723,114.32,0.33067,-0.94355,-0.019031,102.83

> view matrix models
> #1,0.74225,-0.1389,0.65557,123.62,-0.66974,-0.12076,0.73271,112.12,-0.022608,-0.98292,-0.18266,99.155

> select subtract #1

Nothing selected  

> select add #2

2 models selected  

> view matrix models
> #2,0.9995,0.0074953,0.030735,-3.5727,-0.008337,0.99959,0.027347,-1.4932,-0.030517,-0.027589,0.99915,6.62

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.9995,0.0074953,0.030735,23.671,-0.008337,0.99959,0.027347,4.4973,-0.030517,-0.027589,0.99915,5.6597

> ui mousemode right rotate

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.97796,-0.014894,-0.20826,50.426,0.05381,0.98174,0.18248,-14.843,0.20174,-0.18966,0.9609,0.28557

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.97796,-0.014894,-0.20826,53.888,0.05381,0.98174,0.18248,-19.638,0.20174,-0.18966,0.9609,2.2334

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.98566,-0.0079441,-0.16857,48.617,0.044096,0.97631,0.21182,-20.604,0.1629,-0.21622,0.96266,9.4578

> view matrix models
> #2,0.95291,-0.0044741,-0.30321,64.289,0.14917,0.87746,0.45586,-44.084,0.26402,-0.47962,0.83681,38.3

> view matrix models
> #2,0.92066,-0.20279,-0.33356,92.584,0.33574,0.8473,0.41154,-58.164,0.19917,-0.49088,0.84816,45.955

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.92066,-0.20279,-0.33356,83.602,0.33574,0.8473,0.41154,-56.096,0.19917,-0.49088,0.84816,44.316

> select add #2

3 models selected  

> ui mousemode right translate

> ui mousemode right "translate selected atoms"

> ui mousemode right "move picked models"

> ui mousemode right select

> select subtract #2

Nothing selected  

> ui mousemode right "translate selected models"

> select add #2

3 models selected  

> select subtract #2

Nothing selected  

> ui mousemode right "move picked models"

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> select add #1

16827 atoms, 17253 bonds, 2103 residues, 1 model selected  

> view matrix models
> #1,0.74225,-0.1389,0.65557,125.13,-0.66974,-0.12076,0.73271,107.13,-0.022608,-0.98292,-0.18266,95.753

> select subtract #1

Nothing selected  

> isolde start

> clipper associate #2 toModel #1

Opened DeepEMhancer_Danielle_4_9.mrc as #1.1.1.1, grid size 128,128,128, pixel
1.66, shown at level 0.191, step 1, values float32  
Chain information for fold_202411_11_fresh_model_0.cif  
---  
Chain | Description  
1.2/A 1.2/B 1.2/C | .  
  

> isolde start

> set bgColor white

> set bgColor #ffffff00

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 277 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: created disulfide bonds between the following residues:  
B125-B137; B276-B309; C181-C416; B48-B68; C276-C309; C355-C428; A355-A428;
A362-A401; C484-C590; A276-A309; A181-A416; B583-B589; A125-A137; C113-C185;
B484-B590; C583-C589; B362-B401; B113-B185; C208-C219; A48-A68; C48-C68;
A113-A185; C198-C227; B208-B219; B181-B416; A583-A589; A208-A219; B198-B227;
B355-B428; C125-C137; A198-A227; C362-C401; B120-B176; A484-A590; A120-A176;
C120-C176  

> set silhouettes false

> ~select

Nothing selected  

> set silhouettes false

> delete ~protein

> addh

Summary of feedback from adding hydrogens to fold_202411_11_fresh_model_0.cif
#1.2  
---  
notes | Termini for fold_202411_11_fresh_model_0.cif (#1.2) chain A determined from SEQRES records  
Termini for fold_202411_11_fresh_model_0.cif (#1.2) chain B determined from
SEQRES records  
Termini for fold_202411_11_fresh_model_0.cif (#1.2) chain C determined from
SEQRES records  
Chain-initial residues that are actual N termini: /A MET 1, /B MET 1, /C MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A HIS 677, /B HIS 677, /C HIS
677  
Chain-final residues that are not actual C termini:  
1630 hydrogen bonds  
15663 hydrogens added  
  

> select #1

31698 atoms, 32088 bonds, 2031 residues, 16 models selected  

> clipper isolate #1 maskRadius 16

> view matrix models #1,1,0,0,7.0869,0,1,0,-0.39389,0,0,1,2.602

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.95983,0.26995,-0.076557,-10.994,-0.24059,0.93216,0.27052,16.377,0.14439,-0.24124,0.95966,14.374

> view matrix models
> #1,0.9876,-0.040147,-0.15174,25.439,0.021063,0.99189,-0.12534,6.9079,0.15554,0.1206,0.98044,-28.405

> view matrix models
> #1,0.99163,-0.083691,-0.098314,25.632,0.09889,0.98189,0.16158,-23.443,0.08301,-0.16995,0.98195,12.399

> hide atoms

> save "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
> model/316W_diss_1.cxs"

> show ~HC

> isolde restrain distances "#1/A,G"

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain distances "#1/B,F"

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> select #1

31698 atoms, 32088 bonds, 2031 residues, 17 models selected  

> isolde sim start sel

ISOLDE: started sim  

> ui mousemode right "isolde tug selection"

> select /B,F@CA

677 atoms, 677 residues, 1 model selected  

> select /A,H@CA

677 atoms, 677 residues, 1 model selected  

> select /A,B,C

31698 atoms, 32088 bonds, 2031 residues, 1 model selected  

> ui hideFloating toggle

[Repeated 1 time(s)]

> ~select

Nothing selected  

> ~select

Nothing selected  

> isolde sim pause

> select #1

31698 atoms, 32088 bonds, 2031 residues, 21 models selected  

> ui mousemode right "move picked models"

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.99163,-0.083691,-0.098314,22.128,0.09889,0.98189,0.16158,-23.116,0.08301,-0.16995,0.98195,10.873

> ui mousemode right "move picked models"

> isolde sim resume

> select A

Expected an objects specifier or a keyword  

> select /A

10566 atoms, 10696 bonds, 677 residues, 1 model selected  

> view matrix models
> #1.2,1,3.4694e-17,9.7145e-17,-0.57951,2.0817e-17,1,-5.5511e-17,0.97731,0,-8.3267e-17,1,0.16641

> view matrix models
> #1.2,1,6.0715e-17,1.1102e-16,-3.7199,1.3878e-17,1,-1.3878e-16,0.75132,1.3878e-17,-8.3267e-17,1,-1.2135

> view matrix models
> #1.2,1,-5.6725e-16,-4.1633e-17,-4.514,-4.4929e-16,1,-4.1633e-16,6.3267,-5.4123e-16,2.498e-16,1,0.76486

> select /A

10566 atoms, 10696 bonds, 677 residues, 1 model selected  

> ui mousemode right "isolde tug selection"

> ~select

Nothing selected  

> ~select

Nothing selected  

> chains

Unknown command: chains  

> chains/

Unknown command: chains/  

> /

Unknown command: /  

> select add #1.2

31698 atoms, 32088 bonds, 2031 residues, 14 models selected  

> select add #1.1.1

31698 atoms, 32088 bonds, 2031 residues, 17 models selected  

> select add #1

31698 atoms, 32088 bonds, 2031 residues, 21 models selected  

> select subtract #1.1.1

31698 atoms, 32088 bonds, 2031 residues, 16 models selected  

> select add #1.2

31698 atoms, 32088 bonds, 2031 residues, 17 models selected  

> select subtract #1.3

31698 atoms, 32088 bonds, 2031 residues, 15 models selected  

> select add #1.2

31698 atoms, 32088 bonds, 2031 residues, 16 models selected  

> ~select

Nothing selected  

> select add #1.1.1

4 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #1.1.1,1,-5.0307e-17,2.6368e-16,0.51738,-1.1796e-16,1,-6.3838e-16,-5.7231,6.9389e-17,1.3878e-16,1,0.10217

> ui mousemode right "rotate selected models"

> view matrix models
> #1.1.1,0.98912,-0.14707,-0.0035996,18.306,0.1471,0.9884,0.037814,-25.16,-0.0020035,-0.037932,0.99928,4.5772

> view matrix models
> #1.1.1,0.86583,-0.49895,-0.037256,74.567,0.49933,0.85694,0.1278,-60.241,-0.031839,-0.12925,0.9911,18.874

> view matrix models
> #1.1.1,0.9799,-0.19939,-0.0062574,25.388,0.19945,0.97857,0.05124,-31.446,-0.0040934,-0.051458,0.99867,6.3666

> view matrix models
> #1.1.1,0.99258,0.12162,-0.0012517,-11.88,-0.1216,0.99208,-0.031353,12.279,-0.0025713,0.031273,0.99951,-2.9923

> view matrix models
> #1.1.1,0.9998,-0.020045,-0.0001605,2.7614,0.020046,0.99979,0.0051605,-8.5229,5.7023e-05,-0.0051627,0.99999,0.66479

> view matrix models
> #1.1.1,0.99427,0.018958,-0.1052,8.6924,-0.019023,0.99982,0.00038549,-3.5055,0.10519,0.0016179,0.99445,-11.917

> view matrix models
> #1.1.1,0.98647,-0.12373,-0.10757,25.525,0.12676,0.99169,0.021827,-21.678,0.10397,-0.035167,0.99396,-7.6817

> ui mousemode right "translate selected models"

> view matrix models
> #1.1.1,0.98647,-0.12373,-0.10757,30.35,0.12676,0.99169,0.021827,-13.388,0.10397,-0.035167,0.99396,-6.3941

> ~select

Nothing selected  

> ui mousemode right rotate

> ~select

Nothing selected  

> ui mousemode right "move picked models"

> ui mousemode right "translate selected models"

> select add #1.1.1

4 models selected  

> view matrix models
> #1.1.1,0.98647,-0.12373,-0.10757,33.311,0.12676,0.99169,0.021827,-17.645,0.10397,-0.035167,0.99396,-5.3485

> select subtract #1.1.1

Nothing selected  

> ~select

Nothing selected  

> select /A

10566 atoms, 10696 bonds, 677 residues, 1 model selected  

> select /c

10566 atoms, 10696 bonds, 677 residues, 1 model selected  

> select /C

10566 atoms, 10696 bonds, 677 residues, 1 model selected  

> ui mousemode right "isolde tug selection"

[Repeated 1 time(s)]

> select /A

10566 atoms, 10696 bonds, 677 residues, 1 model selected  

> select /B

10566 atoms, 10696 bonds, 677 residues, 1 model selected  

> ~select

Nothing selected  

> select /B

10566 atoms, 10696 bonds, 677 residues, 1 model selected  

> ui mousemode right "isolde tug selection"

[Repeated 1 time(s)]

> ~select

Nothing selected  

> ui mousemode right "translate selected models"

> hide atoms

> show atoms

> select add #1.2

31698 atoms, 32088 bonds, 2031 residues, 14 models selected  

> select add #1.2

31698 atoms, 32088 bonds, 2031 residues, 14 models selected  

> select add #1.2

31698 atoms, 32088 bonds, 2031 residues, 14 models selected  

> ~select

Nothing selected  

> select add #1.2

31698 atoms, 32088 bonds, 2031 residues, 14 models selected  

> select add #1.2

31698 atoms, 32088 bonds, 2031 residues, 14 models selected  

> ~select

Nothing selected  

> select add #1.1.1

4 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #1.1.1,0.95386,-0.26947,-0.13243,55.464,0.27868,0.95872,0.056438,-35.107,0.11175,-0.090739,0.98958,0.24681

> view matrix models
> #1.1.1,0.86816,-0.46394,-0.17625,90.975,0.48447,0.86928,0.098215,-53.367,0.10765,-0.17066,0.97943,10.451

> view matrix models
> #1.1.1,0.72836,-0.29898,-0.61652,129.46,0.4368,0.89585,0.081589,-49.148,0.52792,-0.32872,0.7831,-3.8769

> ui mousemode right "move picked models"

> ui mousemode right "rotate selected models"

> view matrix models
> #1.1.1,0.85765,-0.27788,-0.43269,95.102,0.37939,0.90992,0.16766,-51.769,0.34712,-0.30795,0.88582,5.8133

> view matrix models
> #1.1.1,0.648,-0.46752,-0.60126,156.1,0.73192,0.6006,0.32181,-73.411,0.21067,-0.64861,0.73138,73.494

> view matrix models
> #1.1.1,0.73896,-0.48429,-0.4684,135.09,0.66602,0.63004,0.39933,-75.941,0.10172,-0.60706,0.78812,76.608

> view matrix models
> #1.1.1,0.81976,-0.49328,-0.29098,110.35,0.57131,0.66885,0.47565,-75.991,-0.040005,-0.55616,0.83011,83.909

> view matrix models
> #1.1.1,0.85593,-0.49206,-0.15894,93.907,0.49686,0.69745,0.51643,-74.068,-0.14326,-0.52099,0.84145,91.195

> view matrix models
> #1.1.1,0.82413,-0.49343,-0.2781,108.68,0.56418,0.67165,0.48019,-75.872,-0.050157,-0.55263,0.83191,84.555

> isolde sim pause

> view matrix models
> #1.1.1,0.97678,-0.058664,-0.20603,36.223,0.14599,0.88615,0.43981,-46.365,0.15678,-0.45967,0.87414,46.017

> ui mousemode right "move picked models"

