restore_snapshot for "Redust" returned None

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Darwin-19.6.0-x86_64-i386-64bit
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open "/Users/jyeeles/ownCloud/Human replisome
> structure/300920_LrrCul2/Joe_ChimeraXa.cxs" format session

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

Log from Fri Oct 2 17:02:52 2020 Startup Errors  
---  
error | Bundle 'ChimeraX-Registration' custom initialization failed  
warnings | 'clip' is a prefix of an existing command 'clipper'  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 432, in initialize  
api._api_caller.initialize(api, session, self)  
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1625, in initialize  
return cls._get_func(api, "initialize")(session, bi)  
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/registration/__init__.py", line 41, in initialize  
nag(session)  
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 28, in nag  
if not check_registration(logger=session.logger):  
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 49, in check_registration  
return _check_expiration(param, logger)  
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 140, in _check_expiration  
logger.warning("Registration file %r has expired" % reg_file)  
NameError: name 'reg_file' is not defined  
  
UCSF ChimeraX version: 0.93 (2020-04-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open2 "/Users/jyeeles/Nextcloud/Human replisome
> structure/300920_LrrCul2/postprocess_masked_0110.mrc"

Opened postprocess_masked_0110.mrc, grid size 440,440,440, pixel 1.07, shown
at level 0.0158, step 2, values float32  

> volume #1 step 1

> volume #1 level 0.03037

> volume #1 level 0.02687

> volume #1 level 0.02068

> volume #1 level 0.02822

> volume #1 level 0.02257

> volume #1 level 0.02472

> open2 "/Users/jyeeles/Nextcloud/Human replisome
> structure/300920_LrrCul2/postprocess_masked.mrc"

Opened postprocess_masked.mrc, grid size 220,220,220, pixel 2.14, shown at
level 0.0329, step 1, values float32  

> volume #2 level 0.04704

> volume #1 level 0.02768

> open2 "/Users/jyeeles/Nextcloud/Human replisome
> structure/300920_LrrCul2/run_class001.mrc"

Opened run_class001.mrc, grid size 440,440,440, pixel 1.07, shown at level
0.0149, step 2, values float32  

> volume #3 step 1

> volume #3 level 0.01813

> volume #3 level 0.01983

> volume #1 level 0.02983

> volume #1 level 0.02579

> open 5n4w format mmCIF fromDatabase pdb

5n4w title:  
Crystal structure of the Cul2-Rbx1-EloBC-VHL ubiquitin ligase complex [more
info...]  
  
Chain information for 5n4w #4  
---  
Chain | Description  
A | Cullin-2  
B | Elongin-B  
C | Elongin-C  
R | E3 ubiquitin-protein ligase RBX1  
V | Von Hippel-Lindau disease tumor suppressor  
  
Non-standard residues in 5n4w #4  
---  
ZN — zinc ion  
  
  

> hide atoms

> show cartoons

> set bgColor white

> ui mousemode rightMode select

> select /A:716

6 atoms, 5 bonds, 1 model selected  

> ui mousemode rightMode zoom

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> toolshed show "Fit in Map"

Fit molecule 5n4w (#4) to map postprocess_masked_0110.mrc (#1) using 7719
atoms  
average map value = 0.01015, steps = 172  
shifted from previous position = 8.93  
rotated from previous position = 10.1 degrees  
atoms outside contour = 7216, contour level = 0.025794  
  
Position of 5n4w (#4) relative to postprocess_masked_0110.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.36687554 -0.51365176 -0.77560569 180.88574536  
-0.54236684 -0.55927665 0.62693527 269.48070716  
-0.75580457 0.65067003 -0.07340276 119.17600644  
Axis 0.56257123 -0.46933433 -0.68061655  
Axis point 141.39939379 91.78701151 0.00000000  
Rotation angle (degrees) 178.79126165  
Shift along axis -105.82859459  
  

> open2 "/Users/jyeeles/Nextcloud/Human replisome
> structure/300920_LrrCul2/3009_ep_no_edit-coot-1.pdb"

Summary of feedback from opening <_io.textiowrapper
name="/Users/jyeeles/Nextcloud/Human replisome
structure/300920_LrrCul2/3009_ep_no_edit-coot-1.pdb" mode="rt"
encoding="utf-8">  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ALA 91
ASP 93 1 3  
Start residue of secondary structure not found: HELIX 2 2 LEU 109 MET 111 1 3  
Start residue of secondary structure not found: HELIX 3 3 PRO 123 HIS 142 1 20  
Start residue of secondary structure not found: HELIX 4 4 ILE 168 GLY 173 1 6  
Start residue of secondary structure not found: HELIX 5 5 SER 248 TYR 255 1 8  
29 messages similar to the above omitted  
note | Combining 2 symmetry atoms into ZN /F:1000 ZN  
  
Chain information for 3009_ep_no_edit-coot-1.pdb #5  
---  
Chain | Description  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
K | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
S | No description available  
T U | No description available  
V | No description available  
W | No description available  
  

> hide sel atoms

> hide sel atoms

> hide sel atoms

> hide sel atoms

> hide sel atoms

> ui mousemode rightMode select

> select #5/3:62@NH2

1 atom, 1 model selected  

> hide sel atoms

> hide sel atoms

> hide sel atoms

> hide sel atoms

> hide #5 target a2

Invalid "target" argument: Target option can only include letters a = atoms, b
= bonds, p = pseudobonds, c = cartoons, r = cartoons, s = surfaces, m =
models, got 2  

> hide #5 target a

> show sel cartoons

> show #5 target c

Fit molecule 3009_ep_no_edit-coot-1.pdb (#5) to map
postprocess_masked_0110.mrc (#1) using 67249 atoms  
average map value = 0.02186, steps = 76  
shifted from previous position = 2.59  
rotated from previous position = 3.76 degrees  
atoms outside contour = 42799, contour level = 0.025794  
  
Position of 3009_ep_no_edit-coot-1.pdb (#5) relative to
postprocess_masked_0110.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99836054 -0.05027978 -0.02735296 18.62535802  
0.05112618 0.99820541 0.03117802 -18.06907144  
0.02573624 -0.03252536 0.99913950 4.14645232  
Axis -0.48630305 -0.40527579 0.77411942  
Axis point 354.82435150 373.13307735 0.00000000  
Rotation angle (degrees) 3.75542554  
Shift along axis 1.47523804  
  

