ChimeraX bug report submission

[wenhewang@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26200
ChimeraX Version: 1.11 (2025-12-17 06:45:39 UTC)
Description
It is impossible to activate ChimeraX by using the "right-click - open with - ChimeraX" method, and the corresponding operation file cannot be opened.

Log:
> cd "D:/My Documents/Projects"

Current working directory is: D:\My Documents\Projects  

> ui tool show CliX

UCSF ChimeraX version: 1.11 (2025-12-17)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "D:\\\My Documents\\\Projects\\\494\\\494apo\\\494apo_double_4.46.mrc"

Opened 494apo_double_4.46.mrc as #1, grid size 600,600,600, pixel 0.74, shown
at level 0.0419, step 4, values float32  

> open "D:/My Documents/Projects/494/494apo/494apo_J437_2.42_flip.mrc"

Opened 494apo_J437_2.42_flip.mrc as #2, grid size 432,432,432, pixel 0.844,
shown at level 0.0993, step 2, values float32  

> lighting soft

> surface dust #1 size 7.4

> surface dust #2 size 8.44

> select add #2

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,28.158,0,1,0,-27.897,0,0,1,6.9622

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.41587,-0.89871,-0.13918,325.46,0.90277,0.42644,-0.056149,-75.193,0.10981,-0.10229,0.98867,8.0406

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.41587,-0.89871,-0.13918,333.5,0.90277,0.42644,-0.056149,-58.975,0.10981,-0.10229,0.98867,-3.5369

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.58035,-0.78806,0.20533,426.2,0.80023,-0.59863,-0.035779,143.26,0.15111,0.14354,0.97804,-53.936

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.58035,-0.78806,0.20533,431.6,0.80023,-0.59863,-0.035779,142.59,0.15111,0.14354,0.97804,-35.661

> volume #1 step 2

> ui tool show "Fit in Map"

> fitmap #1 inMap #2

Fit map 494apo_double_4.46.mrc in map 494apo_J437_2.42_flip.mrc using 270340
points  
correlation = 0.1551, correlation about mean = 0.0175, overlap = 255.1  
steps = 212, shift = 5.37, angle = 8.21 degrees  
  
Position of 494apo_double_4.46.mrc (#1) relative to 494apo_J437_2.42_flip.mrc
(#2) coordinates:  
Matrix rotation and translation  
-0.59035943 0.80677812 0.02418273 175.09212899  
-0.80328875 -0.59020195 0.07993022 446.13181953  
0.07875864 0.02776184 0.99650708 -40.40135526  
Axis -0.03236581 -0.03385947 -0.99890239  
Axis point 201.41340768 179.22365535 0.00000000  
Rotation angle (degrees) 126.30099335  
Shift along axis 19.58422480  
  

> view matrix models
> #2,-0.58035,-0.78806,0.20533,432.67,0.80023,-0.59863,-0.035779,144.97,0.15111,0.14354,0.97804,-40.589

> fitmap #1 inMap #2

Fit map 494apo_double_4.46.mrc in map 494apo_J437_2.42_flip.mrc using 270340
points  
correlation = 0.1583, correlation about mean = 0.01699, overlap = 261.1  
steps = 108, shift = 4.47, angle = 1.56 degrees  
  
Position of 494apo_double_4.46.mrc (#1) relative to 494apo_J437_2.42_flip.mrc
(#2) coordinates:  
Matrix rotation and translation  
-0.59300844 0.80489798 0.02191435 174.92525623  
-0.80327069 -0.59325226 0.05299014 453.94244508  
0.05565239 0.01382044 0.99835455 -23.78799521  
Axis -0.02434413 -0.02096834 -0.99948371  
Axis point 202.42131042 182.99236533 0.00000000  
Rotation angle (degrees) 126.43803493  
Shift along axis 9.99889211  
  

> fitmap #1 inMap #2

Fit map 494apo_double_4.46.mrc in map 494apo_J437_2.42_flip.mrc using 270340
points  
correlation = 0.1583, correlation about mean = 0.01698, overlap = 261.1  
steps = 68, shift = 0.012, angle = 0.00456 degrees  
  
Position of 494apo_double_4.46.mrc (#1) relative to 494apo_J437_2.42_flip.mrc
(#2) coordinates:  
Matrix rotation and translation  
-0.59300479 0.80490121 0.02189409 174.93534229  
-0.80327847 -0.59324855 0.05291364 453.95075416  
0.05557889 0.01379099 0.99835905 -23.76363793  
Axis -0.02431476 -0.02093513 -0.99948512  
Axis point 202.42858555 182.99308201 0.00000000  
Rotation angle (degrees) 126.43761289  
Shift along axis 9.99437203  
  

> fitmap #2 inMap #1

Fit map 494apo_J437_2.42_flip.mrc in map 494apo_double_4.46.mrc using 100135
points  
correlation = 0.592, correlation about mean = 0.3081, overlap = 448.7  
steps = 92, shift = 1.46, angle = 2.71 degrees  
  