> view matrix models
> #1.2,1,-2.5847e-16,5.8287e-16,-6.4386,-2.949e-16,1,-1.9429e-16,6.691,-5.8287e-16,-3.3307e-16,1,-0.1065

> isolde sim resume

> ui mousemode right "translate selected models"

> ui mousemode right rotate

> ~select

Nothing selected  

> ~select

Nothing selected  

> ~select

Nothing selected  

> select /A

10566 atoms, 10696 bonds, 677 residues, 1 model selected  

> ui mousemode right "isolde tug selection"

> select add #1

31698 atoms, 32088 bonds, 2031 residues, 21 models selected  

> select add #1

31698 atoms, 32088 bonds, 2031 residues, 21 models selected  

> select add #1

31698 atoms, 32088 bonds, 2031 residues, 21 models selected  

> ~select

Nothing selected  

> select /C

10566 atoms, 10696 bonds, 677 residues, 1 model selected  

> ~select

Nothing selected  

> rotate 30

Unknown command: rotate 30  

> rotate x 30

Unknown command: rotate x 30  

> turn 30

Expected an axis vector or a keyword  

> help help:user

> turn y 30

[Repeated 1 time(s)]

> select /B

10566 atoms, 10696 bonds, 677 residues, 1 model selected  

> isolde sim pause

> select

31698 atoms, 32088 bonds, 2031 residues, 21 models selected  

> ~select

Nothing selected  

> select add #1.1.1

4 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #1.1.1,0.97678,-0.058664,-0.20603,36.443,0.14599,0.88615,0.43981,-47.931,0.15678,-0.45967,0.87414,43.486

> ui mousemode right "rotate selected models"

> view matrix models
> #1.1.1,0.93878,-0.072118,-0.33688,54.349,0.21104,0.89328,0.39687,-52.488,0.27231,-0.44367,0.85382,29.924

> select add #1.1.1

4 models selected  

> select subtract #1.1.1

Nothing selected  

> ~select

Nothing selected  

> select add #1.2

31698 atoms, 32088 bonds, 2031 residues, 14 models selected  

> view matrix models
> #1.2,0.98911,-0.053048,-0.13729,11.919,0.074733,0.98461,0.15797,-14.293,0.1268,-0.16651,0.97785,3.142

> view matrix models
> #1.2,0.98948,0.016677,-0.14373,5.221,0.0055592,0.98822,0.15294,-5.6294,0.14458,-0.15213,0.97773,-0.5454

> view matrix models
> #1.2,0.98685,0.0096553,-0.16132,7.7496,0.012471,0.99069,0.13558,-5.287,0.16113,-0.13581,0.97754,-4.2736

> view matrix models
> #1.2,0.98778,0.006444,-0.15574,7.4975,0.02641,0.97778,0.20796,-11.769,0.15362,-0.20953,0.96566,5.2641

> view matrix models
> #1.2,0.8593,-0.4953,-0.12761,72.895,0.51115,0.8227,0.24878,-59.558,-0.018234,-0.27901,0.96012,34.297

> view matrix models
> #1.2,0.98861,0.0059789,-0.15036,6.9894,0.020811,0.98418,0.17597,-9.0452,0.14903,-0.17709,0.97284,1.8859

> ui mousemode right "move picked models"

> ui mousemode right "translate selected models"

> view matrix models
> #1.2,0.98861,0.0059789,-0.15036,15.778,0.020811,0.98418,0.17597,-19.022,0.14903,-0.17709,0.97284,-8.0522

> view matrix models
> #1.2,0.98861,0.0059789,-0.15036,12.948,0.020811,0.98418,0.17597,-19.55,0.14903,-0.17709,0.97284,-4.7808

> view matrix models
> #1.2,0.98861,0.0059789,-0.15036,8.191,0.020811,0.98418,0.17597,-20.422,0.14903,-0.17709,0.97284,-0.82751

> isolde sim resume

> select /A

10566 atoms, 10696 bonds, 677 residues, 1 model selected  

> ui mousemode right "isolde tug selection"

[Repeated 1 time(s)]

> ~select

Nothing selected  

> volume #1.1.1.1 level 0.1688

> volume #1.1.1.1 level 0.1198

> ui mousemode right "isolde tug selection"

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 61 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde start

> save "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
> model/316W_diss_2.cxs"

——— End of log from Wed Nov 13 21:10:41 2024 ———

opened ChimeraX session  

> clipper isolate #1 maskRadius 16

> isolde start

> isolde sim start /A-C

ISOLDE: started sim  

> ui mousemode right "isolde tug atom"

> ~select

Nothing selected  

> select /B

10566 atoms, 10696 bonds, 677 residues, 1 model selected  

> ui mousemode right "isolde tug selection"

> select

31698 atoms, 32088 bonds, 2031 residues, 24 models selected  

> ~select

Nothing selected  

> select /A

10566 atoms, 10696 bonds, 677 residues, 1 model selected  

> ui mousemode right "isolde tug selection"

[Repeated 1 time(s)]

> isolde restrain distances "#1/C"

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 8 residues in model #1.2 to IUPAC-IUB
standards.  

> ~select

Nothing selected  

> ui mousemode right "isolde tug residue"

> help help:user

> select add #1.2

31698 atoms, 32088 bonds, 2031 residues, 17 models selected  

> show ribbons

> ~select

Nothing selected  

> ui mousemode right swapaa

> swapaa mousemode /C:59 VAL

Sim termination reason: coord length mismatch  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 17 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> save "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
> model/316W_diss_3.cxs"

[Repeated 1 time(s)]

——— End of log from Wed Nov 13 21:59:07 2024 ———

opened ChimeraX session  

> open "D:\Dissertation final 316W model\316W_diss_3.cxs" format session

Opened DeepEMhancer_Danielle_4_9.mrc as #1.1.1.1, grid size 128,128,128, pixel
1.66, shown at level 0.12, step 1, values float32  
Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9rc202411130312\bin\Lib\site-
packages\chimerax\core\session.py", line 854, in restore  
self.add_state_manager(name, data)  
File "C:\Program Files\ChimeraX 1.9rc202411130312\bin\Lib\site-
packages\chimerax\core\session.py", line 647, in add_state_manager  
raise ValueError(  
ValueError: container "Isolde Residue Stepper Manager" of type "<class
'NoneType'>" does not have snapshot methods and does not have clear method  
  
Log from Wed Nov 13 21:59:07 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "C:\Users\daniellem\Desktop\CryoEM workshop\Dissertation final 316W
> model\316W_diss_2.cxs" format session

Opened DeepEMhancer_Danielle_4_9.mrc as #1.1.1.1, grid size 128,128,128, pixel
1.66, shown at level 0.12, step 1, values float32  
Log from Wed Nov 13 21:10:41 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "C:\Users\daniellem\Desktop\CryoEM workshop\Dissertation final 316W
> model\Isolde_316W.cxs" format session

Opened DeepEMhancer_Danielle_4_9.mrc as #1, grid size 128,128,128, pixel 1.66,
shown at level 0.171, step 1, values float32  
Log from Wed Nov 13 16:05:25 2024 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> C:\\\Users\\\daniellem\\\Downloads\\\ChimeraX_ISOLDE-1.8-cp311-cp311-win_amd64.whl

Unrecognized file suffix '.whl'  

> open "C:/Users/daniellem/Desktop/CryoEM
> workshop/DeepEMhancer_Danielle_4_9.mrc"

Opened DeepEMhancer_Danielle_4_9.mrc as #1, grid size 128,128,128, pixel 1.66,
shown at level 0.171, step 1, values float32  

> open
> C:/Users/daniellem/Downloads/fold_202411_11_fresh/fold_202411_11_fresh_model_0.cif

Chain information for fold_202411_11_fresh_model_0.cif #2  
---  
Chain | Description  
A B C | .  
  

> fitmap #2 inMap #1

Fit molecule fold_202411_11_fresh_model_0.cif (#2) to map
DeepEMhancer_Danielle_4_9.mrc (#1) using 16827 atoms  
average map value = 0.07522, steps = 844  
shifted from previous position = 175  
rotated from previous position = 54.2 degrees  
atoms outside contour = 14504, contour level = 0.17065  
  
Position of fold_202411_11_fresh_model_0.cif (#2) relative to
DeepEMhancer_Danielle_4_9.mrc (#1) coordinates:  
Matrix rotation and translation  
0.64792760 -0.62354966 -0.43746502 96.82197592  
0.74386964 0.64153909 0.18731140 110.82058535  
0.16385295 -0.44678117 0.87951055 97.73764625  
Axis -0.39073889 -0.37054262 0.84262761  
Axis point -58.82632784 190.65888686 0.00000000  
Rotation angle (degrees) 54.23312860  
Shift along axis 3.46057824  
  

> select add #2

16827 atoms, 17253 bonds, 2103 residues, 1 model selected  

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.90908,-0.24195,0.33917,98.645,-0.23659,0.3703,0.89828,112.27,-0.34293,-0.89685,0.27939,96.701

> view matrix models
> #2,0.53124,-0.06761,0.84452,97.684,-0.82947,0.1615,0.5347,110.22,-0.17254,-0.98455,0.029713,96.843

> view matrix models
> #2,0.41491,-0.042433,0.90887,97.121,-0.90723,-0.095219,0.40971,113.02,0.069157,-0.99455,-0.078003,97.834

> view matrix models
> #2,0.75288,0.027834,0.65757,97.316,-0.63298,-0.24308,0.73502,119.44,0.1803,-0.96961,-0.16539,97.49

> ui mousemode right "move picked models"

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.87103,0.31614,0.37598,92.913,-0.28071,-0.30778,0.90911,123.97,0.40312,-0.8974,-0.17934,97.549

> view matrix models
> #2,0.91536,0.086966,0.39313,97.148,-0.39835,0.053566,0.91567,117.07,0.058573,-0.99477,0.083675,97.517

> view matrix models
> #2,0.69172,-0.58695,0.42073,107.25,-0.39031,0.18632,0.90163,114.71,-0.60761,-0.78789,-0.10021,89.196

> view matrix models
> #2,0.65444,-0.63502,0.41045,107.75,-0.39395,0.17697,0.90193,114.84,-0.64538,-0.75195,-0.13435,88.167

> view matrix models
> #2,0.74125,-0.50299,0.44446,106.36,-0.46474,0.093202,0.88053,115.65,-0.48433,-0.85925,-0.16467,90.397

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.74125,-0.50299,0.44446,122.67,-0.46474,0.093202,0.88053,118.02,-0.48433,-0.85925,-0.16467,90.501

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.83206,-0.25682,0.49165,119.4,-0.49196,0.067772,0.86798,118.23,-0.25624,-0.96408,-0.069956,93.922

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.83206,-0.25682,0.49165,110.78,-0.49196,0.067772,0.86798,107.87,-0.25624,-0.96408,-0.069956,93.209

> select subtract #2

Nothing selected  

> 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  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 277 residues in model #2 to IUPAC-IUB
standards.  
Chain information for fold_202411_11_fresh_model_0.cif  
---  
Chain | Description  
2.2/A 2.2/B 2.2/C | .  
  
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: created disulfide bonds between the following residues:  
B125-B137; A125-A137; B484-B590; A120-A176; B355-B428; C484-C590; C181-C416;
A208-A219; A276-A309; B198-B227; B120-B176; A113-A185; B181-B416; B208-B219;
A181-A416; C120-C176; C125-C137; C198-C227; A484-A590; A362-A401; B583-B589;
A583-A589; C362-C401; A48-A68; B113-B185; B276-B309; C113-C185; C208-C219;
B362-B401; B48-B68; C48-C68; C276-C309; A198-A227; A355-A428; C355-C428;
C583-C589  

> save "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
> model/Isolde_316W.cxs"

> select add #2

16827 atoms, 17289 bonds, 2103 residues, 14 models selected  

> select subtract #1

16827 atoms, 17289 bonds, 2103 residues, 12 models selected  

> select add #2

16827 atoms, 17289 bonds, 2103 residues, 12 models selected  

> select add #2

16827 atoms, 17289 bonds, 2103 residues, 12 models selected  

> select add #2

16827 atoms, 17289 bonds, 2103 residues, 12 models selected  

> select subtract #2.1

16827 atoms, 17289 bonds, 2103 residues, 11 models selected  

> select add #2

16827 atoms, 17289 bonds, 2103 residues, 12 models selected  

> save "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
> model/Isolde_316W.cxs"

——— End of log from Wed Nov 13 16:05:25 2024 ———

opened ChimeraX session  

> ui mousemode right "rotate selected models"

> ui mousemode right rotate

> select add #2

16827 atoms, 17289 bonds, 2103 residues, 15 models selected  

> select add #2

16827 atoms, 17289 bonds, 2103 residues, 15 models selected  

> select subtract #2.1

16827 atoms, 17289 bonds, 2103 residues, 14 models selected  

> select #2

16827 atoms, 17289 bonds, 2103 residues, 15 models selected  

> select subtract #2.1

16827 atoms, 17289 bonds, 2103 residues, 14 models selected  

> select subtract #2.3

16827 atoms, 17289 bonds, 2103 residues, 13 models selected  

> ui mousemode right "move picked models"

> ui mousemode right "rotate selected models"

> stop isolde

Expected fewer arguments  

> select add #2

16827 atoms, 17289 bonds, 2103 residues, 15 models selected  

> deselect all

Unknown command: deselect all  

> deselect

Unknown command: deselect  

> ~select

Nothing selected  

> select add #2

16827 atoms, 17289 bonds, 2103 residues, 15 models selected  

> view matrix models
> #2,0.99575,-0.015637,0.090722,-4.4839,0.0014031,0.98793,0.15488,-10.121,-0.092049,-0.1541,0.98376,27.255