> volume #1 level 0.02275

> transparency 30

Drag select of 1 residues  

> toolshed show "Side View"

Drag select of 1 postprocess_masked_0110.mrc  
Drag select of 1 postprocess_masked_0110.mrc , 4 residues  

> volume #1 level 0.02164

> select clear

> color red #5 target c

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color #5 red target c

> surface dust #5

No surfaces specified  

> surface dust #1

> color #5/2-7 blue target c

> color #5/H blue target c

> color #5/G grey target c

> color #5/C,E,F grey target c

> color #5/C,E,F, Dgrey target c

> color #5/C,E,F,D grey target c

> color #5/v, w pale green target c

> color #5/s, t, u palegreen orange target c

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color #5/s, t, u orange target c

> color #5/s, t, u cyan target c

> undo

> color #5/k cyan target c

> color #5/P lime green target c

> color #4/A red target c

> color #4/R orange target c

> color #4/B magenta target c

> color #4/C purple target c

> color #4/C magenta\ target c

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

> color #4/C magenta target c

> color #4/B purple target c

> color #4/B darkred purple target c

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color #4/B lilac target c

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

> color #4/B mauve target c

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

> color #4/B indigo target c

> color #4/V maroon target c

> color #5/O, N black target c

> color #5/M black target c

> volume #1 level 0.02524

> color #4/V dark cyan target c

> transparency 0

> transparency 20

> select #5/K:102

9 atoms, 8 bonds, 1 model selected  

> style sel stick

Changed 9 atom styles  

> show sel atoms

> select #5/K:104

7 atoms, 7 bonds, 1 model selected  

> show sel atoms

> style sel stick

Changed 7 atom styles  

> select #5/K:102

9 atoms, 8 bonds, 1 model selected  

> select clear

> select #5/K:101

7 atoms, 7 bonds, 1 model selected  

> show sel atoms

> style sel stick

Changed 7 atom styles  

> select #5/K:103

9 atoms, 8 bonds, 1 model selected  

> show sel atoms

> style sel stick

Changed 9 atom styles  

> select #5/K:102

9 atoms, 8 bonds, 1 model selected  

> select #5/K:102

9 atoms, 8 bonds, 1 model selected  

> select #5/K:101

7 atoms, 7 bonds, 1 model selected  

> volume #1 level 0.02219

Drag select of 1 postprocess_masked_0110.mrc , 1 residues  

> select clear

> select #5/3:555

7 atoms, 7 bonds, 1 model selected  

> select #5/W:523

9 atoms, 8 bonds, 1 model selected  

> open2 "/Users/jyeeles/Nextcloud/Human replisome
> structure/20200811_Human_replisome/Consensus_Refinement/3.24A_LocalFiltered/relion_locres_filtered.mrc"

Opened relion_locres_filtered.mrc, grid size 440,440,440, pixel 1.07, shown at
level 0.0182, step 2, values float32  

> volume #6 step 1

Fit map relion_locres_filtered.mrc in map postprocess_masked_0110.mrc using
849976 points  
correlation = 0.7963, correlation about mean = 0.3799, overlap = 708.3  
steps = 72, shift = 2.57, angle = 3.82 degrees  
  
Position of relion_locres_filtered.mrc (#6) relative to
postprocess_masked_0110.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99832353 -0.05193804 -0.02554546 18.70964174  
0.05275082 0.99808699 0.03224457 -18.65947210  
0.02382187 -0.03353806 0.99915350 4.77058865  
Axis -0.49411421 -0.37081373 0.78635128  
Axis point 356.84352267 362.27659912 0.00000000  
Rotation angle (degrees) 3.81678537  
Shift along axis 1.42584714  
  

> volume #6 level 0.0313

> volume #1 level 0.01942

> transparency

Missing or invalid "percent" argument: Expected a number  

> transparency 0

> volume #1 level 0.02081

> volume #1 level 0.02469

> volume #1 level 0.02607

> select #5/K:46

4 atoms, 3 bonds, 1 model selected  

> select #5/K:44

10 atoms, 10 bonds, 1 model selected  

> select #5/K:45

4 atoms, 3 bonds, 1 model selected  

> select #5/K:46

4 atoms, 3 bonds, 1 model selected  

> save2 "/Users/jyeeles/Nextcloud/Human replisome
> structure/300920_LrrCul2/Joe_ChimeraX.cxs"

> hide #!4 models

> volume #1 level 0.01693

> show #!4 models

> transparency 20

> volume #1 level 0.01915

> transparency 0

> transparency 20

> select clear

> hide #!4 models

Drag select of 3 residues  

> volume #1 level 0.02164

> transparency 0

> show #!4 models

> open2 "/Users/jyeeles/Nextcloud/Human replisome
> structure/300920_LrrCul2/LRR_C.pdb"

Chain information for LRR_C.pdb #7  
---  
Chain | Description  
A | No description available  
  
Drag select of  
Drag select of 260 residues  

> ui mousemode rightMode "translate selected models"

> hide #!5 models

> show #!5 models

> hide #!4 models

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

Fit molecule LRR_C.pdb (#7) to map postprocess_masked_0110.mrc (#1) using 4170
atoms  
average map value = 0.01789, steps = 156  
shifted from previous position = 7.1  
rotated from previous position = 22.9 degrees  
atoms outside contour = 2604, contour level = 0.02164  
  
Position of LRR_C.pdb (#7) relative to postprocess_masked_0110.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.69853195 -0.12455597 -0.70465517 232.06043463  
-0.60815148 0.41560704 -0.67633021 332.16558512  
0.37710062 0.90097535 0.21456590 64.85855161  
Axis 0.79952498 -0.54833433 -0.24513113  
Axis point 0.00000000 200.04289916 308.14615115  
Rotation angle (degrees) 80.54038129  
Shift along axis -12.49852764  
  

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

Fit molecule LRR_C.pdb (#7) to map postprocess_masked_0110.mrc (#1) using 4170
atoms  
average map value = 0.01895, steps = 212  
shifted from previous position = 4.44  
rotated from previous position = 34.8 degrees  
atoms outside contour = 2392, contour level = 0.02164  
  
Position of LRR_C.pdb (#7) relative to postprocess_masked_0110.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.70331364 -0.35475637 -0.61603395 337.95218033  
0.03040247 0.85077638 -0.52464771 245.47731255  
0.71022925 -0.38772085 -0.58757717 203.77763850  
Axis 0.09866261 -0.95563851 0.27752607  
Axis point 130.15944627 0.00000000 211.88017742  
Rotation angle (degrees) 136.05920476  
Shift along axis -144.69072373  
  

