Opened 4 years ago

Closed 4 years ago

#4791 closed defect (fixed)

Map Fit: local variable 'm' referenced before assignment

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/YoyoHuang/Desktop/for binding analysis map.ccp4"

Opened for binding analysis map.ccp4 as #1, grid size 193,225,289, pixel
0.6,0.574,0.585, shown at level 15.3, step 1, values float32  

> volume #1 level 15.33

> volume #1 level 15

> volume #1 level 20

> volume #1 level 29.22

> volume #1 level 75.32

> open "/Users/YoyoHuang/Desktop/RNAP-PmrA/20210511 for binding analysis.pdb"

Chain information for 20210511 for binding analysis.pdb #2  
---  
Chain | Description  
1 | No description available  
2 | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
  

> move #1 sameas #2

Missing or invalid "axis" argument: Expected 3 floats or "x", or "y", or "z"
or two atoms  

> move position #1 sameas #2

Missing or invalid "axis" argument: Expected 3 floats or "x", or "y", or "z"
or two atoms  

> position #1 sameas #2

Unknown command: position #1 sameas #2  

> view position #1 sameAsModels #2

> view #1 sameas #2

Expected an integer >= 1 or a keyword  

> view position #1 sameAsModels #2

> select #1

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #1,1,0,0,-31.907,0,1,0,112.71,0,0,1,45.26

> view position #1 sameAsModels #2

> open /Users/YoyoHuang/Desktop/ech.pdb

Chain information for ech.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
F | No description available  
G | No description available  
H I | No description available  
  

> hide #!2 models

> hide #!3 models

> show #!3 models

> close #2

> close #1

> open "/Users/YoyoHuang/Desktop/RNAP-PmrA/20210511 for binding analysis.pdb"

Chain information for 20210511 for binding analysis.pdb #1  
---  
Chain | Description  
1 | No description available  
2 | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
  

> open /Users/YoyoHuang/Desktop/for_binding_analysis_e_map.ccp4

Opened for_binding_analysis_e_map.ccp4 as #2, grid size 43,43,50, pixel
2.1,2.1,2.1, shown at level 31.7, step 1, values float32  

> open /Users/YoyoHuang/Desktop/apbs_map01.ccp4

Opened apbs_map01.ccp4 as #4, grid size 193,225,289, pixel 0.6,0.574,0.585,
shown at level 15.3, step 1, values float32  

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> volume #2 level 9.861

> volume #2 level 2.567

> hide #!3 models

> show #!3 models

> hide #!3 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> select #4

2 models selected  

> view matrix models #4,1,0,0,63.182,0,1,0,66.492,0,0,1,39.91

> view matrix models #4,1,0,0,136.52,0,1,0,122.41,0,0,1,60.972

> view matrix models #4,1,0,0,139.53,0,1,0,125.72,0,0,1,53.608

> view matrix models #4,1,0,0,138.28,0,1,0,125.4,0,0,1,52.605

> view matrix models #4,1,0,0,138.91,0,1,0,125.31,0,0,1,52.315

> view matrix models #4,1,0,0,136.95,0,1,0,125.86,0,0,1,51.193

> view matrix models #4,1,0,0,137.06,0,1,0,125.81,0,0,1,51.426

> ~select #4

Nothing selected  

> hide #!1 cartoons

> hide #!1 atoms

> show #!1 cartoons

> hide #!1 cartoons

> show #!1 atoms

> style #!1 stick

Changed 7726 atom styles  

> color #!1 byhetero

> volume #4 level 93.7

> ui tool show "Fit in Map"

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> close #2

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

Fit molecule 20210511 for binding analysis.pdb (#1) to map apbs_map01.ccp4
(#4) using 7726 atoms  
average map value = -6.791, steps = 84  
shifted from previous position = 1.34  
rotated from previous position = 0.296 degrees  
atoms outside contour = 7544, contour level = 93.7  
  
Position of 20210511 for binding analysis.pdb (#1) relative to apbs_map01.ccp4
(#4) coordinates:  
Matrix rotation and translation  
0.99999930 -0.00115782 -0.00023303 -136.37854544  
0.00115898 0.99998673 0.00502030 -126.24189403  
0.00022722 -0.00502057 0.99998737 -51.60342015  
Axis -0.97342761 -0.04461926 0.22460591  
Axis point 0.00000000 -16011.25157118 23977.00000337  
Rotation angle (degrees) 0.29550326  
Shift along axis 126.79702800  
  
Fit molecule 20210511 for binding analysis.pdb (#1) to map apbs_map01.ccp4
(#4) using 7726 atoms  
average map value = -6.768, steps = 48  
shifted from previous position = 0.00993  
rotated from previous position = 0.00448 degrees  
atoms outside contour = 7540, contour level = 93.7  
  
Position of 20210511 for binding analysis.pdb (#1) relative to apbs_map01.ccp4
(#4) coordinates:  
Matrix rotation and translation  
0.99999929 -0.00115128 -0.00030977 -136.37892499  
0.00115283 0.99998666 0.00503423 -126.24228478  
0.00030397 -0.00503458 0.99998728 -51.61862755  
Axis -0.97308611 -0.05931328 0.22267770  
Axis point 0.00000000 -16004.67087236 23518.02328150  
Rotation angle (degrees) 0.29642954  
Shift along axis 128.70196449  
  
Fit molecule 20210511 for binding analysis.pdb (#1) to map apbs_map01.ccp4
(#4) using 7726 atoms  
average map value = -6.803, steps = 28  
shifted from previous position = 0.0121  
rotated from previous position = 0.003 degrees  
atoms outside contour = 7547, contour level = 93.7  
  
Position of 20210511 for binding analysis.pdb (#1) relative to apbs_map01.ccp4
(#4) coordinates:  
Matrix rotation and translation  
0.99999926 -0.00116038 -0.00035363 -136.35926524  
0.00116214 0.99998679 0.00500728 -126.23843418  
0.00034782 -0.00500768 0.99998740 -51.63106759  
Axis -0.97188864 -0.06807099 0.22538590  
Axis point 0.00000000 -16197.00355952 23408.02703060  
Rotation angle (degrees) 0.29520741  
Shift along axis 129.48228154  
  
Fit molecule 20210511 for binding analysis.pdb (#1) to map apbs_map01.ccp4
(#4) using 7726 atoms  
average map value = -6.801, steps = 44  
shifted from previous position = 0.0016  
rotated from previous position = 0.00656 degrees  
atoms outside contour = 7546, contour level = 93.7  
  
Position of 20210511 for binding analysis.pdb (#1) relative to apbs_map01.ccp4
(#4) coordinates:  
Matrix rotation and translation  
0.99999927 -0.00118417 -0.00024521 -136.36795001  
0.00118539 0.99998662 0.00503507 -126.24562452  
0.00023924 -0.00503535 0.99998729 -51.60355228  
Axis -0.97235050 -0.04677617 0.22879358  
Axis point 0.00000000 -16065.19299077 23853.57938268  
Rotation angle (degrees) 0.29670115  
Shift along axis 126.69616962  
  
Fit molecule 20210511 for binding analysis.pdb (#1) to map apbs_map01.ccp4
(#4) using 7726 atoms  
average map value = -6.804, steps = 44  
shifted from previous position = 0.00133  
rotated from previous position = 0.00618 degrees  
atoms outside contour = 7546, contour level = 93.7  
  