> view matrix models
> #2,0.78145,0.090022,-0.61745,60.114,0.035975,0.98139,0.18861,-15.794,0.62294,-0.1696,0.76367,-35.953

> view matrix models
> #2,0.71305,0.10657,-0.69297,71.605,-0.27531,0.95155,-0.13695,45.9,0.6448,0.28843,0.70784,-81.031

> view matrix models
> #2,0.89446,0.22625,-0.38569,16.741,-0.28596,0.95254,-0.10439,44.648,0.34377,0.20366,0.9167,-53.518

> view matrix models
> #2,0.94709,0.31726,0.048693,-29.856,-0.31545,0.94804,-0.041416,43.885,-0.059302,0.023864,0.99795,4.4102

> ui mousemode right "move picked models"

> view matrix models
> #2.2,1,5.6986e-16,-2.4286e-16,-9.5814,8.4893e-16,1,1.9082e-16,0.6637,-9.7145e-17,3.1225e-17,1,-0.41905

> select add #2

16827 atoms, 17289 bonds, 2103 residues, 15 models selected  

> ~select

Nothing selected  

> select add #1

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.99565,0.0035698,-0.093147,8.6107,0.0040819,0.99664,0.081827,-7.5691,0.093126,-0.081851,0.99228,-0.9953

> view matrix models
> #1,0.99643,0.0065949,-0.084219,7.3734,0.0032596,0.9932,0.11634,-10.247,0.084414,-0.1162,0.98963,4.0265

> ui mousemode right rotate

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.98436,-0.16331,-0.066065,25.793,0.1716,0.97369,0.14993,-30.516,0.039841,-0.15892,0.98649,14.137

> select subtract #1

Nothing selected  

> ~select

Nothing selected  

> select add #2

16827 atoms, 17289 bonds, 2103 residues, 15 models selected  

> ui mousemode right select

> ~select

Nothing selected  

> ~select

Nothing selected  

> clipper associate #1 toModel #2

Opened DeepEMhancer_Danielle_4_9.mrc as #2.1.1.1, grid size 128,128,128, pixel
1.66, shown at step 1, values float32  

> clipper associate #1 toModel #2

> volume #2.1.1.1 level 0.01818

> volume #2.1.1.1 level 0.006197

> volume #2.1.1.1 level 0.01884

> volume #2.1.1.1 level 0.01019

> volume #2.1.1.1 level 0.0042

> fitmap #2.2 inMap #2.1.1.1

Fit molecule fold_202411_11_fresh_model_0.cif (#2.2) to map
DeepEMhancer_Danielle_4_9.mrc (#2.1.1.1) using 16827 atoms  
average map value = 0, steps = 24  
shifted from previous position = 0  
rotated from previous position = 0 degrees  
atoms outside contour = 16827, contour level = 0.0042003  
  
Position of fold_202411_11_fresh_model_0.cif (#2.2) relative to
DeepEMhancer_Danielle_4_9.mrc (#2.1.1.1) coordinates:  
Matrix rotation and translation  
1.00000000 0.00000000 0.00000000 0.00000000  
0.00000000 1.00000000 0.00000000 0.00000000  
0.00000000 0.00000000 1.00000000 0.00000000  
Axis 0.00000000 0.00000000 1.00000000  
Axis point 0.00000000 0.00000000 0.00000000  
Rotation angle (degrees) 0.00000000  
Shift along axis 0.00000000  
  

> volume #2.1.1.1 color #ff6f82

> volume #2.1.1.1 orthoplanes xyz positionPlanes 64,64,64 style image region
> all

> mousemode rightMode "move planes"

> volume #2.1.1.1 orthoplanes xyz positionPlanes 64,64,64 style image region
> all

> mousemode rightMode "move planes"

> volume #2.1.1.1 orthoplanes xyz positionPlanes 64,64,64 style image region
> all

> mousemode rightMode "move planes"

> volume #2.1.1.1 orthoplanes xyz positionPlanes 64,64,64 style image region
> all

> mousemode rightMode "move planes"

> volume planes z style image imageMode "full region"

> mousemode rightMode "move planes"

> volume style mesh

[Repeated 1 time(s)]

> volume #2.1.1.1 style image region all imageMode "tilted slab"
> tiltedSlabAxis 0,0,1 tiltedSlabOffset 106.1 tiltedSlabSpacing 1.658
> tiltedSlabPlaneCount 10

> mousemode rightMode "rotate slab"

> volume planes z style image imageMode "full region"

> mousemode rightMode "move planes"

> volume #2.1.1.1 style image region all imageMode "tilted slab"
> tiltedSlabAxis 0,0,1 tiltedSlabOffset 106.1 tiltedSlabSpacing 1.658
> tiltedSlabPlaneCount 10

> mousemode rightMode "rotate slab"

> volume style mesh

> volume #2.1.1.1 change image level -0.0001408,0 level 0.1705,0.8 level
> 2.096,1

> volume #2.1.1.1 level 0.3019

> volume #2.1.1.1 orthoplanes xyz positionPlanes 64,64,64 style image region
> all

> mousemode rightMode "move planes"

> volume #2.1.1.1 orthoplanes xyz positionPlanes 64,64,64 style image region
> all

> mousemode rightMode "move planes"

> volume zone #2.1.1.1 nearAtoms #2.2 range 9.95

> volume region all imageMode "full region"

> volume unzone

> mousemode rightMode "crop volume"

> close #2.1.1.1

> select #1

Nothing selected  

> clipper associate #1 toModel #2

> close session

> open
> C:/Users/daniellem/Downloads/fold_202411_11_fresh/fold_202411_11_fresh_model_1.cif

Chain information for fold_202411_11_fresh_model_1.cif #1  
---  
Chain | Description  
A B C | .  
  

> open "C:/Users/daniellem/Desktop/CryoEM
> workshop/DeepEMhancer_Danielle_4_9.mrc"

Opened DeepEMhancer_Danielle_4_9.mrc as #2, grid size 128,128,128, pixel 1.66,
shown at level 0.171, step 1, values float32  

> clipper associate #2 toModel #1

Opened DeepEMhancer_Danielle_4_9.mrc as #1.1.1.1, grid size 128,128,128, pixel
1.66, shown at level 0, step 1, values float32  
Chain information for fold_202411_11_fresh_model_1.cif  
---  
Chain | Description  
1.2/A 1.2/B 1.2/C | .  
  

> zoom

Pixel size at center of rotation is 0.252  

> zoom

Pixel size at center of rotation is 0.252  

> volume #1.1.1.1 level 2.378e-07

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 286 residues in model #1.2 to IUPAC-IUB
standards.  
Done loading forcefield  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  

> volume #1.1.1.1 region 0,2,0,11,15,12

> set bgColor white

> set bgColor #ffffff00

> select add #1

16827 atoms, 17253 bonds, 2103 residues, 15 models selected  

> select add #1.2

16827 atoms, 17253 bonds, 2103 residues, 15 models selected  

> select add #1

16827 atoms, 17253 bonds, 2103 residues, 15 models selected  

> select add #1.2

16827 atoms, 17253 bonds, 2103 residues, 15 models selected  

> ~select

Nothing selected  

> view #1.1.1.1.2 clip false

No displayed objects specified.  

> view #1.1.1.1.2 clip false

No displayed objects specified.  

> view #1.1.1.1.2 clip false

No displayed objects specified.  

> show #1.1.1.1.2 target m

> hide #1.1.1.1.2 target m

> close #1.1.1.1.2

> hide target m

[Repeated 1 time(s)]

> close

> open
> C:\Users\daniellem\Downloads\fold_202411_11_fresh\fold_202411_11_fresh_model_1.cif
> format mmcif

Chain information for fold_202411_11_fresh_model_1.cif #1  
---  
Chain | Description  
A B C | .  
  

> open "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
> model/DeepEMhancer_Danielle_4_9.mrc"

Opened DeepEMhancer_Danielle_4_9.mrc as #2, grid size 128,128,128, pixel 1.66,
shown at level 0.171, step 1, values float32  

> volume #2 region 0,6,0,127,127,127

> select add #1

16827 atoms, 17253 bonds, 2103 residues, 1 model selected  

> volume #2 region 0,9,0,127,127,127

> volume #2 region 0,31,0,127,127,127

> volume #2 region 0,2,0,127,127,127

> volume #2 region 2,2,0,127,127,127

> volume #2 region 0,2,0,127,127,127

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.66525,-0.10274,0.73952,-3.3498,-0.70987,0.21988,0.66913,6.6393,-0.23135,-0.9701,0.073343,18.122

> view matrix models
> #1,0.66436,-0.098392,0.74091,-3.4057,-0.70806,0.23457,0.66606,6.4683,-0.23933,-0.96711,0.086172,18.055

> view matrix models
> #1,0.73489,-0.0012862,0.67819,-3.9016,-0.49398,0.68416,0.53657,1.0277,-0.46468,-0.72933,0.50214,14.374

> view matrix models
> #1,0.48401,-0.29693,0.82315,-0.71801,-0.38327,0.77371,0.50446,-0.064179,-0.78666,-0.55965,0.26068,14.723

> view matrix models
> #1,0.45881,-0.3301,0.82494,-0.27877,-0.38342,0.76399,0.51895,-0.033803,-0.80155,-0.5544,0.22396,14.879

> view matrix models
> #1,0.58787,-0.42542,0.68806,1.4842,-0.33441,0.64668,0.68555,-0.022276,-0.7366,-0.63311,0.2379,15.786

> ui mousemode right "move picked models"

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.58787,-0.42542,0.68806,89.581,-0.33441,0.64668,0.68555,125,-0.7366,-0.63311,0.2379,28.389

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.69323,-0.26637,0.66969,87.572,-0.39958,0.63127,0.6647,125.4,-0.59981,-0.72838,0.33118,28.789

> view matrix models
> #1,0.68673,-0.25861,0.67936,87.446,-0.37136,0.67861,0.63371,124.95,-0.6249,-0.68747,0.36998,28.176

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.68673,-0.25861,0.67936,89.311,-0.37136,0.67861,0.63371,114.2,-0.6249,-0.68747,0.36998,81.84

> ui mousemode right "move picked models"

> view matrix models #2,1,0,0,-3.1953,0,1,0,8.6026,0,0,1,-26.98

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.71675,0.27424,0.64114,83.225,-0.50588,0.8373,0.20739,115.63,-0.47996,-0.47299,0.73887,76.524

> view matrix models
> #1,-0.12708,0.40435,0.90573,81.28,-0.68048,0.62882,-0.3762,118.42,-0.72166,-0.66414,0.19524,82.162

> ui mousemode right "translate selected atoms"

> ui mousemode right "move picked models"

> view matrix models #2,1,0,0,74.792,0,1,0,-99.562,0,0,1,-42.19

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.064661,0.98545,0.15717,76.985,0.45325,0.16932,-0.87516,123.44,-0.88904,0.014648,-0.4576,79.166

> view matrix models
> #1,0.20735,0.96008,0.18775,76.042,0.080933,0.17443,-0.98134,125.61,-0.97491,0.21868,-0.041534,73.66

> view matrix models
> #1,0.52905,0.84743,0.044425,76.673,-0.40974,0.30094,-0.86113,125.75,-0.74312,0.43737,0.50644,66.766

> view matrix models
> #1,0.66252,0.74875,-0.021062,77.638,-0.32016,0.25765,-0.91165,126.14,-0.67717,0.61073,0.41042,64.875

> ui mousemode right "move picked models"

> select subtract #1

Nothing selected  

> select add #2

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.36714,-0.13671,-0.92007,246.56,-0.46121,0.83223,-0.3077,-0.0059004,0.80777,0.53731,0.24249,-124.99

> view matrix models
> #2,0.52398,-0.03222,-0.85112,210.75,-0.71814,0.52057,-0.46182,77.879,0.45795,0.85321,0.24963,-120.19

> view matrix models
> #2,0.30109,-0.16473,-0.93926,258.99,-0.83534,0.42952,-0.3431,90.528,0.45995,0.8879,-0.0082803,-100.69

> ui mousemode right "move picked models"

> view matrix models
> #2,0.30109,-0.16473,-0.93926,198.41,-0.83534,0.42952,-0.3431,218.9,0.45995,0.8879,-0.0082803,-85.192

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.18816,-0.14391,-0.97154,212.04,-0.86165,0.45054,-0.23362,209.62,0.47133,0.88108,-0.039224,-82.925

> view matrix models
> #2,0.18599,-0.16879,-0.96794,214.7,-0.86627,0.43672,-0.24261,212.49,0.46367,0.88362,-0.064991,-79.971

> view matrix models
> #2,0.1282,-0.10727,-0.98593,216.22,-0.87167,0.46198,-0.16361,203.12,0.47303,0.88038,-0.034277,-83.494

> select subtract #2

Nothing selected  

> fitmap map

Missing or invalid "atomsOrMap" argument: invalid objects specifier  

> fitmap

Missing or invalid "atomsOrMap" argument: empty atom specifier  

> fitmap

Missing or invalid "atomsOrMap" argument: empty atom specifier  

> ui mousemode right "move picked models"

> view matrix models
> #1,0.66252,0.74875,-0.021062,121.8,-0.32016,0.25765,-0.91165,144.36,-0.67717,0.61073,0.41042,58.518

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> roll

> stop

> ui mousemode right "translate selected models"

> undo

> redo

> ui mousemode right rotate

> ui mousemode right "move picked models"

> volume #2 level 0.2875

> volume #2 level 0.06889

> clipper associate #2 toModel #1

Opened DeepEMhancer_Danielle_4_9.mrc as #1.1.1.1, grid size 128,128,128, pixel
1.66, shown at level 0.0215, step 1, values float32  
Chain information for fold_202411_11_fresh_model_1.cif  
---  
Chain | Description  
1.2/A 1.2/B 1.2/C | .  
  