> transparency 20

> volume #1 level 0.03189

> volume #1 level 0.02829

Fit molecule LRR_C.pdb (#7) to map postprocess_masked_0110.mrc (#1) using 4170
atoms  
average map value = 0.01895, steps = 60  
shifted from previous position = 0.303  
rotated from previous position = 0.0416 degrees  
atoms outside contour = 3189, contour level = 0.028287  
  
Position of LRR_C.pdb (#7) relative to postprocess_masked_0110.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.70380066 -0.35431919 -0.61572926 337.94261127  
0.03048189 0.85087877 -0.52447703 245.45157688  
0.70974324 -0.38789588 -0.58804872 203.84983477  
Axis 0.09847659 -0.95568095 0.27744602  
Axis point 130.16148245 0.00000000 211.82452704  
Rotation angle (degrees) 136.09456308  
Shift along axis -144.73663565  
  
Fit molecule LRR_C.pdb (#7) to map postprocess_masked_0110.mrc (#1) using 4170
atoms  
average map value = 0.01895, steps = 40  
shifted from previous position = 0.0253  
rotated from previous position = 0.0343 degrees  
atoms outside contour = 3184, contour level = 0.028287  
  
Position of LRR_C.pdb (#7) relative to postprocess_masked_0110.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.70339322 -0.35466332 -0.61599666 337.94932080  
0.03035132 0.85084654 -0.52453689 245.46682787  
0.71015263 -0.38765201 -0.58771519 203.79629155  
Axis 0.09864323 -0.95566180 0.27745277  
Axis point 130.16139817 0.00000000 211.86356504  
Rotation angle (degrees) 136.06529242  
Shift along axis -144.70301226  
  

> show #!4 models

> open2 "/Users/jyeeles/Nextcloud/Human replisome
> structure/300920_LrrCul2/LRR_C2.pdb"

Chain information for LRR_C2.pdb #8  
---  
Chain | Description  
A | No description available  
  

> ui mousemode rightMode select

Drag select of 283 residues  

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "translate selected models"

> hide #!4 models

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

Fit molecule LRR_C2.pdb (#8) to map postprocess_masked_0110.mrc (#1) using
4522 atoms  
average map value = 0.01914, steps = 104  
shifted from previous position = 1.89  
rotated from previous position = 27 degrees  
atoms outside contour = 3489, contour level = 0.028287  
  
Position of LRR_C2.pdb (#8) relative to postprocess_masked_0110.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.17779502 -0.36837394 -0.91251829 327.17296438  
-0.10899894 0.92895842 -0.35377329 232.72332877  
0.97801238 0.03656440 -0.20531654 124.54016775  
Axis 0.20040402 -0.97062093 0.13316621  
Axis point 128.86929495 0.00000000 223.77238354  
Rotation angle (degrees) 103.12501778  
Shift along axis -143.73481618  
  

> select #8

4522 atoms, 4560 bonds, 1 model selected  

> close #8

Fit molecule LRR_C.pdb (#7) to map postprocess_masked_0110.mrc (#1) using 4170
atoms  
average map value = 0.01895, steps = 60  
shifted from previous position = 0.00279  
rotated from previous position = 0.0349 degrees  
atoms outside contour = 3185, contour level = 0.028287  
  
Position of LRR_C.pdb (#7) relative to postprocess_masked_0110.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.70381681 -0.35434536 -0.61569574 337.93311330  
0.03042871 0.85087803 -0.52448132 245.45630793  
0.70972950 -0.38787360 -0.58808000 203.87440787  
Axis 0.09849929 -0.95568136 0.27743654  
Axis point 130.15800390 0.00000000 211.83106201  
Rotation angle (degrees) 136.09655286  
Shift along axis -144.72963307  
  

> ui mousemode rightMode select

> select #1

4 models selected  

> select clear

> select #7/A:167

16 atoms, 15 bonds, 1 model selected  

> ui mousemode rightMode "translate selected models"

Fit molecule LRR_C.pdb (#7) to map postprocess_masked_0110.mrc (#1) using 4170
atoms  
average map value = 0.01882, steps = 76  
shifted from previous position = 1.96  
rotated from previous position = 11.1 degrees  
atoms outside contour = 3259, contour level = 0.028287  
  
Position of LRR_C.pdb (#7) relative to postprocess_masked_0110.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.67519913 -0.44115188 -0.59117776 342.11762296  
-0.15254892 0.86763497 -0.47322127 257.39612827  
0.72168895 -0.22933506 -0.65312362 198.80253330  
Axis 0.17851960 -0.96099096 0.21125132  
Axis point 147.87308837 0.00000000 203.25216521  
Rotation angle (degrees) 136.91523201  
Shift along axis -144.28335244  
  
Fit molecule LRR_C.pdb (#7) to map postprocess_masked_0110.mrc (#1) using 4170
atoms  
average map value = 0.01894, steps = 108  
shifted from previous position = 3.09  
rotated from previous position = 11.3 degrees  
atoms outside contour = 3231, contour level = 0.028287  
  
Position of LRR_C.pdb (#7) relative to postprocess_masked_0110.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.74801786 -0.33494925 -0.57295572 336.58723065  
0.01291961 0.85579048 -0.51716122 246.33117271  
0.66355281 -0.39424820 -0.63581916 212.45513479  
Axis 0.09525355 -0.95825344 0.26958693  
Axis point 132.44344471 0.00000000 207.77959398  
Rotation angle (degrees) 139.82017663  
Shift along axis -146.71143893  
  
Fit molecule LRR_C.pdb (#7) to map postprocess_masked_0110.mrc (#1) using 4170
atoms  
average map value = 0.01895, steps = 72  
shifted from previous position = 5.78  
rotated from previous position = 3.86 degrees  
atoms outside contour = 3184, contour level = 0.028287  
  
Position of LRR_C.pdb (#7) relative to postprocess_masked_0110.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.70355754 -0.35448304 -0.61591277 337.94821542  
0.03037926 0.85090841 -0.52443490 245.45202715  
0.70998864 -0.38768111 -0.58789410 203.81126627  
Axis 0.09856951 -0.95568433 0.27740137  
Axis point 130.16365379 0.00000000 211.83597865  
Rotation angle (degrees) 136.07691036  
Shift along axis -144.72573957  
  