Position of 494apo_J437_2.42_flip.mrc (#2) relative to 494apo_double_4.46.mrc
(#1) coordinates:  
Matrix rotation and translation  
-0.55448057 -0.83010032 0.05903179 467.31307237  
0.83197709 -0.55456728 0.01640894 115.23896417  
0.01911604 0.05821154 0.99812123 -3.66795657  
Axis 0.02513562 0.02400108 0.99939589  
Axis point 202.95065020 182.57745134 0.00000000  
Rotation angle (degrees) 123.74263222  
Shift along axis 10.84632188  
  

> fitmap #2 inMap #1

Fit map 494apo_J437_2.42_flip.mrc in map 494apo_double_4.46.mrc using 100135
points  
correlation = 0.592, correlation about mean = 0.3081, overlap = 448.7  
steps = 28, shift = 0.0183, angle = 0.00287 degrees  
  
Position of 494apo_J437_2.42_flip.mrc (#2) relative to 494apo_double_4.46.mrc
(#1) coordinates:  
Matrix rotation and translation  
-0.55447389 -0.83010128 0.05908100 467.28493367  
0.83198079 -0.55456193 0.01640222 115.23776214  
0.01914857 0.05824886 0.99811843 -3.67769896  
Axis 0.02516201 0.02401101 0.99939499  
Axis point 202.93688851 182.57030956 0.00000000  
Rotation angle (degrees) 123.74231416  
Shift along axis 10.84932840  
  

> view matrix models
> #2,-0.54258,-0.81365,0.20876,432.56,0.82758,-0.56037,-0.033144,132.95,0.14395,0.15478,0.97741,-38.742

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.45237,-0.88224,0.13044,444.08,0.88778,-0.4594,-0.028326,102.64,0.084917,0.10299,0.99105,-21.246

> fitmap #2 inMap #1

Fit map 494apo_J437_2.42_flip.mrc in map 494apo_double_4.46.mrc using 100135
points  
correlation = 0.592, correlation about mean = 0.3081, overlap = 448.7  
steps = 224, shift = 3.94, angle = 8.03 degrees  
  
Position of 494apo_J437_2.42_flip.mrc (#2) relative to 494apo_double_4.46.mrc
(#1) coordinates:  
Matrix rotation and translation  
-0.55445807 -0.83010813 0.05913329 467.27070344  
0.83199026 -0.55454840 0.01637962 115.23874896  
0.01919541 0.05828013 0.99811571 -3.69011755  
Axis 0.02519413 0.02401403 0.99939411  
Axis point 202.92913152 182.56955573 0.00000000  
Rotation angle (degrees) 123.74139693  
Shift along axis 10.85194355  
  

> fitmap #2 inMap #1

Fit map 494apo_J437_2.42_flip.mrc in map 494apo_double_4.46.mrc using 100135
points  
correlation = 0.592, correlation about mean = 0.3081, overlap = 448.7  
steps = 28, shift = 0.0251, angle = 0.011 degrees  
  
Position of 494apo_J437_2.42_flip.mrc (#2) relative to 494apo_double_4.46.mrc
(#1) coordinates:  
Matrix rotation and translation  
-0.55445470 -0.83012295 0.05895653 467.32967695  
0.83199620 -0.55453727 0.01645425 115.21784407  
0.01903454 0.05817474 0.99812494 -3.64679859  
Axis 0.02508565 0.02400425 0.99939707  
Axis point 202.96295232 182.57647655 0.00000000  
Rotation angle (degrees) 123.74057953  
Shift along axis 10.84438710  
  

> fitmap #2 inMap #1

Fit map 494apo_J437_2.42_flip.mrc in map 494apo_double_4.46.mrc using 100135
points  
correlation = 0.592, correlation about mean = 0.3081, overlap = 448.7  
steps = 40, shift = 0.0074, angle = 0.00308 degrees  
  
Position of 494apo_J437_2.42_flip.mrc (#2) relative to 494apo_double_4.46.mrc
(#1) coordinates:  
Matrix rotation and translation  
-0.55446992 -0.83011035 0.05899082 467.31848946  
0.83198492 -0.55455523 0.01641907 115.23456384  
0.01908403 0.05818336 0.99812349 -3.65588684  
Axis 0.02511233 0.02399545 0.99939661  
Axis point 202.95379589 182.57877205 0.00000000  
Rotation angle (degrees) 123.74177270  
Shift along axis 10.84687916  
  

> fitmap #2 inMap #1

Fit map 494apo_J437_2.42_flip.mrc in map 494apo_double_4.46.mrc using 100135
points  
correlation = 0.592, correlation about mean = 0.3081, overlap = 448.7  
steps = 28, shift = 0.0156, angle = 0.00266 degrees  
  