> volume #1.1.1.1 level 0.02788

> color #1.1.1.1 #1dffd9ff models

> set bgColor black

> set bgColor transparent

> save "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
> model/316W_diss_1.cxs"

> select add #1

16827 atoms, 17253 bonds, 2103 residues, 7 models selected  

> select subtract #1

Nothing selected  

> select add #1.2

16827 atoms, 17253 bonds, 2103 residues, 1 model selected  

> select subtract #1.2

Nothing selected  

> select add #1.2

16827 atoms, 17253 bonds, 2103 residues, 1 model selected  

> select subtract #1.2

Nothing selected  

> close #1

> open
> C:/Users/daniellem/Downloads/fold_202411_11_fresh/fold_202411_11_fresh_model_0.cif

Chain information for fold_202411_11_fresh_model_0.cif #1  
---  
Chain | Description  
A B C | .  
  

> open "C:/Users/daniellem/Desktop/CryoEM
> workshop/DeepEMhancer_Danielle_4_9.mrc"

Opened DeepEMhancer_Danielle_4_9.mrc as #2, grid size 128,128,128, pixel 1.66,
shown at level 0.171, step 1, values float32  

> fitmap #1 inMap #2

Fit molecule fold_202411_11_fresh_model_0.cif (#1) to map
DeepEMhancer_Danielle_4_9.mrc (#2) using 16827 atoms  
average map value = 0.07522, steps = 844  
shifted from previous position = 175  
rotated from previous position = 54.2 degrees  
atoms outside contour = 14504, contour level = 0.17065  
  
Position of fold_202411_11_fresh_model_0.cif (#1) relative to
DeepEMhancer_Danielle_4_9.mrc (#2) coordinates:  
Matrix rotation and translation  
0.64792760 -0.62354966 -0.43746502 96.82197592  
0.74386964 0.64153909 0.18731140 110.82058535  
0.16385295 -0.44678117 0.87951055 97.73764625  
Axis -0.39073889 -0.37054262 0.84262761  
Axis point -58.82632784 190.65888686 0.00000000  
Rotation angle (degrees) 54.23312860  
Shift along axis 3.46057824  
  

> select add #1

16827 atoms, 17253 bonds, 2103 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.99713,0.047993,-0.058537,89.39,0.058353,0.0052358,0.99828,118.88,0.048217,-0.99883,0.0024202,98.244

> view matrix models
> #1,0.8632,-0.0503,0.50236,89.98,-0.50441,-0.12817,0.8539,116.49,0.021437,-0.99048,-0.13601,96.623

> ui mousemode right "move picked models"

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.8632,-0.0503,0.50236,89.369,-0.50441,-0.12817,0.8539,114.78,0.021437,-0.99048,-0.13601,96.141

> view matrix models
> #1,0.8632,-0.0503,0.50236,51.119,-0.50441,-0.12817,0.8539,133.03,0.021437,-0.99048,-0.13601,97.843

> view matrix models
> #1,0.8632,-0.0503,0.50236,11.287,-0.50441,-0.12817,0.8539,109.46,0.021437,-0.99048,-0.13601,101.2

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.8632,-0.0503,0.50236,73.284,-0.50441,-0.12817,0.8539,117.42,0.021437,-0.99048,-0.13601,99.791

> view matrix models
> #1,0.8632,-0.0503,0.50236,70.626,-0.50441,-0.12817,0.8539,117.88,0.021437,-0.99048,-0.13601,99.742

> view matrix models
> #1,0.8632,-0.0503,0.50236,121.46,-0.50441,-0.12817,0.8539,114.41,0.021437,-0.99048,-0.13601,99.952

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.8253,-0.28919,0.48503,125.06,-0.54795,-0.20249,0.81163,115.12,-0.1365,-0.93561,-0.32557,97.173

> view matrix models
> #1,0.8233,-0.30662,0.47766,125.28,-0.55534,-0.26109,0.78958,115.9,-0.11739,-0.91532,-0.38523,96.754

> view matrix models
> #1,0.69075,0.22823,0.68613,117.35,-0.64306,-0.24003,0.72723,114.32,0.33067,-0.94355,-0.019031,102.83

> view matrix models
> #1,0.74225,-0.1389,0.65557,123.62,-0.66974,-0.12076,0.73271,112.12,-0.022608,-0.98292,-0.18266,99.155

> select subtract #1

Nothing selected  

> select add #2

2 models selected  

> view matrix models
> #2,0.9995,0.0074953,0.030735,-3.5727,-0.008337,0.99959,0.027347,-1.4932,-0.030517,-0.027589,0.99915,6.62

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.9995,0.0074953,0.030735,23.671,-0.008337,0.99959,0.027347,4.4973,-0.030517,-0.027589,0.99915,5.6597

> ui mousemode right rotate

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.97796,-0.014894,-0.20826,50.426,0.05381,0.98174,0.18248,-14.843,0.20174,-0.18966,0.9609,0.28557

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.97796,-0.014894,-0.20826,53.888,0.05381,0.98174,0.18248,-19.638,0.20174,-0.18966,0.9609,2.2334

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.98566,-0.0079441,-0.16857,48.617,0.044096,0.97631,0.21182,-20.604,0.1629,-0.21622,0.96266,9.4578

> view matrix models
> #2,0.95291,-0.0044741,-0.30321,64.289,0.14917,0.87746,0.45586,-44.084,0.26402,-0.47962,0.83681,38.3

> view matrix models
> #2,0.92066,-0.20279,-0.33356,92.584,0.33574,0.8473,0.41154,-58.164,0.19917,-0.49088,0.84816,45.955

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.92066,-0.20279,-0.33356,83.602,0.33574,0.8473,0.41154,-56.096,0.19917,-0.49088,0.84816,44.316

> select add #2

3 models selected  

> ui mousemode right translate

> ui mousemode right "translate selected atoms"

> ui mousemode right "move picked models"

> ui mousemode right select

> select subtract #2

Nothing selected  

> ui mousemode right "translate selected models"

> select add #2

3 models selected  

> select subtract #2

Nothing selected  

> ui mousemode right "move picked models"

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> select add #1

16827 atoms, 17253 bonds, 2103 residues, 1 model selected  

> view matrix models
> #1,0.74225,-0.1389,0.65557,125.13,-0.66974,-0.12076,0.73271,107.13,-0.022608,-0.98292,-0.18266,95.753

> select subtract #1

Nothing selected  

> isolde start

> clipper associate #2 toModel #1

Opened DeepEMhancer_Danielle_4_9.mrc as #1.1.1.1, grid size 128,128,128, pixel
1.66, shown at level 0.191, step 1, values float32  
Chain information for fold_202411_11_fresh_model_0.cif  
---  
Chain | Description  
1.2/A 1.2/B 1.2/C | .  
  

> isolde start

> set bgColor white

> set bgColor #ffffff00

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 277 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: created disulfide bonds between the following residues:  
B125-B137; B276-B309; C181-C416; B48-B68; C276-C309; C355-C428; A355-A428;
A362-A401; C484-C590; A276-A309; A181-A416; B583-B589; A125-A137; C113-C185;
B484-B590; C583-C589; B362-B401; B113-B185; C208-C219; A48-A68; C48-C68;
A113-A185; C198-C227; B208-B219; B181-B416; A583-A589; A208-A219; B198-B227;
B355-B428; C125-C137; A198-A227; C362-C401; B120-B176; A484-A590; A120-A176;
C120-C176  

> set silhouettes false

> ~select

Nothing selected  

> set silhouettes false

> delete ~protein

> addh

Summary of feedback from adding hydrogens to fold_202411_11_fresh_model_0.cif
#1.2  
---  
notes | Termini for fold_202411_11_fresh_model_0.cif (#1.2) chain A determined from SEQRES records  
Termini for fold_202411_11_fresh_model_0.cif (#1.2) chain B determined from
SEQRES records  
Termini for fold_202411_11_fresh_model_0.cif (#1.2) chain C determined from
SEQRES records  
Chain-initial residues that are actual N termini: /A MET 1, /B MET 1, /C MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A HIS 677, /B HIS 677, /C HIS
677  
Chain-final residues that are not actual C termini:  
1630 hydrogen bonds  
15663 hydrogens added  
  

> select #1

31698 atoms, 32088 bonds, 2031 residues, 16 models selected  

> clipper isolate #1 maskRadius 16

> view matrix models #1,1,0,0,7.0869,0,1,0,-0.39389,0,0,1,2.602

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.95983,0.26995,-0.076557,-10.994,-0.24059,0.93216,0.27052,16.377,0.14439,-0.24124,0.95966,14.374

> view matrix models
> #1,0.9876,-0.040147,-0.15174,25.439,0.021063,0.99189,-0.12534,6.9079,0.15554,0.1206,0.98044,-28.405

> view matrix models
> #1,0.99163,-0.083691,-0.098314,25.632,0.09889,0.98189,0.16158,-23.443,0.08301,-0.16995,0.98195,12.399

> hide atoms

> save "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
> model/316W_diss_1.cxs"

> show ~HC

> isolde restrain distances "#1/A,G"

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain distances "#1/B,F"

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> select #1

31698 atoms, 32088 bonds, 2031 residues, 17 models selected  

> isolde sim start sel

ISOLDE: started sim  

> ui mousemode right "isolde tug selection"

> select /B,F@CA

677 atoms, 677 residues, 1 model selected  

> select /A,H@CA

677 atoms, 677 residues, 1 model selected  

> select /A,B,C

31698 atoms, 32088 bonds, 2031 residues, 1 model selected  

> ui hideFloating toggle

[Repeated 1 time(s)]

> ~select

Nothing selected  

> ~select

Nothing selected  

> isolde sim pause

> select #1

31698 atoms, 32088 bonds, 2031 residues, 21 models selected  

[deleted to fit within ticket limits]

> view matrix models
> #1.1.1,0.98647,-0.12373,-0.10757,30.35,0.12676,0.99169,0.021827,-13.388,0.10397,-0.035167,0.99396,-6.3941

> ~select

Nothing selected  

> ui mousemode right rotate

> ~select

Nothing selected  

> ui mousemode right "move picked models"

> ui mousemode right "translate selected models"

> select add #1.1.1

4 models selected  

> view matrix models
> #1.1.1,0.98647,-0.12373,-0.10757,33.311,0.12676,0.99169,0.021827,-17.645,0.10397,-0.035167,0.99396,-5.3485

> select subtract #1.1.1

Nothing selected  

> ~select

Nothing selected  

> select /A

10566 atoms, 10696 bonds, 677 residues, 1 model selected  

> select /c

10566 atoms, 10696 bonds, 677 residues, 1 model selected  

> select /C

10566 atoms, 10696 bonds, 677 residues, 1 model selected  

> ui mousemode right "isolde tug selection"

[Repeated 1 time(s)]

> select /A

10566 atoms, 10696 bonds, 677 residues, 1 model selected  

> select /B

10566 atoms, 10696 bonds, 677 residues, 1 model selected  

> ~select

Nothing selected  

> select /B

10566 atoms, 10696 bonds, 677 residues, 1 model selected  

> ui mousemode right "isolde tug selection"

[Repeated 1 time(s)]

> ~select

Nothing selected  

> ui mousemode right "translate selected models"

> hide atoms

> show atoms

> select add #1.2

31698 atoms, 32088 bonds, 2031 residues, 14 models selected  

> select add #1.2

31698 atoms, 32088 bonds, 2031 residues, 14 models selected  

> select add #1.2

31698 atoms, 32088 bonds, 2031 residues, 14 models selected  

> ~select

Nothing selected  

> select add #1.2

31698 atoms, 32088 bonds, 2031 residues, 14 models selected  

> select add #1.2

31698 atoms, 32088 bonds, 2031 residues, 14 models selected  

> ~select

Nothing selected  

> select add #1.1.1

4 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #1.1.1,0.95386,-0.26947,-0.13243,55.464,0.27868,0.95872,0.056438,-35.107,0.11175,-0.090739,0.98958,0.24681

> view matrix models
> #1.1.1,0.86816,-0.46394,-0.17625,90.975,0.48447,0.86928,0.098215,-53.367,0.10765,-0.17066,0.97943,10.451

> view matrix models
> #1.1.1,0.72836,-0.29898,-0.61652,129.46,0.4368,0.89585,0.081589,-49.148,0.52792,-0.32872,0.7831,-3.8769

> ui mousemode right "move picked models"

> ui mousemode right "rotate selected models"

> view matrix models
> #1.1.1,0.85765,-0.27788,-0.43269,95.102,0.37939,0.90992,0.16766,-51.769,0.34712,-0.30795,0.88582,5.8133

> view matrix models
> #1.1.1,0.648,-0.46752,-0.60126,156.1,0.73192,0.6006,0.32181,-73.411,0.21067,-0.64861,0.73138,73.494