Fit molecule LRR_C.pdb (#7) to map postprocess_masked_0110.mrc (#1) using 4170
atoms  
average map value = 0.01894, steps = 160  
shifted from previous position = 6.7  
rotated from previous position = 3.85 degrees  
atoms outside contour = 3231, contour level = 0.028287  
  
Position of LRR_C.pdb (#7) relative to postprocess_masked_0110.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.74790165 -0.33498896 -0.57308420 336.58904023  
0.01297465 0.85578426 -0.51717013 246.32521149  
0.66368273 -0.39422796 -0.63569610 212.42948978  
Axis 0.09525577 -0.95824878 0.26960270  
Axis point 132.43537299 0.00000000 207.78751139  
Rotation angle (degrees) 139.80982940  
Shift along axis -146.70722315  
  
Fit molecule LRR_C.pdb (#7) to map postprocess_masked_0110.mrc (#1) using 4170
atoms  
average map value = 0.01894, steps = 112  
shifted from previous position = 3.55  
rotated from previous position = 0.0414 degrees  
atoms outside contour = 3231, contour level = 0.028287  
  
Position of LRR_C.pdb (#7) relative to postprocess_masked_0110.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.74826553 -0.33517136 -0.57250226 336.58468844  
0.01253978 0.85568268 -0.51734890 246.38290368  
0.66328081 -0.39429340 -0.63607489 212.49558915  
Axis 0.09541751 -0.95822895 0.26961599  
Axis point 132.49315818 0.00000000 207.76788984  
Rotation angle (degrees) 139.84732234  
Shift along axis -146.68294956  
  
Fit molecule LRR_C.pdb (#7) to map postprocess_masked_0110.mrc (#1) using 4170
atoms  
average map value = 0.01879, steps = 88  
shifted from previous position = 7.59  
rotated from previous position = 16 degrees  
atoms outside contour = 3156, contour level = 0.028287  
  
Position of LRR_C.pdb (#7) relative to postprocess_masked_0110.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.65564935 -0.35809084 -0.66475173 337.37290698  
0.21564663 0.75491516 -0.61935419 243.49770083  
0.72361623 -0.54943065 -0.41773855 201.60263487  
Axis 0.04649569 -0.92319585 0.38150697  
Axis point 112.95784463 0.00000000 235.42760432  
Rotation angle (degrees) 131.24166039  
Shift along axis -132.19687200  
  
Fit molecule LRR_C.pdb (#7) to map postprocess_masked_0110.mrc (#1) using 4170
atoms  
average map value = 0.01879, steps = 100  
shifted from previous position = 6.33  
rotated from previous position = 0.00855 degrees  
atoms outside contour = 3155, contour level = 0.028287  
  
Position of LRR_C.pdb (#7) relative to postprocess_masked_0110.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.65570063 -0.35800797 -0.66474579 337.36929566  
0.21575963 0.75487027 -0.61936955 243.49289567  
0.72353607 -0.54954631 -0.41772525 201.61452921  
Axis 0.04643124 -0.92318320 0.38154544  
Axis point 112.94682294 0.00000000 235.43034508  
Rotation angle (degrees) 131.24481745  
Shift along axis -132.19897395  
  
Fit molecule LRR_C.pdb (#7) to map postprocess_masked_0110.mrc (#1) using 4170
atoms  
average map value = 0.01879, steps = 68  
shifted from previous position = 1.26  
rotated from previous position = 0.0427 degrees  
atoms outside contour = 3158, contour level = 0.028287  
  
Position of LRR_C.pdb (#7) relative to postprocess_masked_0110.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.65553233 -0.35836467 -0.66471957 337.36344749  
0.21513955 0.75512756 -0.61927161 243.51571983  
0.72387314 -0.54896004 -0.41791211 201.57593638  
Axis 0.04674947 -0.92326143 0.38131723  
Axis point 112.99556636 0.00000000 235.40087891  
Rotation angle (degrees) 131.23572270  
Shift along axis -132.19273285  
  
Fit molecule LRR_C.pdb (#7) to map postprocess_masked_0110.mrc (#1) using 4170
atoms  
average map value = 0.01868, steps = 128  
shifted from previous position = 4.83  
rotated from previous position = 8.54 degrees  
atoms outside contour = 3228, contour level = 0.028287  
  
Position of LRR_C.pdb (#7) relative to postprocess_masked_0110.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.68130948 -0.42858901 -0.59340445 339.61789846  
0.22231941 0.65121648 -0.72559710 261.32407513  
0.69741771 -0.62628152 -0.34839631 202.43727775  
Axis 0.06853807 -0.89080129 0.44919439  
Axis point 118.30390466 0.00000000 250.82300195  
Rotation angle (degrees) 133.57034648  
Shift along axis -118.57738092  
  

> open2 "/Users/jyeeles/Nextcloud/Human replisome
> structure/300920_LrrCul2/LRRs1.pdb"

Chain information for LRRs1.pdb #8  
---  
Chain | Description  
A | No description available  
  

> ui mousemode rightMode select

Drag select of 162 residues  
Drag select of 21 residues  
Drag select of 162 residues  

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

Fit molecule LRR_C.pdb (#7) to map postprocess_masked_0110.mrc (#1) using 4170
atoms  
average map value = 0.01868, steps = 108  
shifted from previous position = 2.51  
rotated from previous position = 0.014 degrees  
atoms outside contour = 3227, contour level = 0.028287  
  
Position of LRR_C.pdb (#7) relative to postprocess_masked_0110.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.68117208 -0.42874157 -0.59345197 339.62359977  
0.22220942 0.65127951 -0.72557422 261.32926973  
0.69758695 -0.62611153 -0.34836301 202.40793857  
Axis 0.06862906 -0.89081422 0.44915486  
Axis point 118.31576727 0.00000000 250.82424493  
Rotation angle (degrees) 133.56110570  
Shift along axis -118.57527275  
  
Fit molecule LRRs1.pdb (#8) to map postprocess_masked_0110.mrc (#1) using 2673
atoms  
average map value = 0.02173, steps = 136  
shifted from previous position = 7.1  
rotated from previous position = 37.5 degrees  
atoms outside contour = 1916, contour level = 0.028287  
  