Position of 20210511 for binding analysis.pdb (#1) relative to apbs_map01.ccp4
(#4) coordinates:  
Matrix rotation and translation  
0.99999932 -0.00112052 -0.00032202 -136.37075746  
0.00112214 0.99998649 0.00507621 -126.23915079  
0.00031633 -0.00507657 0.99998706 -51.61132686  
Axis -0.97462638 -0.06127860 0.21528666  
Axis point 0.00000000 -15719.17634851 23263.23292252  
Rotation angle (degrees) 0.29842906  
Shift along axis 129.53506685  
  
Fit molecule 20210511 for binding analysis.pdb (#1) to map apbs_map01.ccp4
(#4) using 7726 atoms  
average map value = -6.791, steps = 44  
shifted from previous position = 0.00295  
rotated from previous position = 0.00368 degrees  
atoms outside contour = 7544, contour level = 93.7  
  
Position of 20210511 for binding analysis.pdb (#1) relative to apbs_map01.ccp4
(#4) coordinates:  
Matrix rotation and translation  
0.99999933 -0.00112082 -0.00027709 -136.37933025  
0.00112222 0.99998625 0.00512218 -126.24406822  
0.00027135 -0.00512248 0.99998684 -51.59207674  
Axis -0.97552682 -0.05222436 0.21358848  
Axis point 0.00000000 -15494.29633473 23293.65460681  
Rotation angle (degrees) 0.30085204  
Shift along axis 128.61523758  
  
Fit molecule 20210511 for binding analysis.pdb (#1) to map apbs_map01.ccp4
(#4) using 7726 atoms  
average map value = -6.802, steps = 44  
shifted from previous position = 0.00308  
rotated from previous position = 0.00236 degrees  
atoms outside contour = 7545, contour level = 93.7  
  
Position of 20210511 for binding analysis.pdb (#1) relative to apbs_map01.ccp4
(#4) coordinates:  
Matrix rotation and translation  
0.99999932 -0.00113746 -0.00026501 -136.37444907  
0.00113879 0.99998642 0.00508643 -126.24293996  
0.00025922 -0.00508673 0.99998703 -51.59709584  
Axis -0.97463861 -0.05022359 0.21807607  
Axis point 0.00000000 -15691.15827215 23513.71498352  
Rotation angle (degrees) 0.29902475  
Shift along axis 128.00408570  
  
Fit molecule 20210511 for binding analysis.pdb (#1) to map apbs_map01.ccp4
(#4) using 7726 atoms  
average map value = -6.8, steps = 44  
shifted from previous position = 0.00102  
rotated from previous position = 0.00225 degrees  
atoms outside contour = 7546, contour level = 93.7  
  
Position of 20210511 for binding analysis.pdb (#1) relative to apbs_map01.ccp4
(#4) coordinates:  
Matrix rotation and translation  
0.99999934 -0.00111182 -0.00028301 -136.37826102  
0.00111325 0.99998632 0.00511009 -126.24132587  
0.00027733 -0.00511041 0.99998690 -51.59613116  
Axis -0.97571331 -0.05349365 0.21241933  
Axis point 0.00000000 -15512.20297474 23313.86375002  
Rotation angle (degrees) 0.30008515  
Shift along axis 128.85917794  
  
Fit molecule 20210511 for binding analysis.pdb (#1) to map apbs_map01.ccp4
(#4) using 7726 atoms  
average map value = -6.8, steps = 44  
shifted from previous position = 0.00222  
rotated from previous position = 0.00683 degrees  
atoms outside contour = 7545, contour level = 93.7  
  
Position of 20210511 for binding analysis.pdb (#1) relative to apbs_map01.ccp4
(#4) coordinates:  
Matrix rotation and translation  
0.99999928 -0.00117979 -0.00023064 -136.37136478  
0.00118094 0.99998667 0.00502722 -126.24529480  
0.00022470 -0.00502749 0.99998734 -51.60198021  
Axis -0.97258201 -0.04404456 0.22835129  
Axis point 0.00000000 -16065.89134017 23962.21332272  
Rotation angle (degrees) 0.29616807  
Shift along axis 126.40937512  
  
Fit molecule 20210511 for binding analysis.pdb (#1) to map apbs_map01.ccp4
(#4) using 7726 atoms  
average map value = -6.751, steps = 48  
shifted from previous position = 0.0161  
rotated from previous position = 0.0134 degrees  
atoms outside contour = 7541, contour level = 93.7  
  
Position of 20210511 for binding analysis.pdb (#1) relative to apbs_map01.ccp4
(#4) coordinates:  
Matrix rotation and translation  
0.99999941 -0.00104787 -0.00029116 -136.40628771  
0.00104937 0.99998587 0.00521135 -126.24313278  
0.00028570 -0.00521165 0.99998638 -51.57940378  
Axis -0.97891147 -0.05417799 0.19696974  
Axis point 0.00000000 -14877.76396542 22830.62343723  
Rotation angle (degrees) 0.30503121  
Shift along axis 130.20969704  
  
Fit molecule 20210511 for binding analysis.pdb (#1) to map apbs_map01.ccp4
(#4) using 7726 atoms  
average map value = -6.797, steps = 28  
shifted from previous position = 0.0149  
rotated from previous position = 0.0135 degrees  
atoms outside contour = 7547, contour level = 93.7  
  
Position of 20210511 for binding analysis.pdb (#1) relative to apbs_map01.ccp4
(#4) coordinates:  
Matrix rotation and translation  
0.99999926 -0.00116092 -0.00036393 -136.35865285  
0.00116273 0.99998673 0.00501805 -126.23935355  
0.00035810 -0.00501847 0.99998734 -51.62915747  
Axis -0.97184674 -0.06991424 0.22500203  
Axis point 0.00000000 -16162.96974391 23306.85000779  
Rotation angle (degrees) 0.29585590  
Shift along axis 129.72897540  
  
Fit molecule 20210511 for binding analysis.pdb (#1) to map apbs_map01.ccp4
(#4) using 7726 atoms  
average map value = -6.764, steps = 44  
shifted from previous position = 0.011  
rotated from previous position = 0.00752 degrees  
atoms outside contour = 7541, contour level = 93.7  
  
Position of 20210511 for binding analysis.pdb (#1) relative to apbs_map01.ccp4
(#4) coordinates:  
Matrix rotation and translation  
0.99999933 -0.00112580 -0.00026750 -136.38961480  
0.00112715 0.99998636 0.00509978 -126.24442339  
0.00026175 -0.00510008 0.99998696 -51.59622953  
Axis -0.97521276 -0.05060199 0.21540544  
Axis point 0.00000000 -15594.81073341 23440.29800083  
Rotation angle (degrees) 0.29963277  
Shift along axis 128.28300401  
  
Fit molecule 20210511 for binding analysis.pdb (#1) to map apbs_map01.ccp4
(#4) using 7726 atoms  
average map value = -6.801, steps = 28  
shifted from previous position = 0.0119  
rotated from previous position = 0.00909 degrees  
atoms outside contour = 7547, contour level = 93.7  
  
Position of 20210511 for binding analysis.pdb (#1) relative to apbs_map01.ccp4
(#4) coordinates:  
Matrix rotation and translation  
0.99999924 -0.00118535 -0.00035074 -136.35439363  
0.00118709 0.99998690 0.00497851 -126.23951965  
0.00034483 -0.00497892 0.99998755 -51.63466042  
Axis -0.97053230 -0.06779606 0.23123741  
Axis point 0.00000000 -16418.68001566 23557.63356885  
Rotation angle (degrees) 0.29392168  
Shift along axis 128.95502091  
  