> view matrix models
> #1.1.1,0.73896,-0.48429,-0.4684,135.09,0.66602,0.63004,0.39933,-75.941,0.10172,-0.60706,0.78812,76.608

> view matrix models
> #1.1.1,0.81976,-0.49328,-0.29098,110.35,0.57131,0.66885,0.47565,-75.991,-0.040005,-0.55616,0.83011,83.909

> view matrix models
> #1.1.1,0.85593,-0.49206,-0.15894,93.907,0.49686,0.69745,0.51643,-74.068,-0.14326,-0.52099,0.84145,91.195

> view matrix models
> #1.1.1,0.82413,-0.49343,-0.2781,108.68,0.56418,0.67165,0.48019,-75.872,-0.050157,-0.55263,0.83191,84.555

> isolde sim pause

> view matrix models
> #1.1.1,0.97678,-0.058664,-0.20603,36.223,0.14599,0.88615,0.43981,-46.365,0.15678,-0.45967,0.87414,46.017

> ui mousemode right "move picked models"

> view matrix models
> #1.2,1,-2.5847e-16,5.8287e-16,-6.4386,-2.949e-16,1,-1.9429e-16,6.691,-5.8287e-16,-3.3307e-16,1,-0.1065

> isolde sim resume

> ui mousemode right "translate selected models"

> ui mousemode right rotate

> ~select

Nothing selected  

> ~select

Nothing selected  

> ~select

Nothing selected  

> select /A

10566 atoms, 10696 bonds, 677 residues, 1 model selected  

> ui mousemode right "isolde tug selection"

> select add #1

31698 atoms, 32088 bonds, 2031 residues, 21 models selected  

> select add #1

31698 atoms, 32088 bonds, 2031 residues, 21 models selected  

> select add #1

31698 atoms, 32088 bonds, 2031 residues, 21 models selected  

> ~select

Nothing selected  

> select /C

10566 atoms, 10696 bonds, 677 residues, 1 model selected  

> ~select

Nothing selected  

> rotate 30

Unknown command: rotate 30  

> rotate x 30

Unknown command: rotate x 30  

> turn 30

Expected an axis vector or a keyword  

> help help:user

> turn y 30

[Repeated 1 time(s)]

> select /B

10566 atoms, 10696 bonds, 677 residues, 1 model selected  

> isolde sim pause

> select

31698 atoms, 32088 bonds, 2031 residues, 21 models selected  

> ~select

Nothing selected  

> select add #1.1.1

4 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #1.1.1,0.97678,-0.058664,-0.20603,36.443,0.14599,0.88615,0.43981,-47.931,0.15678,-0.45967,0.87414,43.486

> ui mousemode right "rotate selected models"

> view matrix models
> #1.1.1,0.93878,-0.072118,-0.33688,54.349,0.21104,0.89328,0.39687,-52.488,0.27231,-0.44367,0.85382,29.924

> select add #1.1.1

4 models selected  

> select subtract #1.1.1

Nothing selected  

> ~select

Nothing selected  

> select add #1.2

31698 atoms, 32088 bonds, 2031 residues, 14 models selected  

> view matrix models
> #1.2,0.98911,-0.053048,-0.13729,11.919,0.074733,0.98461,0.15797,-14.293,0.1268,-0.16651,0.97785,3.142

> view matrix models
> #1.2,0.98948,0.016677,-0.14373,5.221,0.0055592,0.98822,0.15294,-5.6294,0.14458,-0.15213,0.97773,-0.5454

> view matrix models
> #1.2,0.98685,0.0096553,-0.16132,7.7496,0.012471,0.99069,0.13558,-5.287,0.16113,-0.13581,0.97754,-4.2736

> view matrix models
> #1.2,0.98778,0.006444,-0.15574,7.4975,0.02641,0.97778,0.20796,-11.769,0.15362,-0.20953,0.96566,5.2641

> view matrix models
> #1.2,0.8593,-0.4953,-0.12761,72.895,0.51115,0.8227,0.24878,-59.558,-0.018234,-0.27901,0.96012,34.297

> view matrix models
> #1.2,0.98861,0.0059789,-0.15036,6.9894,0.020811,0.98418,0.17597,-9.0452,0.14903,-0.17709,0.97284,1.8859

> ui mousemode right "move picked models"

> ui mousemode right "translate selected models"

> view matrix models
> #1.2,0.98861,0.0059789,-0.15036,15.778,0.020811,0.98418,0.17597,-19.022,0.14903,-0.17709,0.97284,-8.0522

> view matrix models
> #1.2,0.98861,0.0059789,-0.15036,12.948,0.020811,0.98418,0.17597,-19.55,0.14903,-0.17709,0.97284,-4.7808

> view matrix models
> #1.2,0.98861,0.0059789,-0.15036,8.191,0.020811,0.98418,0.17597,-20.422,0.14903,-0.17709,0.97284,-0.82751

> isolde sim resume

> select /A

10566 atoms, 10696 bonds, 677 residues, 1 model selected  

> ui mousemode right "isolde tug selection"

[Repeated 1 time(s)]

> ~select

Nothing selected  

> volume #1.1.1.1 level 0.1688

> volume #1.1.1.1 level 0.1198

> ui mousemode right "isolde tug selection"

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 61 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde start

> save "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
> model/316W_diss_2.cxs"

——— End of log from Wed Nov 13 21:10:41 2024 ———

opened ChimeraX session  

> clipper isolate #1 maskRadius 16

> isolde start

> isolde sim start /A-C

ISOLDE: started sim  

> ui mousemode right "isolde tug atom"

> ~select

Nothing selected  

> select /B

10566 atoms, 10696 bonds, 677 residues, 1 model selected  

> ui mousemode right "isolde tug selection"

> select

31698 atoms, 32088 bonds, 2031 residues, 24 models selected  

> ~select

Nothing selected  

> select /A

10566 atoms, 10696 bonds, 677 residues, 1 model selected  

> ui mousemode right "isolde tug selection"

[Repeated 1 time(s)]

> isolde restrain distances "#1/C"

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 8 residues in model #1.2 to IUPAC-IUB
standards.  

> ~select

Nothing selected  

> ui mousemode right "isolde tug residue"

> help help:user

> select add #1.2

31698 atoms, 32088 bonds, 2031 residues, 17 models selected  

> show ribbons

> ~select

Nothing selected  

> ui mousemode right swapaa

> swapaa mousemode /C:59 VAL

Sim termination reason: coord length mismatch  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 17 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> save "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
> model/316W_diss_3.cxs"

[Repeated 1 time(s)]

——— End of log from Wed Nov 13 21:59:07 2024 ———

opened ChimeraX session  

> open "D:\Dissertation final 316W model\316W_diss_3.cxs" format session

Opened DeepEMhancer_Danielle_4_9.mrc as #1.1.1.1, grid size 128,128,128, pixel
1.66, shown at level 0.12, step 1, values float32  
Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9rc202411130312\bin\Lib\site-
packages\chimerax\core\session.py", line 854, in restore  
self.add_state_manager(name, data)  
File "C:\Program Files\ChimeraX 1.9rc202411130312\bin\Lib\site-
packages\chimerax\core\session.py", line 647, in add_state_manager  
raise ValueError(  
ValueError: container "Isolde Residue Stepper Manager" of type "<class
'NoneType'>" does not have snapshot methods and does not have clear method  
  
Log from Wed Nov 13 21:59:07 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "C:\Users\daniellem\Desktop\CryoEM workshop\Dissertation final 316W
> model\316W_diss_2.cxs" format session

Opened DeepEMhancer_Danielle_4_9.mrc as #1.1.1.1, grid size 128,128,128, pixel
1.66, shown at level 0.12, step 1, values float32  
Log from Wed Nov 13 21:10:41 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "C:\Users\daniellem\Desktop\CryoEM workshop\Dissertation final 316W
> model\Isolde_316W.cxs" format session

Opened DeepEMhancer_Danielle_4_9.mrc as #1, grid size 128,128,128, pixel 1.66,
shown at level 0.171, step 1, values float32  
Log from Wed Nov 13 16:05:25 2024 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> C:\\\Users\\\daniellem\\\Downloads\\\ChimeraX_ISOLDE-1.8-cp311-cp311-win_amd64.whl

Unrecognized file suffix '.whl'  

> open "C:/Users/daniellem/Desktop/CryoEM
> workshop/DeepEMhancer_Danielle_4_9.mrc"

Opened DeepEMhancer_Danielle_4_9.mrc as #1, grid size 128,128,128, pixel 1.66,
shown at level 0.171, step 1, values float32  

> open
> C:/Users/daniellem/Downloads/fold_202411_11_fresh/fold_202411_11_fresh_model_0.cif

Chain information for fold_202411_11_fresh_model_0.cif #2  
---  
Chain | Description  
A B C | .  
  

> fitmap #2 inMap #1

Fit molecule fold_202411_11_fresh_model_0.cif (#2) to map
DeepEMhancer_Danielle_4_9.mrc (#1) using 16827 atoms  
average map value = 0.07522, steps = 844  
shifted from previous position = 175  
rotated from previous position = 54.2 degrees  
atoms outside contour = 14504, contour level = 0.17065  
  
Position of fold_202411_11_fresh_model_0.cif (#2) relative to
DeepEMhancer_Danielle_4_9.mrc (#1) coordinates:  
Matrix rotation and translation  
0.64792760 -0.62354966 -0.43746502 96.82197592  
0.74386964 0.64153909 0.18731140 110.82058535  
0.16385295 -0.44678117 0.87951055 97.73764625  
Axis -0.39073889 -0.37054262 0.84262761  
Axis point -58.82632784 190.65888686 0.00000000  
Rotation angle (degrees) 54.23312860  
Shift along axis 3.46057824  
  

> select add #2

16827 atoms, 17253 bonds, 2103 residues, 1 model selected  

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.90908,-0.24195,0.33917,98.645,-0.23659,0.3703,0.89828,112.27,-0.34293,-0.89685,0.27939,96.701

> view matrix models
> #2,0.53124,-0.06761,0.84452,97.684,-0.82947,0.1615,0.5347,110.22,-0.17254,-0.98455,0.029713,96.843

> view matrix models
> #2,0.41491,-0.042433,0.90887,97.121,-0.90723,-0.095219,0.40971,113.02,0.069157,-0.99455,-0.078003,97.834

> view matrix models
> #2,0.75288,0.027834,0.65757,97.316,-0.63298,-0.24308,0.73502,119.44,0.1803,-0.96961,-0.16539,97.49

> ui mousemode right "move picked models"

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.87103,0.31614,0.37598,92.913,-0.28071,-0.30778,0.90911,123.97,0.40312,-0.8974,-0.17934,97.549

> view matrix models
> #2,0.91536,0.086966,0.39313,97.148,-0.39835,0.053566,0.91567,117.07,0.058573,-0.99477,0.083675,97.517

> view matrix models
> #2,0.69172,-0.58695,0.42073,107.25,-0.39031,0.18632,0.90163,114.71,-0.60761,-0.78789,-0.10021,89.196

> view matrix models
> #2,0.65444,-0.63502,0.41045,107.75,-0.39395,0.17697,0.90193,114.84,-0.64538,-0.75195,-0.13435,88.167

> view matrix models
> #2,0.74125,-0.50299,0.44446,106.36,-0.46474,0.093202,0.88053,115.65,-0.48433,-0.85925,-0.16467,90.397

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.74125,-0.50299,0.44446,122.67,-0.46474,0.093202,0.88053,118.02,-0.48433,-0.85925,-0.16467,90.501

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.83206,-0.25682,0.49165,119.4,-0.49196,0.067772,0.86798,118.23,-0.25624,-0.96408,-0.069956,93.922

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.83206,-0.25682,0.49165,110.78,-0.49196,0.067772,0.86798,107.87,-0.25624,-0.96408,-0.069956,93.209

> select subtract #2

Nothing selected  

> 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  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 277 residues in model #2 to IUPAC-IUB
standards.  
Chain information for fold_202411_11_fresh_model_0.cif  
---  
Chain | Description  
2.2/A 2.2/B 2.2/C | .  
  