Position of LRRs1.pdb (#8) relative to postprocess_masked_0110.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.72165426 -0.32290397 -0.61233014 334.43327740  
0.15476047 0.78690368 -0.59735402 242.36012498  
0.67473281 -0.52584756 -0.51789961 210.99986733  
Axis 0.05201594 -0.93624821 0.34746745  
Axis point 119.02032700 0.00000000 223.09188516  
Rotation angle (degrees) 136.57919133  
Shift along axis -136.19778610  
  

> hide #7 models

Fit molecule LRRs1.pdb (#8) to map postprocess_masked_0110.mrc (#1) using 2673
atoms  
average map value = 0.02169, steps = 76  
shifted from previous position = 3.31  
rotated from previous position = 5.63 degrees  
atoms outside contour = 1938, contour level = 0.028287  
  
Position of LRRs1.pdb (#8) relative to postprocess_masked_0110.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.72671107 -0.24094568 -0.64330105 332.10934845  
0.18531289 0.83298922 -0.52133302 231.37094395  
0.66147576 -0.49807045 -0.56069214 213.78119178  
Axis 0.01694490 -0.95042404 0.31049478  
Axis point 113.82068255 0.00000000 214.64287258  
Rotation angle (degrees) 136.65275406  
Shift along axis -147.89500477  
  
Fit molecule LRRs1.pdb (#8) to map postprocess_masked_0110.mrc (#1) using 2673
atoms  
average map value = 0.02169, steps = 104  
shifted from previous position = 8.51  
rotated from previous position = 0.0363 degrees  
atoms outside contour = 1938, contour level = 0.028287  
  
Position of LRRs1.pdb (#8) relative to postprocess_masked_0110.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.72685779 -0.24093151 -0.64314058 332.10415524  
0.18563462 0.83266864 -0.52173054 231.40408869  
0.66122430 -0.49861306 -0.56050644 213.81813656  
Axis 0.01684287 -0.95033055 0.31078637  
Axis point 113.80226050 0.00000000 214.68760578  
Rotation angle (degrees) 136.66450836  
Shift along axis -147.86502441  
  
Fit molecule LRRs1.pdb (#8) to map postprocess_masked_0110.mrc (#1) using 2673
atoms  
average map value = 0.02202, steps = 72  
shifted from previous position = 4.3  
rotated from previous position = 11.1 degrees  
atoms outside contour = 1863, contour level = 0.028287  
  
Position of LRRs1.pdb (#8) relative to postprocess_masked_0110.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.65628120 -0.13476287 -0.74238400 325.44602708  
0.36406191 0.80524773 -0.46801181 212.03502714  
0.66087363 -0.57742108 -0.47940691 213.39077437  
Axis -0.07326704 -0.93970587 0.33404313  
Axis point 91.44911344 0.00000000 219.37120493  
Rotation angle (degrees) 131.69921906  
Shift along axis -151.81330481  
  
Fit molecule LRRs1.pdb (#8) to map postprocess_masked_0110.mrc (#1) using 2673
atoms  
average map value = 0.02202, steps = 56  
shifted from previous position = 3.05  
rotated from previous position = 0.0351 degrees  
atoms outside contour = 1865, contour level = 0.028287  
  
Position of LRRs1.pdb (#8) relative to postprocess_masked_0110.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.65595665 -0.13459058 -0.74270202 325.44634987  
0.36457519 0.80508649 -0.46788963 212.00516967  
0.66091288 -0.57768603 -0.47903344 213.36434487  
Axis -0.07350276 -0.93964431 0.33416450  
Axis point 91.38927408 0.00000000 219.40106744  
Rotation angle (degrees) 131.67862692  
Shift along axis -151.83186696  
  
Fit molecule LRRs1.pdb (#8) to map postprocess_masked_0110.mrc (#1) using 2673
atoms  
average map value = 0.02169, steps = 68  
shifted from previous position = 1.61  
rotated from previous position = 11.1 degrees  
atoms outside contour = 1938, contour level = 0.028287  
  
Position of LRRs1.pdb (#8) relative to postprocess_masked_0110.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.72686457 -0.24092631 -0.64313486 332.10407585  
0.18564949 0.83265750 -0.52174303 231.40427229  
0.66121267 -0.49863417 -0.56050138 213.82065063  
Axis 0.01683675 -0.95032734 0.31079650  
Axis point 113.80129959 0.00000000 214.68932407  
Rotation angle (degrees) 136.66504461  
Shift along axis -147.86354479  
  
Fit molecule LRRs1.pdb (#8) to map postprocess_masked_0110.mrc (#1) using 2673
atoms  
average map value = 0.02169, steps = 104  
shifted from previous position = 4.68  
rotated from previous position = 0.022 degrees  
atoms outside contour = 1941, contour level = 0.028287  
  
Position of LRRs1.pdb (#8) relative to postprocess_masked_0110.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.72675964 -0.24076549 -0.64331365 332.09997707  
0.18601479 0.83257661 -0.52174201 231.39208213  
0.66122535 -0.49884688 -0.56029711 213.80276487  
Axis 0.01667810 -0.95029933 0.31089068  
Axis point 113.76464561 0.00000000 214.70429106  
Rotation angle (degrees) 136.65551539  
Shift along axis -147.88365852  
  

> ui mousemode rightMode "rotate selected models"

Fit molecule LRRs1.pdb (#8) to map postprocess_masked_0110.mrc (#1) using 2673
atoms  
average map value = 0.02169, steps = 84  
shifted from previous position = 5.3  
rotated from previous position = 14.4 degrees  
atoms outside contour = 1938, contour level = 0.028287  
  
Position of LRRs1.pdb (#8) relative to postprocess_masked_0110.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.72672974 -0.24071231 -0.64336732 332.09666361  
0.18613965 0.83254383 -0.52174979 231.38883709  
0.66122307 -0.49892725 -0.56022824 213.79779993  
Axis 0.01662437 -0.95028837 0.31092706  
Axis point 113.75153295 0.00000000 214.70951570  
Rotation angle (degrees) 136.65276124  
Shift along axis -147.88970231  
  
Fit molecule LRRs1.pdb (#8) to map postprocess_masked_0110.mrc (#1) using 2673
atoms  
average map value = 0.02169, steps = 76  
shifted from previous position = 0.47  
rotated from previous position = 14.6 degrees  
atoms outside contour = 1940, contour level = 0.028287  
  