> select #4

2 models selected  

> ~select #4

Nothing selected  

> volume #4 level 321.9

> volume #4 level 29.16

Fit molecule 20210511 for binding analysis.pdb (#1) to map apbs_map01.ccp4
(#4) using 7726 atoms  
average map value = -6.759, steps = 44  
shifted from previous position = 0.0133  
rotated from previous position = 0.0139 degrees  
atoms outside contour = 6750, contour level = 29.162  
  
Position of 20210511 for binding analysis.pdb (#1) relative to apbs_map01.ccp4
(#4) coordinates:  
Matrix rotation and translation  
0.99999939 -0.00106973 -0.00028079 -136.40057923  
0.00107117 0.99998601 0.00518025 -126.24347870  
0.00027524 -0.00518055 0.99998654 -51.58316080  
Axis -0.97796149 -0.05248420 0.20208099  
Axis point 0.00000000 -15072.12221730 23016.42588930  
Rotation angle (degrees) 0.30350518  
Shift along axis 129.59632630  
  
Fit molecule 20210511 for binding analysis.pdb (#1) to map apbs_map01.ccp4
(#4) using 7726 atoms  
average map value = -6.8, steps = 28  
shifted from previous position = 0.013  
rotated from previous position = 0.0129 degrees  
atoms outside contour = 6754, contour level = 29.162  
  
Position of 20210511 for binding analysis.pdb (#1) relative to apbs_map01.ccp4
(#4) coordinates:  
Matrix rotation and translation  
0.99999924 -0.00117656 -0.00035574 -136.35574699  
0.00117832 0.99998683 0.00499596 -126.23968305  
0.00034986 -0.00499638 0.99998746 -51.63209406  
Axis -0.97104503 -0.06856972 0.22884437  
Axis point 0.00000000 -16312.60904731 23451.39642230  
Rotation angle (degrees) 0.29479650  
Shift along axis 129.24807581  
  

> hide #!1 models

> show #!1 models

> select #1

7726 atoms, 8165 bonds, 2 pseudobonds, 734 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #1,1,-0.0011766,-0.00035574,-0.73297,0.0011783,0.99999,0.004996,-0.44887,0.00034986,-0.0049964,0.99999,-0.6714

> ~select #1

Nothing selected  
Fit molecule 20210511 for binding analysis.pdb (#1) to map apbs_map01.ccp4
(#4) using 7726 atoms  
average map value = -6.965, steps = 152  
shifted from previous position = 1.4  
rotated from previous position = 0.793 degrees  
atoms outside contour = 6777, contour level = 29.162  
  
Position of 20210511 for binding analysis.pdb (#1) relative to apbs_map01.ccp4
(#4) coordinates:  
Matrix rotation and translation  
0.99991122 0.00088322 0.01329575 -140.36608199  
-0.00093839 0.99999098 0.00414342 -124.36910061  
-0.01329197 -0.00415553 0.99990302 -49.74283444  
Axis -0.29732214 0.95254419 -0.06526184  
Axis point -4191.94227053 0.00000000 12172.54764553  
Rotation angle (degrees) 0.79965517  
Shift along axis -73.48681088  
  

> select #1

7726 atoms, 8165 bonds, 2 pseudobonds, 734 residues, 2 models selected  

> view matrix models
> #1,0.99991,0.00088322,0.013296,-3.5919,-0.00093839,0.99999,0.0041434,-0.40755,-0.013292,-0.0041555,0.9999,1.3545

> view matrix models
> #1,0.99991,0.00088322,0.013296,-3.4798,-0.00093839,0.99999,0.0041434,-0.3336,-0.013292,-0.0041555,0.9999,1.3866

> view matrix models
> #1,0.99991,0.00088322,0.013296,-3.5635,-0.00093839,0.99999,0.0041434,0.22827,-0.013292,-0.0041555,0.9999,2.2768

> view matrix models
> #1,0.99991,0.00088322,0.013296,-3.267,-0.00093839,0.99999,0.0041434,0.16281,-0.013292,-0.0041555,0.9999,2.331

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.99992,0.00086466,0.012996,-3.2232,-0.00091643,0.99999,0.0039779,0.18107,-0.012992,-0.0039895,0.99991,2.2402

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.99992,0.00086466,0.012996,-3.4522,-0.00091643,0.99999,0.0039779,0.036995,-0.012992,-0.0039895,0.99991,1.9763

> view matrix models
> #1,0.99992,0.00086466,0.012996,-3.5668,-0.00091643,0.99999,0.0039779,-0.32032,-0.012992,-0.0039895,0.99991,1.417

> view matrix models
> #1,0.99992,0.00086466,0.012996,-3.5639,-0.00091643,0.99999,0.0039779,-0.29548,-0.012992,-0.0039895,0.99991,1.3158

Fit molecule 20210511 for binding analysis.pdb (#1) to map apbs_map01.ccp4
(#4) using 7726 atoms  
average map value = -7.429, steps = 76  
shifted from previous position = 1.11  
rotated from previous position = 1.39 degrees  
atoms outside contour = 6771, contour level = 29.162  
  
Position of 20210511 for binding analysis.pdb (#1) relative to apbs_map01.ccp4
(#4) coordinates:  
Matrix rotation and translation  
0.99995977 -0.00312600 -0.00840730 -137.84675577  
0.00325057 0.99988453 0.01484458 -128.63594733  
0.00835992 -0.01487131 0.99985447 -51.52145662  
Axis -0.85610105 -0.48305593 0.18370619  
Axis point 0.00000000 -5602.98212158 3067.71342932  
Rotation angle (degrees) 0.99443881  
Shift along axis 170.68429857  
  

> volume #4 level 1.503

> volume #4 level 0

Fit molecule 20210511 for binding analysis.pdb (#1) to map apbs_map01.ccp4
(#4) using 7726 atoms  
average map value = -7.407, steps = 40  
shifted from previous position = 0.00985  
rotated from previous position = 0.00717 degrees  
atoms outside contour = 4683, contour level = 0  
  
Position of 20210511 for binding analysis.pdb (#1) relative to apbs_map01.ccp4
(#4) coordinates:  
Matrix rotation and translation  
0.99995988 -0.00309944 -0.00840405 -137.84355327  
0.00322499 0.99988279 0.01496702 -128.64437436  
0.00835668 -0.01499352 0.99985267 -51.49708769  
Axis -0.85827642 -0.48014286 0.18117511  
Axis point 0.00000000 -5528.04769837 3074.37083399  
Rotation angle (degrees) 1.00008532  
Shift along axis 170.74555815  
  

> volume #4 level 1

> volume #4 level -0.01

> volume #4 level -0.1

> volume #4 level -0.2

> volume #4 level -0.3

> volume #4 level -0.4

> volume #4 level -0.5

> volume #4 level -0.6

> volume #4 level 17.84

> volume #4 level 27.06

> ~select #1

Nothing selected  

> ui mousemode right "contour level"

> ui mousemode right windowing

> ui mousemode right "play coordinates"

> ui mousemode right "play coordinates"

> ui mousemode right "bond rotation"

> ui mousemode right minimize

> ui mousemode right "next docked"

> show #!3 models

> hide #!3 models

> close #4

> close #3

> hide #!1 models

> show #!1 models

> open "/Users/YoyoHuang/Desktop/20210511center_for_binding analysis.cif"