Position of 494apo_J437_2.42_flip.mrc (#2) relative to 494apo_double_4.46.mrc
(#1) coordinates:  
Matrix rotation and translation  
-0.55445438 -0.83011773 0.05903295 467.29409033  
0.83199457 -0.55454107 0.01640878 115.23109228  
0.01911498 0.05821301 0.99812117 -3.66299505  
Axis 0.02513607 0.02400190 0.99939586  
Axis point 202.94207025 182.57307929 0.00000000  
Rotation angle (degrees) 123.74082914  
Shift along axis 10.85092162  
  

> fitmap #2 inMap #1

Fit map 494apo_J437_2.42_flip.mrc in map 494apo_double_4.46.mrc using 100135
points  
correlation = 0.592, correlation about mean = 0.3081, overlap = 448.7  
steps = 28, shift = 0.0202, angle = 0.00559 degrees  
  
Position of 494apo_J437_2.42_flip.mrc (#2) relative to 494apo_double_4.46.mrc
(#1) coordinates:  
Matrix rotation and translation  
-0.55446985 -0.83011348 0.05894736 467.33141048  
0.83198618 -0.55455232 0.01645366 115.22560637  
0.01903099 0.05816645 0.99812549 -3.64467966  
Axis 0.02508132 0.02400115 0.99939725  
Axis point 202.96236409 182.57810188 0.00000000  
Rotation angle (degrees) 123.74160102  
Shift along axis 10.84435153  
  

> fitmap #2 inMap #1

Fit map 494apo_J437_2.42_flip.mrc in map 494apo_double_4.46.mrc using 100135
points  
correlation = 0.592, correlation about mean = 0.3081, overlap = 448.7  
steps = 28, shift = 0.0208, angle = 0.00623 degrees  
  
Position of 494apo_J437_2.42_flip.mrc (#2) relative to 494apo_double_4.46.mrc
(#1) coordinates:  
Matrix rotation and translation  
-0.55445666 -0.83011530 0.05904574 467.29098128  
0.83199287 -0.55454362 0.01640848 115.23151514  
0.01912251 0.05822342 0.99812042 -3.66651899  
Axis 0.02514257 0.02400512 0.99939562  
Axis point 202.94058385 182.57201524 0.00000000  
Rotation angle (degrees) 123.74102160  
Shift along axis 10.85074016  
  

> fitmap #2 inMap #1

Fit map 494apo_J437_2.42_flip.mrc in map 494apo_double_4.46.mrc using 100135
points  
correlation = 0.592, correlation about mean = 0.3081, overlap = 448.7  
steps = 44, shift = 0.0172, angle = 0.00362 degrees  
  
Position of 494apo_J437_2.42_flip.mrc (#2) relative to 494apo_double_4.46.mrc
(#1) coordinates:  
Matrix rotation and translation  
-0.55447127 -0.83010982 0.05898555 467.32055860  
0.83198411 -0.55455642 0.01642021 115.23476476  
0.01908023 0.05817958 0.99812378 -3.65450833  
Axis 0.02510939 0.02399458 0.99939671  
Axis point 202.95480409 182.57920200 0.00000000  
Rotation angle (degrees) 123.74185002  
Shift along axis 10.84684154  
  

> select clear

> volume #1 level 0.05443

> volume #1 level 0.03342

> ui mousemode right "translate selected models"

> select subtract #2

Nothing selected  

> select add #2

2 models selected  

> view matrix models
> #2,-0.54259,-0.81367,0.20867,430.91,0.82758,-0.56036,-0.033127,131.95,0.14388,0.15471,0.97743,-35.519

> fitmap #2 inMap #1

Fit map 494apo_J437_2.42_flip.mrc in map 494apo_double_4.46.mrc using 100135
points  
correlation = 0.592, correlation about mean = 0.3081, overlap = 448.7  
steps = 88, shift = 4.99, angle = 0.00105 degrees  
  
Position of 494apo_J437_2.42_flip.mrc (#2) relative to 494apo_double_4.46.mrc
(#1) coordinates:  
Matrix rotation and translation  
-0.55447700 -0.83010482 0.05900211 467.31577062  
0.83198010 -0.55456240 0.01642157 115.23507071  
0.01908873 0.05819396 0.99812278 -3.65874705  
Axis 0.02511735 0.02399955 0.99939639  
Axis point 202.95268285 182.57700398 0.00000000  
Rotation angle (degrees) 123.74228772  
Shift along axis 10.84678707  
  

> fitmap #2 inMap #1

Fit map 494apo_J437_2.42_flip.mrc in map 494apo_double_4.46.mrc using 100135
points  
correlation = 0.592, correlation about mean = 0.3081, overlap = 448.7  
steps = 28, shift = 0.0144, angle = 0.00308 degrees  
  
Position of 494apo_J437_2.42_flip.mrc (#2) relative to 494apo_double_4.46.mrc
(#1) coordinates:  
Matrix rotation and translation  
-0.55445685 -0.83011487 0.05904995 467.29085964  
0.83199274 -0.55454374 0.01641101 115.23098625  
0.01912275 0.05822833 0.99812012 -3.66931686  
Axis 0.02514400 0.02400751 0.99939553  
Axis point 202.94070786 182.57172161 0.00000000  
Rotation angle (degrees) 123.74104247  
Shift along axis 10.84887211  
  