Position of LRRs1.pdb (#8) relative to postprocess_masked_0110.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.72689522 -0.24098782 -0.64307717 332.10571190  
0.18534670 0.83281712 -0.52159589 231.40579248  
0.66126392 -0.49833778 -0.56070448 213.81024949  
Axis 0.01694647 -0.95037706 0.31063849  
Axis point 113.82867522 0.00000000 214.65777385  
Rotation angle (degrees) 136.66813948  
Shift along axis -147.87704479  
  

> ui mousemode rightMode "translate selected models"

Fit molecule LRRs1.pdb (#8) to map postprocess_masked_0110.mrc (#1) using 2673
atoms  
average map value = 0.02202, steps = 88  
shifted from previous position = 2.95  
rotated from previous position = 11.1 degrees  
atoms outside contour = 1865, contour level = 0.028287  
  
Position of LRRs1.pdb (#8) relative to postprocess_masked_0110.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.65589507 -0.13486949 -0.74270581 325.44928628  
0.36443621 0.80506613 -0.46803292 212.03063485  
0.66105063 -0.57764937 -0.47888756 213.33894120  
Axis -0.07337411 -0.93963430 0.33422092  
Axis point 91.39881715 -0.00000000 219.41881449  
Rotation angle (degrees) 131.67145130  
Shift along axis -151.80847156  
  
Fit molecule LRRs1.pdb (#8) to map postprocess_masked_0110.mrc (#1) using 2673
atoms  
average map value = 0.02202, steps = 64  
shifted from previous position = 0.57  
rotated from previous position = 0.0193 degrees  
atoms outside contour = 1865, contour level = 0.028287  
  
Position of LRRs1.pdb (#8) relative to postprocess_masked_0110.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.65612751 -0.13483573 -0.74250661 325.45907898  
0.36424844 0.80512347 -0.46808045 212.03775236  
0.66092345 -0.57757733 -0.47914993 213.36800552  
Axis -0.07331318 -0.93966081 0.33415975  
Axis point 91.43259475 0.00000000 219.39971705  
Rotation angle (degrees) 131.68823119  
Shift along axis -151.80500667  
  
Fit molecule LRRs1.pdb (#8) to map postprocess_masked_0110.mrc (#1) using 2673
atoms  
average map value = 0.02202, steps = 92  
shifted from previous position = 2.79  
rotated from previous position = 0.0281 degrees  
atoms outside contour = 1861, contour level = 0.028287  
  
Position of LRRs1.pdb (#8) relative to postprocess_masked_0110.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.65604486 -0.13438289 -0.74266171 325.42009618  
0.36450729 0.80522809 -0.46769883 211.98258732  
0.66086278 -0.57753701 -0.47928220 213.39440519  
Axis -0.07353929 -0.93969322 0.33401891  
Axis point 91.38415875 -0.00000000 219.36871478  
Rotation angle (degrees) 131.68612118  
Shift along axis -151.85199622  
  
Fit molecule LRRs1.pdb (#8) to map postprocess_masked_0110.mrc (#1) using 2673
atoms  
average map value = 0.02202, steps = 52  
shifted from previous position = 0.488  
rotated from previous position = 0.0318 degrees  
atoms outside contour = 1862, contour level = 0.028287  
  
Position of LRRs1.pdb (#8) relative to postprocess_masked_0110.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.65630979 -0.13474556 -0.74236186 325.44237157  
0.36407491 0.80523154 -0.46802956 212.03529007  
0.66083807 -0.57744770 -0.47942385 213.40025456  
Axis -0.07327568 -0.93970185 0.33405255  
Axis point 91.44713999 0.00000000 219.37225586  
Rotation angle (degrees) 131.70158782  
Shift along axis -151.81006645  
  
Fit molecule LRRs1.pdb (#8) to map postprocess_masked_0110.mrc (#1) using 2673
atoms  
average map value = 0.02202, steps = 48  
shifted from previous position = 1.04  
rotated from previous position = 0.0392 degrees  
atoms outside contour = 1865, contour level = 0.028287  
  
Position of LRRs1.pdb (#8) relative to postprocess_masked_0110.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.65596915 -0.13458339 -0.74269228 325.44739085  
0.36465110 0.80501778 -0.46794870 212.00733889  
0.66085859 -0.57778347 -0.47899083 213.37130826  
Axis -0.07353013 -0.93962307 0.33421820  
Axis point 91.38416268 -0.00000000 219.41032877  
Rotation angle (degrees) 131.68010793  
Shift along axis -151.82460083  
  
Fit molecule LRRs1.pdb (#8) to map postprocess_masked_0110.mrc (#1) using 2673
atoms  
average map value = 0.02169, steps = 64  
shifted from previous position = 3.88  
rotated from previous position = 11.1 degrees  
atoms outside contour = 1938, contour level = 0.028287  
  
Position of LRRs1.pdb (#8) relative to postprocess_masked_0110.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.72683702 -0.24105456 -0.64311794 332.11155296  
0.18536036 0.83278828 -0.52163710 231.40526898  
0.66132407 -0.49835372 -0.56061937 213.80802066  
Axis 0.01696338 -0.95036658 0.31066961  
Axis point 113.82692892 0.00000000 214.67174130  
Rotation angle (degrees) 136.66336123  
Shift along axis -147.86244635  
  
Fit molecule LRRs1.pdb (#8) to map postprocess_masked_0110.mrc (#1) using 2673
atoms  
average map value = 0.02169, steps = 48  
shifted from previous position = 0.871  
rotated from previous position = 0.0162 degrees  
atoms outside contour = 1938, contour level = 0.028287  
  
Position of LRRs1.pdb (#8) relative to postprocess_masked_0110.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.72687442 -0.24094880 -0.64311531 332.10487901  
0.18558998 0.83267810 -0.52173132 231.40628456  
0.66121855 -0.49858890 -0.56053471 213.81903362  
Axis 0.01686150 -0.95033395 0.31077495  
Axis point 113.80738072 0.00000000 214.68472923  
Rotation angle (degrees) 136.66598730  
Shift along axis -147.86386236  
  
Fit molecule LRRs1.pdb (#8) to map postprocess_masked_0110.mrc (#1) using 2673
atoms  
average map value = 0.02169, steps = 68  
shifted from previous position = 0.927  
rotated from previous position = 0.0188 degrees  
atoms outside contour = 1941, contour level = 0.028287  
  