Summary of feedback from opening
/Users/YoyoHuang/Desktop/20210511center_for_binding analysis.cif  
---  
warnings | Missing entity information. Treating each chain as a separate
entity.  
Skipping residue with duplicate label_seq_id 13 in chain 2  
Skipping residue with duplicate label_seq_id 14 in chain 2  
Skipping residue with duplicate label_seq_id 15 in chain 2  
Skipping residue with duplicate label_seq_id 16 in chain 2  
Skipping residue with duplicate label_seq_id 17 in chain 2  
43 messages similar to the above omitted  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for 20210511center_for_binding analysis.cif #2  
---  
Chain | Description  
1 | No description available  
2 | No description available  
A | No description available  
B | No description available  
F | No description available  
G | No description available  
I | No description available  
  

> hide #!1 models

> style #!2 stick

Changed 6738 atom styles  

> open "/Users/YoyoHuang/Desktop/20210511center_for_binding analysis.pdb"

Chain information for 20210511center_for_binding analysis.pdb #3  
---  
Chain | Description  
1 | No description available  
2 | No description available  
A | No description available  
B | No description available  
F | No description available  
G | No description available  
H I | No description available  
  

> hide #!2 models

> hide #3 models

> show #3 models

> open /Users/YoyoHuang/Desktop/apbs_map02.ccp4

Opened apbs_map02.ccp4 as #4, grid size 161,161,193, pixel 0.571,0.562,0.571,
shown at level 38.2, step 1, values float32  

> select clear

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> select #3

7726 atoms, 8165 bonds, 734 residues, 1 model selected  

> ~select #3

Nothing selected  

> select #4

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #4,1,0,0,141.25,0,1,0,111.89,0,0,1,77.723

> view matrix models #4,1,0,0,140.99,0,1,0,131.82,0,0,1,76.695

> view matrix models #4,1,0,0,151.22,0,1,0,163.39,0,0,1,72.443

> view matrix models #4,1,0,0,151.6,0,1,0,164.25,0,0,1,73.28

> select clear

Fit molecule 20210511center_for_binding analysis.pdb (#3) to map
apbs_map02.ccp4 (#4) using 7726 atoms  
average map value = 4.304, steps = 148  
shifted from previous position = 1.99  
rotated from previous position = 1.15 degrees  
atoms outside contour = 6978, contour level = 38.222  
  
Position of 20210511center_for_binding analysis.pdb (#3) relative to
apbs_map02.ccp4 (#4) coordinates:  
Matrix rotation and translation  
0.99983172 0.01088862 0.01476353 -157.06045590  
-0.01076807 0.99990823 -0.00822034 -161.93659002  
-0.01485168 0.00805998 0.99985722 -73.30820166  
Axis 0.40560079 0.73782033 -0.53954532  
Axis point -10217.19023803 0.00000000 6575.95897213  
Rotation angle (degrees) 1.14996866  
Shift along axis -143.63085600  
  

> delete #3 /1,2

Fit molecule 20210511center_for_binding analysis.pdb (#3) to map
apbs_map02.ccp4 (#4) using 4605 atoms  
average map value = 5.78, steps = 44  
shifted from previous position = 0.00917  
rotated from previous position = 0.00844 degrees  
atoms outside contour = 3855, contour level = 38.222  
  
Position of 20210511center_for_binding analysis.pdb (#3) relative to
apbs_map02.ccp4 (#4) coordinates:  
Matrix rotation and translation  
0.99983090 0.01093653 0.01478399 -157.06933640  
-0.01081786 0.99990881 -0.00808335 -161.94882036  
-0.01487104 0.00792205 0.99985804 -73.26823641  
Axis 0.39903319 0.73933455 -0.54236237  
Axis point -10193.86210176 0.00000000 6656.83492171  
Rotation angle (degrees) 1.14915629  
Shift along axis -142.67230251  
  
Fit molecule 20210511center_for_binding analysis.pdb (#3) to map
apbs_map02.ccp4 (#4) using 4605 atoms  
average map value = 5.787, steps = 40  
shifted from previous position = 0.0141  
rotated from previous position = 0.0308 degrees  
atoms outside contour = 3854, contour level = 38.222  
  
Position of 20210511center_for_binding analysis.pdb (#3) relative to
apbs_map02.ccp4 (#4) coordinates:  
Matrix rotation and translation  
0.99982487 0.01121534 0.01498171 -157.15173211  
-0.01108881 0.99990237 -0.00850228 -161.82841350  
-0.01507561 0.00833467 0.99985162 -73.31936910  
Axis 0.41024265 0.73236498 -0.54345423  
Axis point -10087.01773601 0.00000000 6452.01122093  
Rotation angle (degrees) 1.17583333  
Shift along axis -143.14208424  
  

> style #3 stick

Changed 4605 atom styles  

> color #3 byhetero

> volume #4 level 38.22

> volume #4 level 56.46

> volume #4 level 26.06

> volume #4 level 26.06 level -45.63 color #b2b2ff color #b2b2ff

> volume #4 level 26.06 level 65.83

> volume #4 level 17.96 level 65.83

> volume #4 level 17.96 level 86.1

> volume #4 level 17.96 level 96.23

> volume #4 level 22.01 level 96.23

> volume #4 level 22.01 level 92.18

> volume #4 level 22.01 color #b2b2ff

> volume #4 level 36.2

> volume #4 showOutlineBox true

> hide #3 models

> show #3 models

> volume #3 showOutlineBox true

No volumes specified  

> show #3 surfaces

> ui tool show "Surface Color"

> color electrostatic #3.6 map #4 palette -2,#ff0000:0,#ffffff:2,#0000ff

Map values for surface "20210511center_for_binding analysis.pdb_I SES
surface": minimum -242.9, mean -2.505, maximum 356.9  

> color electrostatic #3.5 map #4 palette -2,#ff0000:0,#ffffff:2,#0000ff

Map values for surface "20210511center_for_binding analysis.pdb_H SES
surface": minimum -347.2, mean -3.027, maximum 333.3  

> select #3

4605 atoms, 4665 bonds, 582 residues, 1 model selected  

> ~select #3

6 models selected  

> show #!2 models

> show #!1 models

> show surfaces

> hide #!1 models

> hide #!2 models

> show #!2 models

> show #!1 models

> hide surfaces

> hide surfaces

> hide surfaces

> hide #!2 models

> hide #!1 models

> color electrostatic #3.1 map #4 palette -2,#ff0000:0,#ffffff:2,#0000ff

Map values for surface "20210511center_for_binding analysis.pdb_A SES
surface": minimum -317.5, mean 7.755, maximum 308.8  

> color electrostatic #3.4 map #4 palette -2,#ff0000:0,#ffffff:2,#0000ff

Map values for surface "20210511center_for_binding analysis.pdb_G SES
surface": minimum -94.79, mean -0.2755, maximum 96.01  

> color electrostatic #3.1 map #4 palette -2,#ff0000:0,#ffffff:2,#0000ff

Map values for surface "20210511center_for_binding analysis.pdb_A SES
surface": minimum -317.5, mean 7.755, maximum 308.8  

> color electrostatic #3.5 map #4 palette -2,#ff0000:0,#ffffff:2,#0000ff

Map values for surface "20210511center_for_binding analysis.pdb_H SES
surface": minimum -347.2, mean -3.027, maximum 333.3  

> show #!3 surfaces

> hide #!3 atoms

> color electrostatic #3.5 map #4 palette -2,#ff0000:0,#ffffff:2,#0000ff

Map values for surface "20210511center_for_binding analysis.pdb_H SES
surface": minimum -347.2, mean -3.027, maximum 333.3  