> fitmap #2 inMap #1

Fit map 494apo_J437_2.42_flip.mrc in map 494apo_double_4.46.mrc using 100135
points  
correlation = 0.592, correlation about mean = 0.3081, overlap = 448.7  
steps = 44, shift = 0.000406, angle = 0.00394 degrees  
  
Position of 494apo_J437_2.42_flip.mrc (#2) relative to 494apo_double_4.46.mrc
(#1) coordinates:  
Matrix rotation and translation  
-0.55446077 -0.83010760 0.05911534 467.27789043  
0.83198891 -0.55455005 0.01639173 115.23635813  
0.01917552 0.05827188 0.99811657 -3.68606198  
Axis 0.02518192 0.02401523 0.99939439  
Axis point 202.93337176 182.56993020 0.00000000  
Rotation angle (degrees) 123.74151740  
Shift along axis 10.85055474  
  

> fitmap #2 inMap #1

Fit map 494apo_J437_2.42_flip.mrc in map 494apo_double_4.46.mrc using 100135
points  
correlation = 0.592, correlation about mean = 0.3081, overlap = 448.7  
steps = 44, shift = 0.0173, angle = 0.00798 degrees  
  
Position of 494apo_J437_2.42_flip.mrc (#2) relative to 494apo_double_4.46.mrc
(#1) coordinates:  
Matrix rotation and translation  
-0.55447038 -0.83011082 0.05897984 467.32217464  
0.83198482 -0.55455529 0.01642239 115.23408356  
0.01907518 0.05817606 0.99812408 -3.65318914  
Axis 0.02510595 0.02399416 0.99939680  
Axis point 202.95571951 182.57948685 0.00000000  
Rotation angle (degrees) 123.74177001  
Shift along axis 10.84652507  
  

> fitmap #2 inMap #1

Fit map 494apo_J437_2.42_flip.mrc in map 494apo_double_4.46.mrc using 100135
points  
correlation = 0.592, correlation about mean = 0.3081, overlap = 448.7  
steps = 28, shift = 0.0178, angle = 0.00356 degrees  
  
Position of 494apo_J437_2.42_flip.mrc (#2) relative to 494apo_double_4.46.mrc
(#1) coordinates:  
Matrix rotation and translation  
-0.55445647 -0.83011602 0.05903742 467.29259494  
0.83199302 -0.55454354 0.01640371 115.23293465  
0.01912184 0.05821387 0.99812099 -3.66459686  
Axis 0.02513968 0.02400051 0.99939580  
Axis point 202.94095592 182.57318536 0.00000000  
Rotation angle (degrees) 123.74099277  
Shift along axis 10.85085484  
  

> fitmap #2 inMap #1

Fit map 494apo_J437_2.42_flip.mrc in map 494apo_double_4.46.mrc using 100135
points  
correlation = 0.592, correlation about mean = 0.3081, overlap = 448.7  
steps = 28, shift = 0.0206, angle = 0.00584 degrees  
  
Position of 494apo_J437_2.42_flip.mrc (#2) relative to 494apo_double_4.46.mrc
(#1) coordinates:  
Matrix rotation and translation  
-0.55446973 -0.83011350 0.05894818 467.33099664  
0.83198621 -0.55455232 0.01645181 115.22578631  
0.01903298 0.05816611 0.99812547 -3.64464778  
Axis 0.02508222 0.02400045 0.99939725  
Axis point 202.96210822 182.57808413 0.00000000  
Rotation angle (degrees) 123.74159760  
Shift along axis 10.84471809  
  

> fitmap #2 inMap #1

Fit map 494apo_J437_2.42_flip.mrc in map 494apo_double_4.46.mrc using 100135
points  
correlation = 0.592, correlation about mean = 0.3081, overlap = 448.7  
steps = 28, shift = 0.0206, angle = 0.00626 degrees  
  
Position of 494apo_J437_2.42_flip.mrc (#2) relative to 494apo_double_4.46.mrc
(#1) coordinates:  
Matrix rotation and translation  
-0.55445635 -0.83011537 0.05904761 467.29043941  
0.83199305 -0.55454336 0.01640808 115.23154358  
0.01912386 0.05822477 0.99812031 -3.66708232  
Axis 0.02514361 0.02400543 0.99939559  
Axis point 202.94030361 182.57193490 0.00000000  
Rotation angle (degrees) 123.74100578  
Shift along axis 10.85068710  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.97217,-0.22813,0.053395,431.09,0.22741,-0.97361,-0.019256,312.84,0.056379,-0.0065778,0.99839,0.82501

> fitmap #2 inMap #1

Fit map 494apo_J437_2.42_flip.mrc in map 494apo_double_4.46.mrc using 100135
points  
correlation = 0.7207, correlation about mean = 0.4677, overlap = 653  
steps = 280, shift = 18.5, angle = 11 degrees  
  