Position of LRRs1.pdb (#8) relative to postprocess_masked_0110.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.72674675 -0.24083307 -0.64330291 332.10363235  
0.18588562 0.83262712 -0.52170744 231.39570186  
0.66127583 -0.49872994 -0.56034163 213.79240298  
Axis 0.01673785 -0.95031444 0.31084129  
Axis point 113.77716460 0.00000000 214.69599072  
Rotation angle (degrees) 136.65472745  
Shift along axis -147.88446971  
  
Fit molecule LRRs1.pdb (#8) to map postprocess_masked_0110.mrc (#1) using 2673
atoms  
average map value = 0.02169, steps = 64  
shifted from previous position = 1.02  
rotated from previous position = 0.00774 degrees  
atoms outside contour = 1941, contour level = 0.028287  
  
Position of LRRs1.pdb (#8) relative to postprocess_masked_0110.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.72675300 -0.24078253 -0.64331476 332.09964862  
0.18600222 0.83257633 -0.52174693 231.39464517  
0.66123618 -0.49883912 -0.56029125 213.79929451  
Axis 0.01668718 -0.95029907 0.31089100  
Axis point 113.76558213 0.00000000 214.70416553  
Rotation angle (degrees) 136.65500499  
Shift along axis -147.88403142  
  
Fit molecule LRRs1.pdb (#8) to map postprocess_masked_0110.mrc (#1) using 2673
atoms  
average map value = 0.02169, steps = 68  
shifted from previous position = 1.42  
rotated from previous position = 0.00334 degrees  
atoms outside contour = 1942, contour level = 0.028287  
  
Position of LRRs1.pdb (#8) relative to postprocess_masked_0110.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.72674937 -0.24078230 -0.64331896 332.10288264  
0.18596612 0.83260597 -0.52171250 231.39048636  
0.66125033 -0.49878975 -0.56031850 213.79856713  
Axis 0.01669798 -0.95030801 0.31086309  
Axis point 113.76959260 0.00000000 214.70016967  
Rotation angle (degrees) 136.65475317  
Shift along axis -147.88470204  
  

> select #5/3:222

9 atoms, 8 bonds, 1 model selected  

> select #5/3:216

6 atoms, 5 bonds, 1 model selected  

> select #5/3:214

7 atoms, 7 bonds, 1 model selected  

> style sel stick

Changed 7 atom styles  

> show sel atoms

> select #5/3:216

6 atoms, 5 bonds, 1 model selected  

> select #5/3:213

11 atoms, 11 bonds, 1 model selected  

> show sel atoms

> style sel stick

Changed 11 atom styles  

> select #5/3:216

6 atoms, 5 bonds, 1 model selected  

> show sel atoms

> style sel stick

Changed 6 atom styles  

> select #5/3:213

11 atoms, 11 bonds, 1 model selected  

> select #5/3:216

6 atoms, 5 bonds, 1 model selected  

> select #5/3:217

6 atoms, 5 bonds, 1 model selected  

> show sel atoms

> style sel stick

Changed 6 atom styles  

> select #5/3:203

11 atoms, 10 bonds, 1 model selected  

> show sel atoms

> show sel cartoons

> style sel stick

Changed 11 atom styles  
Drag select of  

> volume #1 level 0.02441

> show #!6 models

> volume #6 level 0.05232

> volume #6 level 0.04969

> volume #6 level 0.04838

Fit map relion_locres_filtered.mrc in map postprocess_masked_0110.mrc using
172838 points  
correlation = 0.8595, correlation about mean = 0.2338, overlap = 389.6  
steps = 44, shift = 0.0538, angle = 0.0485 degrees  
  
Position of relion_locres_filtered.mrc (#6) relative to
postprocess_masked_0110.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99832764 -0.05214502 -0.02495630 18.61317930  
0.05295116 0.99805791 0.03281127 -18.79851413  
0.02319689 -0.03407787 0.99914994 4.99283566  
Axis -0.50081969 -0.36053782 0.78688761  
Axis point 358.74662056 358.74229137 -0.00000000  
Rotation angle (degrees) 3.82904245  
Shift along axis 1.38452901  
  

> volume #6 level 0.0313

Fit map relion_locres_filtered.mrc in map postprocess_masked_0110.mrc using
358203 points  
correlation = 0.8317, correlation about mean = 0.3003, overlap = 533.6  
steps = 44, shift = 0.0517, angle = 0.0437 degrees  
  
Position of relion_locres_filtered.mrc (#6) relative to
postprocess_masked_0110.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99832991 -0.05188507 -0.02540323 18.64428600  
0.05269338 0.99808963 0.03225690 -18.63836272  
0.02368105 -0.03354161 0.99915673 4.80340665  
Axis -0.49491650 -0.36919709 0.78660737  
Axis point 356.78499487 361.51582212 0.00000000  
Rotation angle (degrees) 3.81151104  
Shift along axis 1.43225960  
  

> surface dust #4

No surfaces specified  

> surface dust #6

> volume #6 level 0.03458

Fit map relion_locres_filtered.mrc in map postprocess_masked_0110.mrc using
301872 points  
correlation = 0.8382, correlation about mean = 0.2833, overlap = 499.1  
steps = 44, shift = 0.00703, angle = 0.00758 degrees  
  
Position of relion_locres_filtered.mrc (#6) relative to
postprocess_masked_0110.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99833546 -0.05183295 -0.02529136 18.60061318  
0.05263867 0.99809094 0.03230539 -18.63328201  
0.02356860 -0.03358292 0.99915800 4.83410751  
Axis -0.49604781 -0.36784792 0.78652684  
Axis point 357.08958283 361.07072090 0.00000000  
Rotation angle (degrees) 3.80800221  
Shift along axis 1.42957599  
  

> save2 "/Users/jyeeles/Nextcloud/Human replisome
> structure/300920_LrrCul2/Joe_ChimeraXa.cxs"

> surface dust #6

Fit map postprocess_masked_0110.mrc in map relion_locres_filtered.mrc using
406573 points  
correlation = 0.7803, correlation about mean = 0.3552, overlap = 506.7  
steps = 44, shift = 0.0184, angle = 0.023 degrees  
  
Position of postprocess_masked_0110.mrc (#1) relative to
relion_locres_filtered.mrc (#6) coordinates:  
Matrix rotation and translation  
0.99834062 0.05242034 0.02383527 -17.71418945  
-0.05160098 0.99809626 -0.03378153 19.70984200  
-0.02556073 0.03249555 0.99914498 -3.72319840  
Axis 0.49883103 0.37177649 -0.78291114  
Axis point 358.45541397 362.65429655 0.00000000  
Rotation angle (degrees) 3.80910093  
Shift along axis 1.40620197  
  