> color electrostatic #3.6 map #4 palette -2,#ff0000:0,#ffffff:2,#0000ff

Map values for surface "20210511center_for_binding analysis.pdb_I SES
surface": minimum -242.9, mean -2.505, maximum 356.9  

> color electrostatic #3.4 map #4 palette -2,#ff0000:0,#ffffff:2,#0000ff

Map values for surface "20210511center_for_binding analysis.pdb_G SES
surface": minimum -94.79, mean -0.2755, maximum 96.01  

> color electrostatic #3.3 map #4 palette -2,#ff0000:0,#ffffff:2,#0000ff

Map values for surface "20210511center_for_binding analysis.pdb_F SES
surface": minimum -142.3, mean 0.9646, maximum 113  

> color electrostatic #3.2 map #4 palette -2,#ff0000:0,#ffffff:2,#0000ff

Map values for surface "20210511center_for_binding analysis.pdb_B SES
surface": minimum -254.5, mean 4.631, maximum 86.6  

> color electrostatic #3.1 map #4 palette -2,#ff0000:0,#ffffff:2,#0000ff

Map values for surface "20210511center_for_binding analysis.pdb_A SES
surface": minimum -317.5, mean 7.755, maximum 308.8  

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> volume #4 level 136

> volume #4 level 163.5

> volume #4 style image region 0,0,96,160,160,96 step 1

> volume #4 region 0,0,0,160,160,192 step 1

> volume #4 style mesh region 0,0,0,160,160,192 step 1

> volume #4 style surface

> open /Users/YoyoHuang/Desktop/apbs_map01.ccp4

Opened apbs_map01.ccp4 as #5, grid size 193,225,289, pixel 0.6,0.574,0.585,
shown at level 15.3, step 1, values float32  

> volume #4 region 0,0,0,160,160,192

> close #5

> open /Users/YoyoHuang/Desktop/apbs_map01.dx

Incorrect format: blank header line. Comments must begin with # character.  

> open /Users/YoyoHuang/Desktop/apbs_map01.dx

Incorrect format: blank header line. Comments must begin with # character.  

> open /Users/YoyoHuang/Desktop/apbs_map01.cif

mmCIF parsing error: unexpected data value near line 1  

> open /Users/YoyoHuang/Desktop/apbs_map01.ccp4

Opened apbs_map01.ccp4 as #5, grid size 193,225,289, pixel 0.6,0.574,0.585,
shown at level 15.3, step 1, values float32  

> close #5

> show #!3 models

> hide #!3 models

> show #!2 models

> hide #!2 models

> close #2

> show #!1 models

> hide #!1 models

> show #!3 models

> hide #!3 models

> close #1

> open /Users/YoyoHuang/Desktop/RNAP-
> PmrA/0starters/J521_540-3DVA_grp0-frame19-0822A.mrc

Opened J521_540-3DVA_grp0-frame19-0822A.mrc as #1, grid size 400,400,400,
pixel 0.822, shown at level 0.171, step 2, values float32  

> volume #1 level 0.1391

> volume #1 step 1

> volume #1 level 0.3545

> show #!3 models

> hide #!1 models

> hide #!4 models

> hide #!3 models

> show #!3 models

> hide surfaces

> show cartoons

> show #!1 models

Fit molecule 20210511center_for_binding analysis.pdb (#3) to map
J521_540-3DVA_grp0-frame19-0822A.mrc (#1) using 4605 atoms  
average map value = 0.2687, steps = 68  
shifted from previous position = 1.75  
rotated from previous position = 1.14 degrees  
atoms outside contour = 3479, contour level = 0.35453  
  
Position of 20210511center_for_binding analysis.pdb (#3) relative to
J521_540-3DVA_grp0-frame19-0822A.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999829 0.00128685 -0.00132946 -0.16906859  
-0.00129049 0.99999541 -0.00273969 0.61285162  
0.00132592 0.00274140 0.99999536 -1.24503094  
Axis 0.82879460 -0.40151952 -0.38971989  
Axis point -0.00000000 440.48365866 237.46823236  
Rotation angle (degrees) 0.18945830  
Shift along axis 0.09901830  
  
Fit molecule 20210511center_for_binding analysis.pdb (#3) to map
J521_540-3DVA_grp0-frame19-0822A.mrc (#1) using 4605 atoms  
average map value = 0.2687, steps = 48  
shifted from previous position = 0.00318  
rotated from previous position = 0.00145 degrees  
atoms outside contour = 3478, contour level = 0.35453  
  
Position of 20210511center_for_binding analysis.pdb (#3) relative to
J521_540-3DVA_grp0-frame19-0822A.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999828 0.00127282 -0.00134777 -0.16330900  
-0.00127650 0.99999546 -0.00272944 0.60833408  
0.00134429 0.00273116 0.99999537 -1.24957276  
Axis 0.82732199 -0.40786791 -0.38624098  
Axis point 0.00000000 443.86861135 236.99487833  
Rotation angle (degrees) 0.18908600  
Shift along axis 0.09940712  
  

> hide #!3 models

> show #!4 models

> volume #4 change image level -0.6495,0 level 40.18,0.8 level 281,1

> volume #4 level 27.47

Fit map apbs_map02.ccp4 in map J521_540-3DVA_grp0-frame19-0822A.mrc using
79830 points  
correlation = 0.7316, correlation about mean = 0.1053, overlap = 1.29e+06  
steps = 88, shift = 1.71, angle = 0.709 degrees  
  
Position of apbs_map02.ccp4 (#4) relative to
J521_540-3DVA_grp0-frame19-0822A.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99992561 -0.00610492 -0.01055955 152.98412922  
0.00608292 0.99997926 -0.00211399 164.27639454  
0.01057223 0.00204960 0.99994201 74.32249403  
Axis 0.16824410 -0.85390096 0.49249068  
Axis point -10573.71685313 0.00000000 15803.95878070  
Rotation angle (degrees) 0.70897723  
Shift along axis -77.93395850  
  
Fit map apbs_map02.ccp4 in map J521_540-3DVA_grp0-frame19-0822A.mrc using
79830 points  
correlation = 0.7316, correlation about mean = 0.1053, overlap = 1.29e+06  
steps = 48, shift = 0.0149, angle = 0.00526 degrees  
  
Position of apbs_map02.ccp4 (#4) relative to
J521_540-3DVA_grp0-frame19-0822A.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99992612 -0.00611618 -0.01050499 152.97648242  
0.00609353 0.99997904 -0.00218700 164.28565776  
0.01051815 0.00212282 0.99994243 74.33380677  
Axis 0.17455329 -0.85146463 0.49450899  
Axis point -10573.10633819 0.00000000 15906.47561169  
Rotation angle (degrees) 0.70735047  
Shift along axis -76.42214246  
  

> hide #!1 models

> show #!3 models

> hide #!3 models

> hide #!4 models

> show #!1 models

> open /Users/YoyoHuang/Desktop/apbs_map01.ccp4

Opened apbs_map01.ccp4 as #2, grid size 193,225,289, pixel 0.6,0.574,0.585,
shown at level 15.3, step 1, values float32  

> open "/Users/YoyoHuang/Desktop/RNAP-PmrA/20210511 for binding analysis.pdb"

Chain information for 20210511 for binding analysis.pdb #5  
---  
Chain | Description  
1 | No description available  
2 | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
  