Position of 494apo_J437_2.42_flip.mrc (#2) relative to 494apo_double_4.46.mrc
(#1) coordinates:  
Matrix rotation and translation  
-0.98172316 -0.17526371 0.07417732 424.68434814  
0.17302001 -0.98427059 -0.03571398 324.12708938  
0.07926992 -0.02222708 0.99660536 18.77298289  
Axis 0.03869075 -0.01460948 0.99914443  
Axis point 197.71493069 180.81235112 0.00000000  
Rotation angle (degrees) 169.96259990  
Shift along axis 30.45295233  
  

> fitmap #2 inMap #1

Fit map 494apo_J437_2.42_flip.mrc in map 494apo_double_4.46.mrc using 100135
points  
correlation = 0.7207, correlation about mean = 0.4677, overlap = 653  
steps = 44, shift = 0.00212, angle = 0.00253 degrees  
  
Position of 494apo_J437_2.42_flip.mrc (#2) relative to 494apo_double_4.46.mrc
(#1) coordinates:  
Matrix rotation and translation  
-0.98172844 -0.17522553 0.07419763 424.67432859  
0.17298095 -0.98427731 -0.03571798 324.13600859  
0.07928974 -0.02223058 0.99660370 18.76823010  
Axis 0.03870076 -0.01461132 0.99914401  
Axis point 197.71272628 180.81216615 0.00000000  
Rotation angle (degrees) 169.96484489  
Shift along axis 30.45132813  
  

> fitmap #2 inMap #1

Fit map 494apo_J437_2.42_flip.mrc in map 494apo_double_4.46.mrc using 100135
points  
correlation = 0.7207, correlation about mean = 0.4677, overlap = 653  
steps = 44, shift = 0.000896, angle = 0.00206 degrees  
  
Position of 494apo_J437_2.42_flip.mrc (#2) relative to 494apo_double_4.46.mrc
(#1) coordinates:  
Matrix rotation and translation  
-0.98172810 -0.17523971 0.07416860 424.68148873  
0.17299698 -0.98427502 -0.03570341 324.13034156  
0.07925895 -0.02222010 0.99660639 18.77093956  
Axis 0.03868570 -0.01460501 0.99914469  
Axis point 197.71541631 180.81124467 0.00000000  
Rotation angle (degrees) 169.96397178  
Shift along axis 30.45005753  
  

> fitmap #2 inMap #1

Fit map 494apo_J437_2.42_flip.mrc in map 494apo_double_4.46.mrc using 100135
points  
correlation = 0.7207, correlation about mean = 0.4677, overlap = 653  
steps = 44, shift = 0.0162, angle = 0.00432 degrees  
  
Position of 494apo_J437_2.42_flip.mrc (#2) relative to 494apo_double_4.46.mrc
(#1) coordinates:  
Matrix rotation and translation  
-0.98171464 -0.17531011 0.07418040 424.68793540  
0.17306850 -0.98426299 -0.03568833 324.11184833  
0.07926955 -0.02219746 0.99660605 18.74890094  
Axis 0.03869160 -0.01459560 0.99914460  
Axis point 197.71394189 180.80975584 0.00000000  
Rotation angle (degrees) 169.95983873  
Shift along axis 30.43411144  
  

> fitmap #2 inMap #1

Fit map 494apo_J437_2.42_flip.mrc in map 494apo_double_4.46.mrc using 100135
points  
correlation = 0.7207, correlation about mean = 0.4677, overlap = 653  
steps = 44, shift = 0.0179, angle = 0.00778 degrees  
  
Position of 494apo_J437_2.42_flip.mrc (#2) relative to 494apo_double_4.46.mrc
(#1) coordinates:  
Matrix rotation and translation  
-0.98173633 -0.17521095 0.07412756 424.68532852  
0.17296506 -0.98427880 -0.03575380 324.14513568  
0.07922664 -0.02227933 0.99660763 18.78920059  
Axis 0.03866709 -0.01463261 0.99914501  
Axis point 197.71900308 180.81592088 0.00000000  
Rotation angle (degrees) 169.96574199  
Shift along axis 30.45139243  
  

> fitmap #2 inMap #1

Fit map 494apo_J437_2.42_flip.mrc in map 494apo_double_4.46.mrc using 100135
points  
correlation = 0.7207, correlation about mean = 0.4677, overlap = 653  
steps = 48, shift = 0.00227, angle = 0.00486 degrees  
  
Position of 494apo_J437_2.42_flip.mrc (#2) relative to 494apo_double_4.46.mrc
(#1) coordinates:  
Matrix rotation and translation  
-0.98172596 -0.17525125 0.07416967 424.68313906  
0.17300910 -0.98427315 -0.03569620 324.12657234  
0.07925902 -0.02221186 0.99660656 18.76915835  
Axis 0.03868603 -0.01460113 0.99914473  
Axis point 197.71546116 180.81066538 0.00000000  
Rotation angle (degrees) 169.96328334  
Shift along axis 30.44979396  
  