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: created disulfide bonds between the following residues:  
B125-B137; A125-A137; B484-B590; A120-A176; B355-B428; C484-C590; C181-C416;
A208-A219; A276-A309; B198-B227; B120-B176; A113-A185; B181-B416; B208-B219;
A181-A416; C120-C176; C125-C137; C198-C227; A484-A590; A362-A401; B583-B589;
A583-A589; C362-C401; A48-A68; B113-B185; B276-B309; C113-C185; C208-C219;
B362-B401; B48-B68; C48-C68; C276-C309; A198-A227; A355-A428; C355-C428;
C583-C589  

> save "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
> model/Isolde_316W.cxs"

> select add #2

16827 atoms, 17289 bonds, 2103 residues, 14 models selected  

> select subtract #1

16827 atoms, 17289 bonds, 2103 residues, 12 models selected  

> select add #2

16827 atoms, 17289 bonds, 2103 residues, 12 models selected  

> select add #2

16827 atoms, 17289 bonds, 2103 residues, 12 models selected  

> select add #2

16827 atoms, 17289 bonds, 2103 residues, 12 models selected  

> select subtract #2.1

16827 atoms, 17289 bonds, 2103 residues, 11 models selected  

> select add #2

16827 atoms, 17289 bonds, 2103 residues, 12 models selected  

> save "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
> model/Isolde_316W.cxs"

——— End of log from Wed Nov 13 16:05:25 2024 ———

opened ChimeraX session  

> ui mousemode right "rotate selected models"

> ui mousemode right rotate

> select add #2

16827 atoms, 17289 bonds, 2103 residues, 15 models selected  

> select add #2

16827 atoms, 17289 bonds, 2103 residues, 15 models selected  

> select subtract #2.1

16827 atoms, 17289 bonds, 2103 residues, 14 models selected  

> select #2

16827 atoms, 17289 bonds, 2103 residues, 15 models selected  

> select subtract #2.1

16827 atoms, 17289 bonds, 2103 residues, 14 models selected  

> select subtract #2.3

16827 atoms, 17289 bonds, 2103 residues, 13 models selected  

> ui mousemode right "move picked models"

> ui mousemode right "rotate selected models"

> stop isolde

Expected fewer arguments  

> select add #2

16827 atoms, 17289 bonds, 2103 residues, 15 models selected  

> deselect all

Unknown command: deselect all  

> deselect

Unknown command: deselect  

> ~select

Nothing selected  

> select add #2

16827 atoms, 17289 bonds, 2103 residues, 15 models selected  

> view matrix models
> #2,0.99575,-0.015637,0.090722,-4.4839,0.0014031,0.98793,0.15488,-10.121,-0.092049,-0.1541,0.98376,27.255

> view matrix models
> #2,0.78145,0.090022,-0.61745,60.114,0.035975,0.98139,0.18861,-15.794,0.62294,-0.1696,0.76367,-35.953

> view matrix models
> #2,0.71305,0.10657,-0.69297,71.605,-0.27531,0.95155,-0.13695,45.9,0.6448,0.28843,0.70784,-81.031

> view matrix models
> #2,0.89446,0.22625,-0.38569,16.741,-0.28596,0.95254,-0.10439,44.648,0.34377,0.20366,0.9167,-53.518

> view matrix models
> #2,0.94709,0.31726,0.048693,-29.856,-0.31545,0.94804,-0.041416,43.885,-0.059302,0.023864,0.99795,4.4102

> ui mousemode right "move picked models"

> view matrix models
> #2.2,1,5.6986e-16,-2.4286e-16,-9.5814,8.4893e-16,1,1.9082e-16,0.6637,-9.7145e-17,3.1225e-17,1,-0.41905

> select add #2

16827 atoms, 17289 bonds, 2103 residues, 15 models selected  

> ~select

Nothing selected  

> select add #1

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.99565,0.0035698,-0.093147,8.6107,0.0040819,0.99664,0.081827,-7.5691,0.093126,-0.081851,0.99228,-0.9953

> view matrix models
> #1,0.99643,0.0065949,-0.084219,7.3734,0.0032596,0.9932,0.11634,-10.247,0.084414,-0.1162,0.98963,4.0265

> ui mousemode right rotate

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.98436,-0.16331,-0.066065,25.793,0.1716,0.97369,0.14993,-30.516,0.039841,-0.15892,0.98649,14.137

> select subtract #1

Nothing selected  

> ~select

Nothing selected  

> select add #2

16827 atoms, 17289 bonds, 2103 residues, 15 models selected  

> ui mousemode right select

> ~select

Nothing selected  

> ~select

Nothing selected  

> clipper associate #1 toModel #2

Opened DeepEMhancer_Danielle_4_9.mrc as #2.1.1.1, grid size 128,128,128, pixel
1.66, shown at step 1, values float32  

> clipper associate #1 toModel #2

> volume #2.1.1.1 level 0.01818

> volume #2.1.1.1 level 0.006197

> volume #2.1.1.1 level 0.01884

> volume #2.1.1.1 level 0.01019

> volume #2.1.1.1 level 0.0042

> fitmap #2.2 inMap #2.1.1.1

Fit molecule fold_202411_11_fresh_model_0.cif (#2.2) to map
DeepEMhancer_Danielle_4_9.mrc (#2.1.1.1) using 16827 atoms  
average map value = 0, steps = 24  
shifted from previous position = 0  
rotated from previous position = 0 degrees  
atoms outside contour = 16827, contour level = 0.0042003  
  
Position of fold_202411_11_fresh_model_0.cif (#2.2) relative to
DeepEMhancer_Danielle_4_9.mrc (#2.1.1.1) coordinates:  
Matrix rotation and translation  
1.00000000 0.00000000 0.00000000 0.00000000  
0.00000000 1.00000000 0.00000000 0.00000000  
0.00000000 0.00000000 1.00000000 0.00000000  
Axis 0.00000000 0.00000000 1.00000000  
Axis point 0.00000000 0.00000000 0.00000000  
Rotation angle (degrees) 0.00000000  
Shift along axis 0.00000000  
  

> volume #2.1.1.1 color #ff6f82

> volume #2.1.1.1 orthoplanes xyz positionPlanes 64,64,64 style image region
> all

> mousemode rightMode "move planes"

> volume #2.1.1.1 orthoplanes xyz positionPlanes 64,64,64 style image region
> all

> mousemode rightMode "move planes"

> volume #2.1.1.1 orthoplanes xyz positionPlanes 64,64,64 style image region
> all

> mousemode rightMode "move planes"

> volume #2.1.1.1 orthoplanes xyz positionPlanes 64,64,64 style image region
> all

> mousemode rightMode "move planes"

> volume planes z style image imageMode "full region"

> mousemode rightMode "move planes"

> volume style mesh

[Repeated 1 time(s)]

> volume #2.1.1.1 style image region all imageMode "tilted slab"
> tiltedSlabAxis 0,0,1 tiltedSlabOffset 106.1 tiltedSlabSpacing 1.658
> tiltedSlabPlaneCount 10

> mousemode rightMode "rotate slab"

> volume planes z style image imageMode "full region"

> mousemode rightMode "move planes"

> volume #2.1.1.1 style image region all imageMode "tilted slab"
> tiltedSlabAxis 0,0,1 tiltedSlabOffset 106.1 tiltedSlabSpacing 1.658
> tiltedSlabPlaneCount 10

> mousemode rightMode "rotate slab"

> volume style mesh

> volume #2.1.1.1 change image level -0.0001408,0 level 0.1705,0.8 level
> 2.096,1

> volume #2.1.1.1 level 0.3019

> volume #2.1.1.1 orthoplanes xyz positionPlanes 64,64,64 style image region
> all

> mousemode rightMode "move planes"

> volume #2.1.1.1 orthoplanes xyz positionPlanes 64,64,64 style image region
> all

> mousemode rightMode "move planes"

> volume zone #2.1.1.1 nearAtoms #2.2 range 9.95

> volume region all imageMode "full region"

> volume unzone

> mousemode rightMode "crop volume"

> close #2.1.1.1

> select #1

Nothing selected  

> clipper associate #1 toModel #2

> close session

> open
> C:/Users/daniellem/Downloads/fold_202411_11_fresh/fold_202411_11_fresh_model_1.cif

Chain information for fold_202411_11_fresh_model_1.cif #1  
---  
Chain | Description  
A B C | .  
  

> open "C:/Users/daniellem/Desktop/CryoEM
> workshop/DeepEMhancer_Danielle_4_9.mrc"

Opened DeepEMhancer_Danielle_4_9.mrc as #2, grid size 128,128,128, pixel 1.66,
shown at level 0.171, step 1, values float32  

> clipper associate #2 toModel #1

Opened DeepEMhancer_Danielle_4_9.mrc as #1.1.1.1, grid size 128,128,128, pixel
1.66, shown at level 0, step 1, values float32  
Chain information for fold_202411_11_fresh_model_1.cif  
---  
Chain | Description  
1.2/A 1.2/B 1.2/C | .  
  

> zoom

Pixel size at center of rotation is 0.252  

> zoom

Pixel size at center of rotation is 0.252  

> volume #1.1.1.1 level 2.378e-07

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 286 residues in model #1.2 to IUPAC-IUB
standards.  
Done loading forcefield  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  

> volume #1.1.1.1 region 0,2,0,11,15,12

> set bgColor white

> set bgColor #ffffff00

> select add #1

16827 atoms, 17253 bonds, 2103 residues, 15 models selected  

> select add #1.2

16827 atoms, 17253 bonds, 2103 residues, 15 models selected  

> select add #1

16827 atoms, 17253 bonds, 2103 residues, 15 models selected  

> select add #1.2

16827 atoms, 17253 bonds, 2103 residues, 15 models selected  

> ~select

Nothing selected  

> view #1.1.1.1.2 clip false

No displayed objects specified.  

> view #1.1.1.1.2 clip false

No displayed objects specified.  

> view #1.1.1.1.2 clip false

No displayed objects specified.  

> show #1.1.1.1.2 target m

> hide #1.1.1.1.2 target m

> close #1.1.1.1.2

> hide target m

[Repeated 1 time(s)]

> close

> open
> C:\Users\daniellem\Downloads\fold_202411_11_fresh\fold_202411_11_fresh_model_1.cif
> format mmcif

Chain information for fold_202411_11_fresh_model_1.cif #1  
---  
Chain | Description  
A B C | .  
  

> open "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
> model/DeepEMhancer_Danielle_4_9.mrc"

Opened DeepEMhancer_Danielle_4_9.mrc as #2, grid size 128,128,128, pixel 1.66,
shown at level 0.171, step 1, values float32  

> volume #2 region 0,6,0,127,127,127

> select add #1

16827 atoms, 17253 bonds, 2103 residues, 1 model selected  

> volume #2 region 0,9,0,127,127,127

> volume #2 region 0,31,0,127,127,127

> volume #2 region 0,2,0,127,127,127

> volume #2 region 2,2,0,127,127,127

> volume #2 region 0,2,0,127,127,127

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.66525,-0.10274,0.73952,-3.3498,-0.70987,0.21988,0.66913,6.6393,-0.23135,-0.9701,0.073343,18.122

> view matrix models
> #1,0.66436,-0.098392,0.74091,-3.4057,-0.70806,0.23457,0.66606,6.4683,-0.23933,-0.96711,0.086172,18.055

> view matrix models
> #1,0.73489,-0.0012862,0.67819,-3.9016,-0.49398,0.68416,0.53657,1.0277,-0.46468,-0.72933,0.50214,14.374

> view matrix models
> #1,0.48401,-0.29693,0.82315,-0.71801,-0.38327,0.77371,0.50446,-0.064179,-0.78666,-0.55965,0.26068,14.723

> view matrix models
> #1,0.45881,-0.3301,0.82494,-0.27877,-0.38342,0.76399,0.51895,-0.033803,-0.80155,-0.5544,0.22396,14.879

> view matrix models
> #1,0.58787,-0.42542,0.68806,1.4842,-0.33441,0.64668,0.68555,-0.022276,-0.7366,-0.63311,0.2379,15.786

> ui mousemode right "move picked models"

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.58787,-0.42542,0.68806,89.581,-0.33441,0.64668,0.68555,125,-0.7366,-0.63311,0.2379,28.389

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.69323,-0.26637,0.66969,87.572,-0.39958,0.63127,0.6647,125.4,-0.59981,-0.72838,0.33118,28.789

> view matrix models
> #1,0.68673,-0.25861,0.67936,87.446,-0.37136,0.67861,0.63371,124.95,-0.6249,-0.68747,0.36998,28.176

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.68673,-0.25861,0.67936,89.311,-0.37136,0.67861,0.63371,114.2,-0.6249,-0.68747,0.36998,81.84

> ui mousemode right "move picked models"

> view matrix models #2,1,0,0,-3.1953,0,1,0,8.6026,0,0,1,-26.98

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.71675,0.27424,0.64114,83.225,-0.50588,0.8373,0.20739,115.63,-0.47996,-0.47299,0.73887,76.524

> view matrix models
> #1,-0.12708,0.40435,0.90573,81.28,-0.68048,0.62882,-0.3762,118.42,-0.72166,-0.66414,0.19524,82.162

> ui mousemode right "translate selected atoms"

> ui mousemode right "move picked models"

> view matrix models #2,1,0,0,74.792,0,1,0,-99.562,0,0,1,-42.19

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.064661,0.98545,0.15717,76.985,0.45325,0.16932,-0.87516,123.44,-0.88904,0.014648,-0.4576,79.166

> view matrix models
> #1,0.20735,0.96008,0.18775,76.042,0.080933,0.17443,-0.98134,125.61,-0.97491,0.21868,-0.041534,73.66

> view matrix models
> #1,0.52905,0.84743,0.044425,76.673,-0.40974,0.30094,-0.86113,125.75,-0.74312,0.43737,0.50644,66.766

> view matrix models
> #1,0.66252,0.74875,-0.021062,77.638,-0.32016,0.25765,-0.91165,126.14,-0.67717,0.61073,0.41042,64.875

> ui mousemode right "move picked models"

> select subtract #1

Nothing selected  

> select add #2

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.36714,-0.13671,-0.92007,246.56,-0.46121,0.83223,-0.3077,-0.0059004,0.80777,0.53731,0.24249,-124.99

> view matrix models
> #2,0.52398,-0.03222,-0.85112,210.75,-0.71814,0.52057,-0.46182,77.879,0.45795,0.85321,0.24963,-120.19

> view matrix models
> #2,0.30109,-0.16473,-0.93926,258.99,-0.83534,0.42952,-0.3431,90.528,0.45995,0.8879,-0.0082803,-100.69

> ui mousemode right "move picked models"

> view matrix models
> #2,0.30109,-0.16473,-0.93926,198.41,-0.83534,0.42952,-0.3431,218.9,0.45995,0.8879,-0.0082803,-85.192

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.18816,-0.14391,-0.97154,212.04,-0.86165,0.45054,-0.23362,209.62,0.47133,0.88108,-0.039224,-82.925

> view matrix models
> #2,0.18599,-0.16879,-0.96794,214.7,-0.86627,0.43672,-0.24261,212.49,0.46367,0.88362,-0.064991,-79.971

> view matrix models
> #2,0.1282,-0.10727,-0.98593,216.22,-0.87167,0.46198,-0.16361,203.12,0.47303,0.88038,-0.034277,-83.494

> select subtract #2

Nothing selected  

> fitmap map

Missing or invalid "atomsOrMap" argument: invalid objects specifier  

> fitmap

Missing or invalid "atomsOrMap" argument: empty atom specifier  

> fitmap

Missing or invalid "atomsOrMap" argument: empty atom specifier  

> ui mousemode right "move picked models"

> view matrix models
> #1,0.66252,0.74875,-0.021062,121.8,-0.32016,0.25765,-0.91165,144.36,-0.67717,0.61073,0.41042,58.518

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> roll

> stop

> ui mousemode right "translate selected models"

> undo

> redo

> ui mousemode right rotate

> ui mousemode right "move picked models"

> volume #2 level 0.2875

> volume #2 level 0.06889

> clipper associate #2 toModel #1

Opened DeepEMhancer_Danielle_4_9.mrc as #1.1.1.1, grid size 128,128,128, pixel
1.66, shown at level 0.0215, step 1, values float32  
Chain information for fold_202411_11_fresh_model_1.cif  
---  
Chain | Description  
1.2/A 1.2/B 1.2/C | .  
  