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!2 models

> hide #!1 models

> style #!5 stick

Changed 7726 atom styles  

> color #!5 byhetero

> show #!1 models

Fit molecule 20210511 for binding analysis.pdb (#5) to map
J521_540-3DVA_grp0-frame19-0822A.mrc (#1) using 7726 atoms  
average map value = 0.2816, steps = 64  
shifted from previous position = 0.283  
rotated from previous position = 0.151 degrees  
atoms outside contour = 5444, contour level = 0.35453  
  
Position of 20210511 for binding analysis.pdb (#5) relative to
J521_540-3DVA_grp0-frame19-0822A.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999703 0.00066920 0.00234542 -0.55350654  
-0.00067155 0.99999928 0.00099879 0.03714452  
-0.00234475 -0.00100037 0.99999675 0.40717801  
Axis -0.37921711 0.88967022 -0.25432515  
Axis point 188.47817490 0.00000000 213.69661205  
Rotation angle (degrees) 0.15102627  
Shift along axis 0.13938992  
  
Fit molecule 20210511 for binding analysis.pdb (#5) to map
J521_540-3DVA_grp0-frame19-0822A.mrc (#1) using 7726 atoms  
average map value = 0.2816, steps = 40  
shifted from previous position = 0.00741  
rotated from previous position = 0.0034 degrees  
atoms outside contour = 5444, contour level = 0.35453  
  
Position of 20210511 for binding analysis.pdb (#5) relative to
J521_540-3DVA_grp0-frame19-0822A.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999692 0.00067761 0.00238839 -0.56363448  
-0.00068010 0.99999923 0.00103880 0.03670673  
-0.00238768 -0.00104042 0.99999661 0.43011497  
Axis -0.38625203 0.88724010 -0.25221891  
Axis point 194.81389954 0.00000000 213.31065193  
Rotation angle (degrees) 0.15421354  
Shift along axis 0.14178952  
  

> hide #!1 models

> hide #!5 models

> show #!5 models

> show #!1 models

> show #!2 models

> hide #!5 models

Fit map apbs_map01.ccp4 in map J521_540-3DVA_grp0-frame19-0822A.mrc using
125268 points  
correlation = -0.02013, correlation about mean = 0.01001, overlap = -191.2  
steps = 300, shift = 13.8, angle = 5.18 degrees  
  
Position of apbs_map01.ccp4 (#2) relative to
J521_540-3DVA_grp0-frame19-0822A.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99782481 -0.05281834 0.03944457 -9.81208608  
0.05027898 0.99675822 0.06280980 -15.35870577  
-0.04263421 -0.06068995 0.99724573 9.01504280  
Axis -0.68381128 0.45446572 0.57084415  
Axis point 0.00000000 89.77271553 284.43984777  
Rotation angle (degrees) 5.18101039  
Shift along axis 4.87579430  
  

> select #2

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.99782,-0.052818,0.039445,11.629,0.050279,0.99676,0.06281,25.257,-0.042634,-0.06069,0.99725,30.75

> view matrix models
> #2,0.99782,-0.052818,0.039445,118.32,0.050279,0.99676,0.06281,103.88,-0.042634,-0.06069,0.99725,103.99

> view matrix models
> #2,0.99782,-0.052818,0.039445,119.15,0.050279,0.99676,0.06281,104.21,-0.042634,-0.06069,0.99725,91.835

> view matrix models
> #2,0.99782,-0.052818,0.039445,131.38,0.050279,0.99676,0.06281,112.6,-0.042634,-0.06069,0.99725,87.173

Fit map apbs_map01.ccp4 in map J521_540-3DVA_grp0-frame19-0822A.mrc using
125268 points  
correlation = 0.4532, correlation about mean = 0.02107, overlap = 8.232e+05  
steps = 208, shift = 4.12, angle = 15.3 degrees  
  
Position of apbs_map01.ccp4 (#2) relative to
J521_540-3DVA_grp0-frame19-0822A.mrc (#1) coordinates:  
Matrix rotation and translation  
0.97844150 -0.18385696 -0.09406832 151.63194311  
0.17096202 0.97659487 -0.13051607 125.58628162  
0.11586292 0.11162023 0.98697351 63.94639001  
Axis 0.50643539 -0.43907753 0.74211463  
Axis point -812.18153204 729.61084206 0.00000000  
Rotation angle (degrees) 13.83103297  
Shift along axis 69.10521841  
  

> view matrix models
> #2,0.97844,-0.18386,-0.094068,163.48,0.17096,0.97659,-0.13052,125.47,0.11586,0.11162,0.98697,36.947

Fit map apbs_map01.ccp4 in map J521_540-3DVA_grp0-frame19-0822A.mrc using
125268 points  
correlation = 0.646, correlation about mean = 0.1084, overlap = 1.58e+06  
steps = 160, shift = 2.75, angle = 13.7 degrees  
  
Position of apbs_map01.ccp4 (#2) relative to
J521_540-3DVA_grp0-frame19-0822A.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999538 -0.00228695 -0.00200159 138.47059785  
0.00229005 0.99999618 0.00154820 125.42386466  
0.00199804 -0.00155278 0.99999680 52.86589752  
Axis -0.45444588 -0.58614401 0.67075640  
Axis point -28854.37121226 40539.67500441 0.00000000  
Rotation angle (degrees) 0.19548333  
Shift along axis -100.98370086  
  

> ~select #2

Nothing selected  

> hide #!1 models

> show #!5 models

> volume #2 level 144.4

Fit molecule 20210511 for binding analysis.pdb (#5) to map apbs_map01.ccp4
(#2) using 7726 atoms  
average map value = -7.116, steps = 72  
shifted from previous position = 1.62  
rotated from previous position = 0.181 degrees  
atoms outside contour = 7692, contour level = 144.41  
  
Position of 20210511 for binding analysis.pdb (#5) relative to apbs_map01.ccp4
(#2) coordinates:  
Matrix rotation and translation  
0.99999567 0.00249385 0.00156189 -139.00576359  
-0.00249098 0.99999520 -0.00184044 -126.52272022  
-0.00156647 0.00183654 0.99999709 -53.20106230  
Axis 0.52986992 0.45081180 -0.71833599  
Axis point -34125.56419910 36031.58018654 0.00000000  
Rotation angle (degrees) 0.19879983  
Shift along axis -92.47667057  
  
Fit molecule 20210511 for binding analysis.pdb (#5) to map apbs_map01.ccp4
(#2) using 7726 atoms  
average map value = -7.116, steps = 72  
shifted from previous position = 1.62  
rotated from previous position = 0.181 degrees  
atoms outside contour = 7692, contour level = 144.41  
  
Position of 20210511 for binding analysis.pdb (#5) relative to apbs_map01.ccp4
(#2) coordinates:  
Matrix rotation and translation  
0.99999567 0.00249385 0.00156189 -139.00576359  
-0.00249098 0.99999520 -0.00184044 -126.52272022  
-0.00156647 0.00183654 0.99999709 -53.20106230  
Axis 0.52986992 0.45081180 -0.71833599  
Axis point -34125.56419910 36031.58018654 0.00000000  
Rotation angle (degrees) 0.19879983  
Shift along axis -92.47667057  
  
Fit molecule 20210511 for binding analysis.pdb (#5) to map apbs_map01.ccp4
(#2) using 7726 atoms  
average map value = -7.116, steps = 72  
shifted from previous position = 1.62  
rotated from previous position = 0.181 degrees  
atoms outside contour = 7692, contour level = 144.41  
  