> fitmap #2 inMap #1

Fit map 494apo_J437_2.42_flip.mrc in map 494apo_double_4.46.mrc using 100135
points  
correlation = 0.7207, correlation about mean = 0.4677, overlap = 653  
steps = 48, shift = 0.00175, angle = 0.00418 degrees  
  
Position of 494apo_J437_2.42_flip.mrc (#2) relative to 494apo_double_4.46.mrc
(#1) coordinates:  
Matrix rotation and translation  
-0.98172481 -0.17527065 0.07413900 424.69176269  
0.17302410 -0.98426817 -0.03576086 324.13390496  
0.07924049 -0.02227948 0.99660653 18.78341266  
Axis 0.03867368 -0.01463451 0.99914472  
Axis point 197.71781618 180.81701496 0.00000000  
Rotation angle (degrees) 169.96228159  
Shift along axis 30.44820128  
  

> select clear

> open "D:/My Documents/Projects/494/494apo/494apo_J423_2.43_flip.mrc"

Opened 494apo_J423_2.43_flip.mrc as #3, grid size 432,432,432, pixel 0.844,
shown at level 0.0949, step 2, values float32  

> surface dust #1 size 7.4

> surface dust #2 size 8.44

> surface dust #3 size 8.44

> ui mousemode right "translate selected models"

> select add #3

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.27228,0.90108,0.3375,-1.5179,-0.94887,-0.19323,-0.24961,438.29,-0.1597,-0.38821,0.90763,117.91

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.27228,0.90108,0.3375,21.26,-0.94887,-0.19323,-0.24961,539.71,-0.1597,-0.38821,0.90763,129.92

> view matrix models
> #3,-0.27228,0.90108,0.3375,48.443,-0.94887,-0.19323,-0.24961,522.52,-0.1597,-0.38821,0.90763,117.43

> fitmap #3 inMap #1

Fit map 494apo_J423_2.43_flip.mrc in map 494apo_double_4.46.mrc using 100153
points  
correlation = 0.6843, correlation about mean = 0.4206, overlap = 631.3  
steps = 432, shift = 9.98, angle = 21.8 degrees  
  
Position of 494apo_J423_2.43_flip.mrc (#3) relative to 494apo_double_4.46.mrc
(#1) coordinates:  
Matrix rotation and translation  
-0.02483042 0.99746008 -0.06675954 66.93278980  
-0.99867026 -0.02776768 -0.04343571 467.73853321  
-0.04517915 0.06559224 0.99682321 -7.40607558  
Axis 0.05453519 -0.01079439 -0.99845350  
Axis point 261.08363498 201.47237154 0.00000000  
Rotation angle (degrees) 91.59804043  
Shift along axis 5.99586071  
  

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.91806,0.30916,0.24815,-42.758,-0.33152,0.94196,0.052929,156.24,-0.21739,-0.13086,0.96727,69.473

> fitmap #3 inMap #1

Fit map 494apo_J423_2.43_flip.mrc in map 494apo_double_4.46.mrc using 100153
points  
correlation = 0.7019, correlation about mean = 0.4455, overlap = 672  
steps = 588, shift = 31.1, angle = 24.4 degrees  
  
Position of 494apo_J423_2.43_flip.mrc (#3) relative to 494apo_double_4.46.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.99649120 -0.04976891 -0.06729296 67.53854735  
0.05308019 0.99741916 0.04834792 72.27302315  
0.06471306 -0.05175020 0.99656116 24.91366534  
Axis -0.51333609 -0.67697032 0.52744407  
Axis point -931.88437255 0.00000000 514.77428523  
Rotation angle (degrees) 5.59509153  
Shift along axis -70.45610033  
  

> fitmap #3 inMap #1

Fit map 494apo_J423_2.43_flip.mrc in map 494apo_double_4.46.mrc using 100153
points  
correlation = 0.7019, correlation about mean = 0.4455, overlap = 672  
steps = 36, shift = 0.0108, angle = 0.00577 degrees  
  
Position of 494apo_J423_2.43_flip.mrc (#3) relative to 494apo_double_4.46.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.99648952 -0.04980475 -0.06729130 67.54289010  
0.05312191 0.99741250 0.04843932 72.24875610  
0.06470468 -0.05184391 0.99655683 24.94356561  
Axis -0.51394490 -0.67647061 0.52749232  
Axis point -932.28892055 0.00000000 514.45815350  
Rotation angle (degrees) 5.59881065  
Shift along axis -70.42994525  
  

> select clear

> hide #!1 models

> show #!1 models

> fitmap #3 inMap #1

Fit map 494apo_J423_2.43_flip.mrc in map 494apo_double_4.46.mrc using 100153
points  
correlation = 0.7019, correlation about mean = 0.4455, overlap = 672  
steps = 48, shift = 0.0142, angle = 0.00508 degrees  
  