> volume #1.1.1.1 level 0.02788

> color #1.1.1.1 #1dffd9ff models

> set bgColor black

> set bgColor transparent

> save "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
> model/316W_diss_1.cxs"

> select add #1

16827 atoms, 17253 bonds, 2103 residues, 7 models selected  

> select subtract #1

Nothing selected  

> select add #1.2

16827 atoms, 17253 bonds, 2103 residues, 1 model selected  

> select subtract #1.2

Nothing selected  

> select add #1.2

16827 atoms, 17253 bonds, 2103 residues, 1 model selected  

> select subtract #1.2

Nothing selected  

> close #1

> open
> C:/Users/daniellem/Downloads/fold_202411_11_fresh/fold_202411_11_fresh_model_0.cif

Chain information for fold_202411_11_fresh_model_0.cif #1  
---  
Chain | Description  
A B C | .  
  

> open "C:/Users/daniellem/Desktop/CryoEM
> workshop/DeepEMhancer_Danielle_4_9.mrc"

Opened DeepEMhancer_Danielle_4_9.mrc as #2, grid size 128,128,128, pixel 1.66,
shown at level 0.171, step 1, values float32  

> fitmap #1 inMap #2

Fit molecule fold_202411_11_fresh_model_0.cif (#1) to map
DeepEMhancer_Danielle_4_9.mrc (#2) using 16827 atoms  
average map value = 0.07522, steps = 844  
shifted from previous position = 175  
rotated from previous position = 54.2 degrees  
atoms outside contour = 14504, contour level = 0.17065  
  
Position of fold_202411_11_fresh_model_0.cif (#1) relative to
DeepEMhancer_Danielle_4_9.mrc (#2) coordinates:  
Matrix rotation and translation  
0.64792760 -0.62354966 -0.43746502 96.82197592  
0.74386964 0.64153909 0.18731140 110.82058535  
0.16385295 -0.44678117 0.87951055 97.73764625  
Axis -0.39073889 -0.37054262 0.84262761  
Axis point -58.82632784 190.65888686 0.00000000  
Rotation angle (degrees) 54.23312860  
Shift along axis 3.46057824  
  

> select add #1

16827 atoms, 17253 bonds, 2103 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.99713,0.047993,-0.058537,89.39,0.058353,0.0052358,0.99828,118.88,0.048217,-0.99883,0.0024202,98.244

> view matrix models
> #1,0.8632,-0.0503,0.50236,89.98,-0.50441,-0.12817,0.8539,116.49,0.021437,-0.99048,-0.13601,96.623

> ui mousemode right "move picked models"

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.8632,-0.0503,0.50236,89.369,-0.50441,-0.12817,0.8539,114.78,0.021437,-0.99048,-0.13601,96.141

> view matrix models
> #1,0.8632,-0.0503,0.50236,51.119,-0.50441,-0.12817,0.8539,133.03,0.021437,-0.99048,-0.13601,97.843

> view matrix models
> #1,0.8632,-0.0503,0.50236,11.287,-0.50441,-0.12817,0.8539,109.46,0.021437,-0.99048,-0.13601,101.2

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.8632,-0.0503,0.50236,73.284,-0.50441,-0.12817,0.8539,117.42,0.021437,-0.99048,-0.13601,99.791

> view matrix models
> #1,0.8632,-0.0503,0.50236,70.626,-0.50441,-0.12817,0.8539,117.88,0.021437,-0.99048,-0.13601,99.742

> view matrix models
> #1,0.8632,-0.0503,0.50236,121.46,-0.50441,-0.12817,0.8539,114.41,0.021437,-0.99048,-0.13601,99.952

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.8253,-0.28919,0.48503,125.06,-0.54795,-0.20249,0.81163,115.12,-0.1365,-0.93561,-0.32557,97.173

> view matrix models
> #1,0.8233,-0.30662,0.47766,125.28,-0.55534,-0.26109,0.78958,115.9,-0.11739,-0.91532,-0.38523,96.754

> view matrix models
> #1,0.69075,0.22823,0.68613,117.35,-0.64306,-0.24003,0.72723,114.32,0.33067,-0.94355,-0.019031,102.83

> view matrix models
> #1,0.74225,-0.1389,0.65557,123.62,-0.66974,-0.12076,0.73271,112.12,-0.022608,-0.98292,-0.18266,99.155

> select subtract #1

Nothing selected  

> select add #2

2 models selected  

> view matrix models
> #2,0.9995,0.0074953,0.030735,-3.5727,-0.008337,0.99959,0.027347,-1.4932,-0.030517,-0.027589,0.99915,6.62

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.9995,0.0074953,0.030735,23.671,-0.008337,0.99959,0.027347,4.4973,-0.030517,-0.027589,0.99915,5.6597

> ui mousemode right rotate

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.97796,-0.014894,-0.20826,50.426,0.05381,0.98174,0.18248,-14.843,0.20174,-0.18966,0.9609,0.28557

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.97796,-0.014894,-0.20826,53.888,0.05381,0.98174,0.18248,-19.638,0.20174,-0.18966,0.9609,2.2334

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.98566,-0.0079441,-0.16857,48.617,0.044096,0.97631,0.21182,-20.604,0.1629,-0.21622,0.96266,9.4578

> view matrix models
> #2,0.95291,-0.0044741,-0.30321,64.289,0.14917,0.87746,0.45586,-44.084,0.26402,-0.47962,0.83681,38.3

> view matrix models
> #2,0.92066,-0.20279,-0.33356,92.584,0.33574,0.8473,0.41154,-58.164,0.19917,-0.49088,0.84816,45.955

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.92066,-0.20279,-0.33356,83.602,0.33574,0.8473,0.41154,-56.096,0.19917,-0.49088,0.84816,44.316

> select add #2

3 models selected  

> ui mousemode right translate

> ui mousemode right "translate selected atoms"

> ui mousemode right "move picked models"

> ui mousemode right select

> select subtract #2

Nothing selected  

> ui mousemode right "translate selected models"

> select add #2

3 models selected  

> select subtract #2

Nothing selected  

> ui mousemode right "move picked models"

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> select add #1

16827 atoms, 17253 bonds, 2103 residues, 1 model selected  

> view matrix models
> #1,0.74225,-0.1389,0.65557,125.13,-0.66974,-0.12076,0.73271,107.13,-0.022608,-0.98292,-0.18266,95.753

> select subtract #1

Nothing selected  

> isolde start

> clipper associate #2 toModel #1

Opened DeepEMhancer_Danielle_4_9.mrc as #1.1.1.1, grid size 128,128,128, pixel
1.66, shown at level 0.191, step 1, values float32  
Chain information for fold_202411_11_fresh_model_0.cif  
---  
Chain | Description  
1.2/A 1.2/B 1.2/C | .  
  

> isolde start

> set bgColor white

> set bgColor #ffffff00

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 277 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: created disulfide bonds between the following residues:  
B125-B137; B276-B309; C181-C416; B48-B68; C276-C309; C355-C428; A355-A428;
A362-A401; C484-C590; A276-A309; A181-A416; B583-B589; A125-A137; C113-C185;
B484-B590; C583-C589; B362-B401; B113-B185; C208-C219; A48-A68; C48-C68;
A113-A185; C198-C227; B208-B219; B181-B416; A583-A589; A208-A219; B198-B227;
B355-B428; C125-C137; A198-A227; C362-C401; B120-B176; A484-A590; A120-A176;
C120-C176  

> set silhouettes false

> ~select

Nothing selected  

> set silhouettes false

> delete ~protein

> addh

Summary of feedback from adding hydrogens to fold_202411_11_fresh_model_0.cif
#1.2  
---  
notes | Termini for fold_202411_11_fresh_model_0.cif (#1.2) chain A determined from SEQRES records  
Termini for fold_202411_11_fresh_model_0.cif (#1.2) chain B determined from
SEQRES records  
Termini for fold_202411_11_fresh_model_0.cif (#1.2) chain C determined from
SEQRES records  
Chain-initial residues that are actual N termini: /A MET 1, /B MET 1, /C MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A HIS 677, /B HIS 677, /C HIS
677  
Chain-final residues that are not actual C termini:  
1630 hydrogen bonds  
15663 hydrogens added  
  

> select #1

31698 atoms, 32088 bonds, 2031 residues, 16 models selected  

> clipper isolate #1 maskRadius 16

> view matrix models #1,1,0,0,7.0869,0,1,0,-0.39389,0,0,1,2.602

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.95983,0.26995,-0.076557,-10.994,-0.24059,0.93216,0.27052,16.377,0.14439,-0.24124,0.95966,14.374

> view matrix models
> #1,0.9876,-0.040147,-0.15174,25.439,0.021063,0.99189,-0.12534,6.9079,0.15554,0.1206,0.98044,-28.405

> view matrix models
> #1,0.99163,-0.083691,-0.098314,25.632,0.09889,0.98189,0.16158,-23.443,0.08301,-0.16995,0.98195,12.399

> hide atoms

> save "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
> model/316W_diss_1.cxs"

> show ~HC

> isolde restrain distances "#1/A,G"

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain distances "#1/B,F"

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> select #1

31698 atoms, 32088 bonds, 2031 residues, 17 models selected  

> isolde sim start sel

ISOLDE: started sim  

> ui mousemode right "isolde tug selection"

> select /B,F@CA

677 atoms, 677 residues, 1 model selected  

> select /A,H@CA

677 atoms, 677 residues, 1 model selected  

> select /A,B,C

31698 atoms, 32088 bonds, 2031 residues, 1 model selected  

> ui hideFloating toggle

[Repeated 1 time(s)]

> ~select

Nothing selected  

> ~select

Nothing selected  

> isolde sim pause

> select #1

31698 atoms, 32088 bonds, 2031 residues, 21 models selected  

> ui mousemode right "move picked models"

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.99163,-0.083691,-0.098314,22.128,0.09889,0.98189,0.16158,-23.116,0.08301,-0.16995,0.98195,10.873

> ui mousemode right "move picked models"

> isolde sim resume

> select A

Expected an objects specifier or a keyword  

> select /A

10566 atoms, 10696 bonds, 677 residues, 1 model selected  

> view matrix models
> #1.2,1,3.4694e-17,9.7145e-17,-0.57951,2.0817e-17,1,-5.5511e-17,0.97731,0,-8.3267e-17,1,0.16641

> view matrix models
> #1.2,1,6.0715e-17,1.1102e-16,-3.7199,1.3878e-17,1,-1.3878e-16,0.75132,1.3878e-17,-8.3267e-17,1,-1.2135

> view matrix models
> #1.2,1,-5.6725e-16,-4.1633e-17,-4.514,-4.4929e-16,1,-4.1633e-16,6.3267,-5.4123e-16,2.498e-16,1,0.76486

> select /A

10566 atoms, 10696 bonds, 677 residues, 1 model selected  

> ui mousemode right "isolde tug selection"

> ~select

Nothing selected  

> ~select

Nothing selected  

> chains

Unknown command: chains  

> chains/

Unknown command: chains/  

> /

Unknown command: /  

> select add #1.2

31698 atoms, 32088 bonds, 2031 residues, 14 models selected  

> select add #1.1.1

31698 atoms, 32088 bonds, 2031 residues, 17 models selected  

> select add #1

31698 atoms, 32088 bonds, 2031 residues, 21 models selected  

> select subtract #1.1.1

31698 atoms, 32088 bonds, 2031 residues, 16 models selected  

> select add #1.2

31698 atoms, 32088 bonds, 2031 residues, 17 models selected  

> select subtract #1.3

31698 atoms, 32088 bonds, 2031 residues, 15 models selected  

> select add #1.2

31698 atoms, 32088 bonds, 2031 residues, 16 models selected  

> ~select

Nothing selected  

> select add #1.1.1

4 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #1.1.1,1,-5.0307e-17,2.6368e-16,0.51738,-1.1796e-16,1,-6.3838e-16,-5.7231,6.9389e-17,1.3878e-16,1,0.10217