Position of 20210511 for binding analysis.pdb (#5) relative to apbs_map01.ccp4
(#2) coordinates:  
Matrix rotation and translation  
0.99999567 0.00249385 0.00156189 -139.00576359  
-0.00249098 0.99999520 -0.00184044 -126.52272022  
-0.00156647 0.00183654 0.99999709 -53.20106230  
Axis 0.52986992 0.45081180 -0.71833599  
Axis point -34125.56419910 36031.58018654 0.00000000  
Rotation angle (degrees) 0.19879983  
Shift along axis -92.47667057  
  
Fit molecule 20210511 for binding analysis.pdb (#5) to map apbs_map01.ccp4
(#2) using 7726 atoms  
average map value = -7.116, steps = 72  
shifted from previous position = 1.62  
rotated from previous position = 0.181 degrees  
atoms outside contour = 7692, contour level = 144.41  
  
Position of 20210511 for binding analysis.pdb (#5) relative to apbs_map01.ccp4
(#2) coordinates:  
Matrix rotation and translation  
0.99999567 0.00249385 0.00156189 -139.00576359  
-0.00249098 0.99999520 -0.00184044 -126.52272022  
-0.00156647 0.00183654 0.99999709 -53.20106230  
Axis 0.52986992 0.45081180 -0.71833599  
Axis point -34125.56419910 36031.58018654 0.00000000  
Rotation angle (degrees) 0.19879983  
Shift along axis -92.47667057  
  
Opened 20210511 for binding analysis.pdb map 10 as #6, grid size 47,51,63,
pixel 3.33, shown at level 0.0536, step 1, values float32  
Fit map 20210511 for binding analysis.pdb map 10 in map apbs_map01.ccp4 using
5847 points  
correlation = -0.1716, correlation about mean = -0.03234, overlap = -7941  
steps = 284, shift = 4.13, angle = 8.88 degrees  
  
Position of 20210511 for binding analysis.pdb map 10 (#6) relative to
apbs_map01.ccp4 (#2) coordinates:  
Matrix rotation and translation  
0.99597109 -0.08429228 0.03060056 -127.54087856  
0.07981533 0.98881431 0.12599912 -156.00563175  
-0.04087902 -0.12304909 0.99155828 -20.65379057  
Axis -0.81202219 0.23305931 0.53507319  
Axis point 0.00000000 -501.05938652 1297.53805126  
Rotation angle (degrees) 8.82115000  
Shift along axis 56.15616864  
  
Average map value = -6.779 for 7726 atoms, 7703 outside contour  
Average map value = -6.779 for 7726 atoms, 7703 outside contour  
Correlation = -0.1716, Correlation about mean = -0.03234, Overlap = -7941  
  
Average map value = -6.779 for 7726 atoms, 7703 outside contour  
Correlation = -0.1716, Correlation about mean = -0.03234, Overlap = -7941  
  

> ui tool show "Fit in Map"

> hide #!1 models

Opened 20210511 for binding analysis.pdb map 5 as #6, grid size 76,83,107,
pixel 1.67, shown at level 0.0925, step 1, values float32  
Fit map 20210511 for binding analysis.pdb map 5 in map apbs_map01.ccp4 using
28892 points  
correlation = -0.02242, correlation about mean = 0.01336, overlap = -5653  
steps = 188, shift = 15.5, angle = 7.93 degrees  
  
Position of 20210511 for binding analysis.pdb map 5 (#6) relative to
apbs_map01.ccp4 (#2) coordinates:  
Matrix rotation and translation  
0.98785440 -0.10270369 0.11660033 -149.02810113  
0.07365599 0.97025768 0.23059669 -163.66294907  
-0.13681549 -0.21920764 0.96603806 19.64701457  
Axis -0.82446728 0.46449765 0.32325785  
Axis point 0.00000000 -113.12459846 802.30586834  
Rotation angle (degrees) 15.83004751  
Shift along axis 53.19879014  
  
Average map value = -0.8289 for 7726 atoms, 7714 outside contour  

> select clear

> select clear

> volume #2 level 111.2

> volume #6 level 0.4982

> volume #2 level 42.37

> hide #!6 models

Opened 20210511 for binding analysis.pdb map 1 as #6, grid size 304,343,462,
pixel 0.333, shown at level 0.797, step 1, values float32  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 401, in _fit  
self._fit_map_in_map(smap, bmap, opt_r, opt_t, atoms = fatoms)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 412, in _fit_map_in_map  
metric = self._metric()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 367, in _metric  
return m  
UnboundLocalError: local variable 'm' referenced before assignment  
  
UnboundLocalError: local variable 'm' referenced before assignment  
  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 367, in _metric  
return m  
  
See log for complete Python traceback.  
  

> ui tool show "Fit in Map"

> close #2

> close #5

> close #6

> open /Users/YoyoHuang/Desktop/apbs_map01.ccp4

Opened apbs_map01.ccp4 as #2, grid size 193,225,289, pixel 0.6,0.574,0.585,
shown at level 15.3, step 1, values float32  

> open "/Users/YoyoHuang/Desktop/RNAP-PmrA/20210511 for binding analysis.pdb"

Chain information for 20210511 for binding analysis.pdb #5  
---  
Chain | Description  
1 | No description available  
2 | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
  

> style #!5 stick

Changed 7726 atom styles  

> color #!5 byhetero

> hide #!5 models

> show #!5 models

Fit molecule 20210511 for binding analysis.pdb (#5) to map apbs_map01.ccp4
(#2) using 7726 atoms  
average map value = 0, steps = 24  
shifted from previous position = 0  
rotated from previous position = 0 degrees  
atoms outside contour = 7726, contour level = 15.332  
  
Position of 20210511 for binding analysis.pdb (#5) relative to apbs_map01.ccp4
(#2) 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  
  

> ui mousemode right "translate selected models"

> select #5

7726 atoms, 8165 bonds, 2 pseudobonds, 734 residues, 2 models selected  

> ~select #5

Nothing selected  

> select #2

2 models selected  

> view matrix models #2,1,0,0,144.62,0,1,0,90.899,0,0,1,56.68

> view matrix models #2,1,0,0,150.75,0,1,0,109.72,0,0,1,59.444

> ~select #2

Nothing selected  
Fit molecule 20210511 for binding analysis.pdb (#5) to map apbs_map01.ccp4
(#2) using 7726 atoms  
average map value = -1.172, steps = 72  
shifted from previous position = 2.22  
rotated from previous position = 0 degrees  
atoms outside contour = 7243, contour level = 15.332  
  
Position of 20210511 for binding analysis.pdb (#5) relative to apbs_map01.ccp4
(#2) coordinates:  
Matrix rotation and translation  
1.00000000 0.00000000 0.00000000 -152.20199252  
0.00000000 1.00000000 0.00000000 -111.06095456  
0.00000000 0.00000000 1.00000000 -58.41638433  
Axis 0.00000000 0.00000000 1.00000000  
Axis point 0.00000000 0.00000000 0.00000000  
Rotation angle (degrees) 0.00000000  
Shift along axis -58.41638433  
  
Fit molecule 20210511 for binding analysis.pdb (#5) to map apbs_map01.ccp4
(#2) using 7726 atoms  
average map value = -1.172, steps = 40  
shifted from previous position = 0.00226  
rotated from previous position = 0 degrees  
atoms outside contour = 7244, contour level = 15.332  
  
Position of 20210511 for binding analysis.pdb (#5) relative to apbs_map01.ccp4
(#2) coordinates:  
Matrix rotation and translation  
1.00000000 0.00000000 0.00000000 -152.20163034  
0.00000000 1.00000000 0.00000000 -111.05972719  
0.00000000 0.00000000 1.00000000 -58.41824454  
Axis 0.00000000 0.00000000 1.00000000  
Axis point 0.00000000 0.00000000 0.00000000  
Rotation angle (degrees) 0.00000000  
Shift along axis -58.41824454  
  