Position of 494apo_J423_2.43_flip.mrc (#3) relative to 494apo_double_4.46.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.99649381 -0.04976194 -0.06725954 67.53232238  
0.05307303 0.99741838 0.04837192 72.27065860  
0.06467882 -0.05177199 0.99656225 24.92066405  
Axis -0.51364927 -0.67672654 0.52745201  
Axis point -932.46814982 0.00000000 514.64312664  
Rotation angle (degrees) 5.59423579  
Shift along axis -70.45094649  
  

> fitmap #3 inMap #1

Fit map 494apo_J423_2.43_flip.mrc in map 494apo_double_4.46.mrc using 100153
points  
correlation = 0.7019, correlation about mean = 0.4455, overlap = 672  
steps = 44, shift = 0.00588, angle = 0.0035 degrees  
  
Position of 494apo_J423_2.43_flip.mrc (#3) relative to 494apo_double_4.46.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.99648974 -0.04981892 -0.06727758 67.54484887  
0.05313150 0.99741489 0.04837959 72.25846505  
0.06469344 -0.05178432 0.99656066 24.92604533  
Axis -0.51350615 -0.67657035 0.52779162  
Axis point -932.39264936 -0.00000000 515.15365897  
Rotation angle (degrees) 5.59692097  
Shift along axis -70.41687257  
  

> fitmap #3 inMap #1

Fit map 494apo_J423_2.43_flip.mrc in map 494apo_double_4.46.mrc using 100153
points  
correlation = 0.7019, correlation about mean = 0.4455, overlap = 672  
steps = 44, shift = 0.0131, angle = 0.00283 degrees  
  
Position of 494apo_J423_2.43_flip.mrc (#3) relative to 494apo_double_4.46.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.99649034 -0.04982729 -0.06726257 67.54125919  
0.05314206 0.99741211 0.04842520 72.24686584  
0.06467560 -0.05182971 0.99655946 24.95059318  
Axis -0.51388173 -0.67628227 0.52779528  
Axis point -932.88473413 0.00000000 514.97844663  
Rotation angle (degrees) 5.59791435  
Shift along axis -70.39868812  
  

> fitmap #3 inMap #1

Fit map 494apo_J423_2.43_flip.mrc in map 494apo_double_4.46.mrc using 100153
points  
correlation = 0.7019, correlation about mean = 0.4455, overlap = 672  
steps = 40, shift = 0.00172, angle = 0.00302 degrees  
  
Position of 494apo_J423_2.43_flip.mrc (#3) relative to 494apo_double_4.46.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.99648726 -0.04982085 -0.06731285 67.54839240  
0.05313918 0.99741156 0.04843972 72.24518402  
0.06472531 -0.05184651 0.99655536 24.94607437  
Axis -0.51383472 -0.67652150 0.52753440  
Axis point -932.01291655 0.00000000 514.55109062  
Rotation angle (degrees) 5.60018312  
Shift along axis -70.42421727  
  

> fitmap #3 inMap #1

Fit map 494apo_J423_2.43_flip.mrc in map 494apo_double_4.46.mrc using 100153
points  
correlation = 0.7019, correlation about mean = 0.4455, overlap = 672  
steps = 44, shift = 0.00188, angle = 0.00217 degrees  
  
Position of 494apo_J423_2.43_flip.mrc (#3) relative to 494apo_double_4.46.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.99648918 -0.04978546 -0.06731069 67.54153121  
0.05310295 0.99741401 0.04842910 72.25320986  
0.06472556 -0.05183347 0.99655602 24.94168804  
Axis -0.51384831 -0.67668933 0.52730585  
Axis point -931.90151240 0.00000000 514.24382652  
Rotation angle (degrees) 5.59870864  
Shift along axis -70.44718022  
  

> open "D:/My Documents/Projects/494/494apo/494apo_J437_2.42-coot-0.pdb"

Summary of feedback from opening D:/My
Documents/Projects/494/494apo/494apo_J437_2.42-coot-0.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 28 28 LEU C 139 GLN C 141 1 3  
Start residue of secondary structure not found: HELIX 41 41 LEU D 139 GLN D
141 1 3  
Start residue of secondary structure not found: HELIX 78 78 LEU G 139 GLN G
141 1 3  
Start residue of secondary structure not found: HELIX 91 91 LEU H 139 GLN H
141 1 3  
  
Chain information for 494apo_J437_2.42-coot-0.pdb #4  
---  
Chain | Description  
A B E F | No description available  
C D G H | No description available  
  

> open "D:/My Documents/Projects/494/494apo/494apo_J437_2.42-coot-0.pdb"

Summary of feedback from opening D:/My
Documents/Projects/494/494apo/494apo_J437_2.42-coot-0.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 28 28 LEU C 139 GLN C 141 1 3  
Start residue of secondary structure not found: HELIX 41 41 LEU D 139 GLN D
141 1 3  
Start residue of secondary structure not found: HELIX 78 78 LEU G 139 GLN G
141 1 3  
Start residue of secondary structure not found: HELIX 91 91 LEU H 139 GLN H
141 1 3  
  
Chain information for 494apo_J437_2.42-coot-0.pdb #5  
---  
Chain | Description  
A B E F | No description available  
C D G H | No description available  
  