> open2 "/Users/jyeeles/Nextcloud/Human replisome
> structure/300920_LrrCul2/88ccc456a9e632f9/c6s6qB_.1.pdb"

Chain information for c6s6qB_.1.pdb #9  
---  
Chain | Description  
| No description available  
  

> ui mousemode rightMode select

Drag select of 182 residues  
Drag select of 102 residues  
Drag select of 182 residues  

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

Fit molecule c6s6qB_.1.pdb (#9) to map relion_locres_filtered.mrc (#6) using
1451 atoms  
average map value = 0.02357, steps = 212  
shifted from previous position = 25.9  
rotated from previous position = 20.7 degrees  
atoms outside contour = 1136, contour level = 0.034583  
  
Position of c6s6qB_.1.pdb (#9) relative to relion_locres_filtered.mrc (#6)
coordinates:  
Matrix rotation and translation  
0.00213692 -0.35051332 0.93655531 187.73838524  
-0.96008308 0.26124300 0.09996289 330.19737716  
-0.27970684 -0.89938451 -0.33596365 287.98951701  
Axis -0.59200758 0.72050662 -0.36110557  
Axis point 342.45637606 -0.00000000 150.02302115  
Rotation angle (degrees) 122.43156496  
Shift along axis 22.77222740  
  

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

Fit molecule c6s6qB_.1.pdb (#9) to map relion_locres_filtered.mrc (#6) using
1451 atoms  
average map value = 0.02021, steps = 376  
shifted from previous position = 24.2  
rotated from previous position = 4.09 degrees  
atoms outside contour = 1216, contour level = 0.034583  
  
Position of c6s6qB_.1.pdb (#9) relative to relion_locres_filtered.mrc (#6)
coordinates:  
Matrix rotation and translation  
-0.66376821 -0.74791738 -0.00560009 297.09699497  
-0.73991438 0.65553502 0.15099856 272.40056701  
-0.10926339 0.10437164 -0.98851812 242.93548509  
Axis -0.40919395 0.90974037 0.07023365  
Axis point 213.45924396 0.00000000 105.37863673  
Rotation angle (degrees) 176.73385545  
Shift along axis 143.30574682  
  
Fit molecule c6s6qB_.1.pdb (#9) to map postprocess_masked_0110.mrc (#1) using
1451 atoms  
average map value = 0.01545, steps = 192  
shifted from previous position = 2.34  
rotated from previous position = 20.2 degrees  
atoms outside contour = 1083, contour level = 0.02441  
  
Position of c6s6qB_.1.pdb (#9) relative to postprocess_masked_0110.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.71694047 -0.66532567 0.20817812 288.44340243  
-0.58594107 0.73688917 0.33714600 245.92101180  
-0.37771609 0.11973350 -0.91814729 257.99135502  
Axis -0.34512436 0.93005861 0.12601649  
Axis point 210.49305651 0.00000000 82.42848953  
Rotation angle (degrees) 161.64057251  
Shift along axis 161.68327465  
  
Fit molecule c6s6qB_.1.pdb (#9) to map postprocess_masked_0110.mrc (#1) using
1451 atoms  
average map value = 0.01983, steps = 160  
shifted from previous position = 20.4  
rotated from previous position = 32.9 degrees  
atoms outside contour = 956, contour level = 0.02441  
  
Position of c6s6qB_.1.pdb (#9) relative to postprocess_masked_0110.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.26941146 -0.86344521 0.42647373 262.76065486  
-0.64003615 0.49143058 0.59063502 268.98175326  
-0.71956321 -0.11383476 -0.68503317 270.14290999  
Axis -0.51659925 0.84040770 0.16382953  
Axis point 272.17587805 0.00000000 31.00749725  
Rotation angle (degrees) 137.01288185  
Shift along axis 134.56976641  
  

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

Fit molecule c6s6qB_.1.pdb (#9) to map postprocess_masked_0110.mrc (#1) using
1451 atoms  
average map value = 0.02312, steps = 264  
shifted from previous position = 2.95  
rotated from previous position = 51.1 degrees  
atoms outside contour = 769, contour level = 0.02441  
  
Position of c6s6qB_.1.pdb (#9) relative to postprocess_masked_0110.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.41180135 -0.70569125 0.57655833 252.75884291  
-0.90931750 0.35964846 -0.20927180 315.61720612  
-0.05967703 -0.61045298 -0.78980112 247.05345682  
Axis -0.51484053 0.81648834 -0.26131596  
Axis point 258.61643380 0.00000000 138.61040617  
Rotation angle (degrees) 157.06933385  
Shift along axis 63.00826051  
  

> ui mousemode rightMode select

> select clear

> transparency 0

> save2 "/Users/jyeeles/Nextcloud/Human replisome
> structure/300920_LrrCul2/Joe_ChimeraXa.cxs"

restore_snapshot for "Redust" returned None  

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 683, in restore  
obj = sm.restore_snapshot(self, data)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/updaters.py", line 26, in restore_snapshot  
return SurfaceUpdaters(data['updaters'])  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/updaters.py", line 10, in __init__  
self._updaters = WeakSet(updaters)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/_weakrefset.py",
line 50, in __init__  
self.update(data)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/_weakrefset.py",
line 120, in update  
self.add(element)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/_weakrefset.py",
line 84, in add  
self.data.add(ref(item, self._remove))  
TypeError: cannot create weak reference to 'NoneType' object  
  
opened ChimeraX session  




OpenGL version: 4.1 INTEL-14.7.8
OpenGL renderer: Intel(R) Iris(TM) Graphics 550
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro13,2
      Processor Name: Dual-Core Intel Core i5
      Processor Speed: 3.1 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 428.0.0.0.0
      SMC Version (system): 2.37f24

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H2)
      Kernel Version: Darwin 19.6.0
      Time since boot: 8:46

Graphics/Displays:

    Intel Iris Graphics 550:

      Chipset Model: Intel Iris Graphics 550
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x1927
      Revision ID: 0x000a
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.0
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.0
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

[Tom Goddard]

Fixed.

Tried to restore a session with a surface dust updater probably on a volume file that was missing and the user chose not to replace. Made code handle missing surface updaters.