> select #2

2 models selected  

> ~select #2

Nothing selected  

> select #5

7726 atoms, 8165 bonds, 2 pseudobonds, 734 residues, 2 models selected  

> view matrix models #5,1,0,0,0.0035882,0,1,0,-16.128,0,0,1,-0.90971

> view matrix models #5,1,0,0,11.14,0,1,0,-20.185,0,0,1,5.3664

> ~select #5

Nothing selected  
Fit molecule 20210511 for binding analysis.pdb (#5) to map apbs_map01.ccp4
(#2) using 7726 atoms  
average map value = -4.059, steps = 76  
shifted from previous position = 6.76  
rotated from previous position = 0 degrees  
atoms outside contour = 7015, contour level = 15.332  
  
Position of 20210511 for binding analysis.pdb (#5) relative to apbs_map01.ccp4
(#2) coordinates:  
Matrix rotation and translation  
1.00000000 0.00000000 0.00000000 -142.41987304  
0.00000000 1.00000000 0.00000000 -135.51135349  
0.00000000 0.00000000 1.00000000 -56.62325496  
Axis 0.00000000 0.00000000 1.00000000  
Axis point 0.00000000 0.00000000 0.00000000  
Rotation angle (degrees) 0.00000000  
Shift along axis -56.62325496  
  
Fit molecule 20210511 for binding analysis.pdb (#5) to map apbs_map01.ccp4
(#2) using 7726 atoms  
average map value = -2.24, steps = 212  
shifted from previous position = 4.1  
rotated from previous position = 7.07 degrees  
atoms outside contour = 7130, contour level = 15.332  
  
Position of 20210511 for binding analysis.pdb (#5) relative to apbs_map01.ccp4
(#2) coordinates:  
Matrix rotation and translation  
0.99461636 0.05792741 -0.08592266 -144.52296433  
-0.06352957 0.99592796 -0.06396482 -114.53471294  
0.08186746 0.06907909 0.99424635 -89.21316379  
Axis 0.54042717 -0.68156700 -0.49336082  
Axis point 684.06714954 0.00000000 -2001.45184161  
Rotation angle (degrees) 7.07055165  
Shift along axis 43.97322373  
  
Fit molecule 20210511 for binding analysis.pdb (#5) to map apbs_map01.ccp4
(#2) using 7726 atoms  
average map value = -1.998, steps = 100  
shifted from previous position = 0.471  
rotated from previous position = 2.36 degrees  
atoms outside contour = 7122, contour level = 15.332  
  
Position of 20210511 for binding analysis.pdb (#5) relative to apbs_map01.ccp4
(#2) coordinates:  
Matrix rotation and translation  
0.99117480 0.09831820 -0.08891598 -152.28033204  
-0.10334975 0.99318547 -0.05386504 -107.74181009  
0.08301415 0.06257912 0.99458157 -88.20032739  
Axis 0.40227567 -0.59396114 -0.69669538  
Axis point -788.39793844 1740.69948603 0.00000000  
Rotation angle (degrees) 8.32174856  
Shift along axis 64.18453638  
  
Fit molecule 20210511 for binding analysis.pdb (#5) to map apbs_map01.ccp4
(#2) using 7726 atoms  
average map value = -2.003, steps = 28  
shifted from previous position = 0.0125  
rotated from previous position = 0.00296 degrees  
atoms outside contour = 7122, contour level = 15.332  
  
Position of 20210511 for binding analysis.pdb (#5) relative to apbs_map01.ccp4
(#2) coordinates:  
Matrix rotation and translation  
0.99117042 0.09834096 -0.08893960 -152.29206635  
-0.10337057 0.99318557 -0.05382333 -107.74180745  
0.08304049 0.06254183 0.99458172 -88.19222066  
Axis 0.40196349 -0.59407571 -0.69677787  
Axis point -787.82429142 1740.46072830 0.00000000  
Rotation angle (degrees) 8.32256697  
Shift along axis 64.24132925  
  
Fit molecule 20210511 for binding analysis.pdb (#5) to map apbs_map01.ccp4
(#2) using 7726 atoms  
average map value = -1.999, steps = 44  
shifted from previous position = 0.0111  
rotated from previous position = 0.00277 degrees  
atoms outside contour = 7122, contour level = 15.332  
  
Position of 20210511 for binding analysis.pdb (#5) relative to apbs_map01.ccp4
(#2) coordinates:  
Matrix rotation and translation  
0.99117612 0.09830190 -0.08891929 -152.27745478  
-0.10333205 0.99318835 -0.05384603 -107.74776450  
0.08302044 0.06255912 0.99458231 -88.19603181  
Axis 0.40218769 -0.59406342 -0.69665897  
Axis point -788.36738471 1741.00837182 0.00000000  
Rotation angle (degrees) 8.32077351  
Shift along axis 64.20744483  
  
Fit molecule 20210511 for binding analysis.pdb (#5) to map apbs_map01.ccp4
(#2) using 7726 atoms  
average map value = -1.999, steps = 36  
shifted from previous position = 8.04e-14  
rotated from previous position = 0.00568 degrees  
atoms outside contour = 7122, contour level = 15.332  
  
Position of 20210511 for binding analysis.pdb (#5) relative to apbs_map01.ccp4
(#2) coordinates:  
Matrix rotation and translation  
0.99117482 0.09824483 -0.08899674 -152.25476048  
-0.10327815 0.99319499 -0.05382696 -107.76232841  
0.08310289 0.06254334 0.99457641 -88.20813076  
Axis 0.40206209 -0.59460821 -0.69626658  
Axis point -788.13490782 1742.00126173 0.00000000  
Rotation angle (degrees) 8.32088166  
Shift along axis 64.27687149  
  
Opened 20210511 for binding analysis.pdb map 10 as #6, grid size 47,51,63,
pixel 3.33, shown at level 0.0536, step 1, values float32  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 401, in _fit  
self._fit_map_in_map(smap, bmap, opt_r, opt_t, atoms = fatoms)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 412, in _fit_map_in_map  
metric = self._metric()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 367, in _metric  
return m  
UnboundLocalError: local variable 'm' referenced before assignment  
  
UnboundLocalError: local variable 'm' referenced before assignment  
  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 367, in _metric  
return m  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-14.7.8
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: Mac mini
      Model Identifier: Macmini8,1
      Processor Name: Quad-Core Intel Core i3
      Processor Speed: 3.6 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Memory: 8 GB
      Boot ROM Version: 1554.60.15.0.0 (iBridge: 18.16.13030.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H2)
      Kernel Version: Darwin 19.6.0
      Time since boot: 8 days 2:12

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0000
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        VA2407 Series:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60 Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: UEP202020711
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Adapter Type: DVI or HDMI
          Automatically Adjust Brightness: No
          Adapter Firmware Version: 2.19

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
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    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    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: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    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: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    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: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    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: 0.29.21
    decorator: 5.0.9
    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: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0

Change History (2)

comment:1 by pett, 4 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Map Fit: local variable 'm' referenced before assignment

comment:2 by Tom Goddard, 4 years ago

Resolution: → fixed
Status: assigned → closed

Fixed.

User turned off overlap and correlation radio buttons in fit in map gui so none were selected. That should not be possible but clicking on the enabled radiobutton turned it off. Made it so clicking the enabled button leaves it on.

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