> ui mousemode right "rotate selected models"

> view matrix models
> #1.1.1,0.98912,-0.14707,-0.0035996,18.306,0.1471,0.9884,0.037814,-25.16,-0.0020035,-0.037932,0.99928,4.5772

> view matrix models
> #1.1.1,0.86583,-0.49895,-0.037256,74.567,0.49933,0.85694,0.1278,-60.241,-0.031839,-0.12925,0.9911,18.874

> view matrix models
> #1.1.1,0.9799,-0.19939,-0.0062574,25.388,0.19945,0.97857,0.05124,-31.446,-0.0040934,-0.051458,0.99867,6.3666

> view matrix models
> #1.1.1,0.99258,0.12162,-0.0012517,-11.88,-0.1216,0.99208,-0.031353,12.279,-0.0025713,0.031273,0.99951,-2.9923

> view matrix models
> #1.1.1,0.9998,-0.020045,-0.0001605,2.7614,0.020046,0.99979,0.0051605,-8.5229,5.7023e-05,-0.0051627,0.99999,0.66479

> view matrix models
> #1.1.1,0.99427,0.018958,-0.1052,8.6924,-0.019023,0.99982,0.00038549,-3.5055,0.10519,0.0016179,0.99445,-11.917

> view matrix models
> #1.1.1,0.98647,-0.12373,-0.10757,25.525,0.12676,0.99169,0.021827,-21.678,0.10397,-0.035167,0.99396,-7.6817

> ui mousemode right "translate selected models"

> view matrix models
> #1.1.1,0.98647,-0.12373,-0.10757,30.35,0.12676,0.99169,0.021827,-13.388,0.10397,-0.035167,0.99396,-6.3941

> ~select

Nothing selected  

> ui mousemode right rotate

> ~select

Nothing selected  

> ui mousemode right "move picked models"

> ui mousemode right "translate selected models"

> select add #1.1.1

4 models selected  

> view matrix models
> #1.1.1,0.98647,-0.12373,-0.10757,33.311,0.12676,0.99169,0.021827,-17.645,0.10397,-0.035167,0.99396,-5.3485

> select subtract #1.1.1

Nothing selected  

> ~select

Nothing selected  

> select /A

10566 atoms, 10696 bonds, 677 residues, 1 model selected  

> select /c

10566 atoms, 10696 bonds, 677 residues, 1 model selected  

> select /C

10566 atoms, 10696 bonds, 677 residues, 1 model selected  

> ui mousemode right "isolde tug selection"

[Repeated 1 time(s)]

> select /A

10566 atoms, 10696 bonds, 677 residues, 1 model selected  

> select /B

10566 atoms, 10696 bonds, 677 residues, 1 model selected  

> ~select

Nothing selected  

> select /B

10566 atoms, 10696 bonds, 677 residues, 1 model selected  

> ui mousemode right "isolde tug selection"

[Repeated 1 time(s)]

> ~select

Nothing selected  

> ui mousemode right "translate selected models"

> hide atoms

> show atoms

> select add #1.2

31698 atoms, 32088 bonds, 2031 residues, 14 models selected  

> select add #1.2

31698 atoms, 32088 bonds, 2031 residues, 14 models selected  

> select add #1.2

31698 atoms, 32088 bonds, 2031 residues, 14 models selected  

> ~select

Nothing selected  

> select add #1.2

31698 atoms, 32088 bonds, 2031 residues, 14 models selected  

> select add #1.2

31698 atoms, 32088 bonds, 2031 residues, 14 models selected  

> ~select

Nothing selected  

> select add #1.1.1

4 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #1.1.1,0.95386,-0.26947,-0.13243,55.464,0.27868,0.95872,0.056438,-35.107,0.11175,-0.090739,0.98958,0.24681

> view matrix models
> #1.1.1,0.86816,-0.46394,-0.17625,90.975,0.48447,0.86928,0.098215,-53.367,0.10765,-0.17066,0.97943,10.451

> view matrix models
> #1.1.1,0.72836,-0.29898,-0.61652,129.46,0.4368,0.89585,0.081589,-49.148,0.52792,-0.32872,0.7831,-3.8769

> ui mousemode right "move picked models"

> ui mousemode right "rotate selected models"

> view matrix models
> #1.1.1,0.85765,-0.27788,-0.43269,95.102,0.37939,0.90992,0.16766,-51.769,0.34712,-0.30795,0.88582,5.8133

> view matrix models
> #1.1.1,0.648,-0.46752,-0.60126,156.1,0.73192,0.6006,0.32181,-73.411,0.21067,-0.64861,0.73138,73.494

> view matrix models
> #1.1.1,0.73896,-0.48429,-0.4684,135.09,0.66602,0.63004,0.39933,-75.941,0.10172,-0.60706,0.78812,76.608

> view matrix models
> #1.1.1,0.81976,-0.49328,-0.29098,110.35,0.57131,0.66885,0.47565,-75.991,-0.040005,-0.55616,0.83011,83.909

> view matrix models
> #1.1.1,0.85593,-0.49206,-0.15894,93.907,0.49686,0.69745,0.51643,-74.068,-0.14326,-0.52099,0.84145,91.195

> view matrix models
> #1.1.1,0.82413,-0.49343,-0.2781,108.68,0.56418,0.67165,0.48019,-75.872,-0.050157,-0.55263,0.83191,84.555

> isolde sim pause

> view matrix models
> #1.1.1,0.97678,-0.058664,-0.20603,36.223,0.14599,0.88615,0.43981,-46.365,0.15678,-0.45967,0.87414,46.017

> ui mousemode right "move picked models"

> view matrix models
> #1.2,1,-2.5847e-16,5.8287e-16,-6.4386,-2.949e-16,1,-1.9429e-16,6.691,-5.8287e-16,-3.3307e-16,1,-0.1065

> isolde sim resume

> ui mousemode right "translate selected models"

> ui mousemode right rotate

> ~select

Nothing selected  

> ~select

Nothing selected  

> ~select

Nothing selected  

> select /A

10566 atoms, 10696 bonds, 677 residues, 1 model selected  

> ui mousemode right "isolde tug selection"

> select add #1

31698 atoms, 32088 bonds, 2031 residues, 21 models selected  

> select add #1

31698 atoms, 32088 bonds, 2031 residues, 21 models selected  

> select add #1

31698 atoms, 32088 bonds, 2031 residues, 21 models selected  

> ~select

Nothing selected  

> select /C

10566 atoms, 10696 bonds, 677 residues, 1 model selected  

> ~select

Nothing selected  

> rotate 30

Unknown command: rotate 30  

> rotate x 30

Unknown command: rotate x 30  

> turn 30

Expected an axis vector or a keyword  

> help help:user

> turn y 30

[Repeated 1 time(s)]

> select /B

10566 atoms, 10696 bonds, 677 residues, 1 model selected  

> isolde sim pause

> select

31698 atoms, 32088 bonds, 2031 residues, 21 models selected  

> ~select

Nothing selected  

> select add #1.1.1

4 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #1.1.1,0.97678,-0.058664,-0.20603,36.443,0.14599,0.88615,0.43981,-47.931,0.15678,-0.45967,0.87414,43.486

> ui mousemode right "rotate selected models"

> view matrix models
> #1.1.1,0.93878,-0.072118,-0.33688,54.349,0.21104,0.89328,0.39687,-52.488,0.27231,-0.44367,0.85382,29.924

> select add #1.1.1

4 models selected  

> select subtract #1.1.1

Nothing selected  

> ~select

Nothing selected  

> select add #1.2

31698 atoms, 32088 bonds, 2031 residues, 14 models selected  

> view matrix models
> #1.2,0.98911,-0.053048,-0.13729,11.919,0.074733,0.98461,0.15797,-14.293,0.1268,-0.16651,0.97785,3.142

> view matrix models
> #1.2,0.98948,0.016677,-0.14373,5.221,0.0055592,0.98822,0.15294,-5.6294,0.14458,-0.15213,0.97773,-0.5454

> view matrix models
> #1.2,0.98685,0.0096553,-0.16132,7.7496,0.012471,0.99069,0.13558,-5.287,0.16113,-0.13581,0.97754,-4.2736

> view matrix models
> #1.2,0.98778,0.006444,-0.15574,7.4975,0.02641,0.97778,0.20796,-11.769,0.15362,-0.20953,0.96566,5.2641

> view matrix models
> #1.2,0.8593,-0.4953,-0.12761,72.895,0.51115,0.8227,0.24878,-59.558,-0.018234,-0.27901,0.96012,34.297

> view matrix models
> #1.2,0.98861,0.0059789,-0.15036,6.9894,0.020811,0.98418,0.17597,-9.0452,0.14903,-0.17709,0.97284,1.8859

> ui mousemode right "move picked models"

> ui mousemode right "translate selected models"

> view matrix models
> #1.2,0.98861,0.0059789,-0.15036,15.778,0.020811,0.98418,0.17597,-19.022,0.14903,-0.17709,0.97284,-8.0522

> view matrix models
> #1.2,0.98861,0.0059789,-0.15036,12.948,0.020811,0.98418,0.17597,-19.55,0.14903,-0.17709,0.97284,-4.7808

> view matrix models
> #1.2,0.98861,0.0059789,-0.15036,8.191,0.020811,0.98418,0.17597,-20.422,0.14903,-0.17709,0.97284,-0.82751

> isolde sim resume

> select /A

10566 atoms, 10696 bonds, 677 residues, 1 model selected  

> ui mousemode right "isolde tug selection"

[Repeated 1 time(s)]

> ~select

Nothing selected  

> volume #1.1.1.1 level 0.1688

> volume #1.1.1.1 level 0.1198

> ui mousemode right "isolde tug selection"

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 61 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde start

> save "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
> model/316W_diss_2.cxs"

——— End of log from Wed Nov 13 21:10:41 2024 ———

opened ChimeraX session  

> clipper isolate #1 maskRadius 16

> isolde start

> isolde sim start /A-C

ISOLDE: started sim  

> ui mousemode right "isolde tug atom"

> ~select

Nothing selected  

> select /B

10566 atoms, 10696 bonds, 677 residues, 1 model selected  

> ui mousemode right "isolde tug selection"

> select

31698 atoms, 32088 bonds, 2031 residues, 24 models selected  

> ~select

Nothing selected  

> select /A

10566 atoms, 10696 bonds, 677 residues, 1 model selected  

> ui mousemode right "isolde tug selection"

[Repeated 1 time(s)]

> isolde restrain distances "#1/C"

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 8 residues in model #1.2 to IUPAC-IUB
standards.  

> ~select

Nothing selected  

> ui mousemode right "isolde tug residue"

> help help:user

> select add #1.2

31698 atoms, 32088 bonds, 2031 residues, 17 models selected  

> show ribbons

> ~select

Nothing selected  

> ui mousemode right swapaa

> swapaa mousemode /C:59 VAL

Sim termination reason: coord length mismatch  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 17 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> save "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
> model/316W_diss_3.cxs"

[Repeated 1 time(s)]

——— End of log from Wed Nov 13 21:59:07 2024 ———

opened ChimeraX session  




OpenGL version: 3.3.14761 Core Profile Forward-Compatible Context 21.30.44.03 30.0.13044.3001
OpenGL renderer: AMD Radeon(TM) Graphics
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.4
Locale: en_ZA.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: ASUSTeK COMPUTER INC.
Model: VivoBook_ASUSLaptop X421UAY_M413UA
OS: Microsoft Windows 11 Home Single Language (Build 22631)
Memory: 7,931,224,064
MaxProcessMemory: 137,438,953,344
CPU: 12 AMD Ryzen 5 5500U with Radeon Graphics         
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 2.4.1
    auditwheel: 6.1.0
    autocommand: 2.2.2
    babel: 2.16.0
    backports.tarfile: 1.2.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.7.1
    build: 1.2.1
    certifi: 2024.8.30
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.7
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.7
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-Clipper: 0.23.0
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9rc202411130312
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.5
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ISOLDE: 1.8.dev0
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.11
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.3.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.5
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.8
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.54.1
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.12.1
    html2text: 2024.2.26
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    importlib_metadata: 8.0.0
    importlib_resources: 6.4.0
    inflect: 7.3.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jaraco.context: 5.3.0
    jaraco.functools: 4.0.1
    jaraco.text: 3.12.1
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    more-itertools: 10.3.0
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.1
    numpy: 1.26.4
    openvr: 1.26.701
    ordered-set: 4.1.0
    packaging: 23.2
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    platformdirs: 4.2.2
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pywin32: 306
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4.1
    traitlets: 5.14.3
    typeguard: 4.3.0
    typing_extensions: 4.12.2
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    WMI: 1.5.1
    zipp: 3.19.2

[Tristan Croll]

Most likely reason for all of this mess is that ISOLDE 1.8.dev0 was never meant to be installable in ChimeraX 1.9. The fault is mine - specifically my failure to rtfm on the ~= operator... ​https://peps.python.org/pep-0440/#compatible-release

If a pre-release, post-release or developmental release is named in a compatible release clause as V.N.suffix, then the suffix is ignored when determining the required prefix match:

~= 2.2.post3
>= 2.2.post3, == 2.*

~= 1.4.5a4
>= 1.4.5a4, == 1.4.*

I've been using it under the assumption that ~=1.8.dev123 would expand to >=1.8.dev123, ==1.8.* where it *actually* makes >=1.8.dev123, ==1.*. Sigh. Will try not to make that mistake again.