> hide atoms

> show cartoons

> select add #5

19604 atoms, 20064 bonds, 8 pseudobonds, 2556 residues, 2 models selected  

> view matrix models
> #5,0.34153,0.93666,0.077549,-64.116,-0.88034,0.34771,-0.32264,341.17,-0.32917,0.041922,0.94334,63.503

> view matrix models
> #5,-0.1183,0.9925,-0.030795,30.491,-0.97152,-0.1221,-0.2031,421.74,-0.20534,0.0058913,0.97867,40.725

> view matrix models
> #5,0.22622,0.90005,-0.37247,47.044,-0.97357,0.19655,-0.11634,347.84,-0.031499,0.38894,0.92072,-50.615

> ui mousemode right "translate selected models"

> view matrix models
> #5,0.22622,0.90005,-0.37247,39.525,-0.97357,0.19655,-0.11634,440.5,-0.031499,0.38894,0.92072,-28.885

> view matrix models
> #5,0.22622,0.90005,-0.37247,81.529,-0.97357,0.19655,-0.11634,442.45,-0.031499,0.38894,0.92072,-37.496

> view matrix models
> #5,0.22622,0.90005,-0.37247,88.269,-0.97357,0.19655,-0.11634,439.25,-0.031499,0.38894,0.92072,-24.211

> ui mousemode right "rotate selected models"

> view matrix models
> #5,0.66307,0.74652,0.055124,-43.277,-0.74354,0.64833,0.16377,262.49,0.086519,-0.14958,0.98496,40.569

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.04517, steps = 64  
shifted from previous position = 2.96  
rotated from previous position = 1.04 degrees  
atoms outside contour = 15044, contour level = 0.094923  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.61103671 0.79156877 -0.00727968 -75.07166721  
-0.78164126 0.60477660 0.15258502 187.39283585  
0.12518412 -0.08754495 0.98826353 -11.10994658  
Axis -0.15036935 -0.08294882 -0.98514392  
Axis point 154.70382910 169.58716008 0.00000000  
Rotation angle (degrees) 52.98397083  
Shift along axis 6.68936057  
  

> view matrix models
> #5,0.65435,0.71714,0.23986,-71.606,-0.75467,0.59921,0.26725,256.75,0.047934,-0.35589,0.9333,93.562

> view matrix models
> #5,0.711,0.69199,0.12501,-56.218,-0.70275,0.69292,0.16126,249.64,0.024969,-0.2025,0.97896,61.32

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.04513, steps = 156  
shifted from previous position = 2.95  
rotated from previous position = 1.73 degrees  
atoms outside contour = 15016, contour level = 0.094923  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.67195736 0.74026650 0.02188147 -82.70093774  
-0.73291647 0.66046260 0.16316429 164.47793889  
0.10633316 -0.12567673 0.98635623 -2.54008087  
Axis -0.19209895 -0.05616613 -0.97976699  
Axis point 144.74398926 173.48868110 0.00000000  
Rotation angle (degrees) 48.74677745  
Shift along axis 9.13736110  
  

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.04501, steps = 104  
shifted from previous position = 0.241  
rotated from previous position = 0.372 degrees  
atoms outside contour = 15000, contour level = 0.094923  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.67631215 0.73633099 0.02045782 -82.45540064  
-0.72910636 0.66520449 0.16095619 163.33373518  
0.10490840 -0.12377255 0.98674950 -2.93560078  
Axis -0.19042487 -0.05648004 -0.98007570  
Axis point 145.13723642 173.36416137 0.00000000  
Rotation angle (degrees) 48.38414824  
Shift along axis 9.35357376  
  

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.045, steps = 76  
shifted from previous position = 0.232  
rotated from previous position = 0.322 degrees  
atoms outside contour = 14960, contour level = 0.094923  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.67963026 0.73331485 0.01876208 -82.16323542  
-0.72622650 0.66901423 0.15816137 162.64986599  
0.10342998 -0.12111677 0.98723500 -3.46999615  
Axis -0.18763261 -0.05688401 -0.98059075  
Axis point 145.74585976 173.26898517 0.00000000  
Rotation angle (degrees) 48.09174721  
Shift along axis 9.56697204  
  

> view matrix models
> #5,0.77224,0.56665,0.28733,-75.021,-0.60806,0.79027,0.075757,228.44,-0.18414,-0.23322,0.95483,107.27

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.0493, steps = 104  
shifted from previous position = 2.42  
rotated from previous position = 2.56 degrees  
atoms outside contour = 14887, contour level = 0.094923  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.76323559 0.62406476 0.16737558 -104.21901006  
-0.64061347 0.76464829 0.07019509 146.10524040  
-0.08417717 -0.16079844 0.98339110 36.95030444  
Axis -0.17633362 0.19202792 -0.96541791  
Axis point 144.47194832 218.77100673 0.00000000  
Rotation angle (degrees) 40.91889569  
Shift along axis 10.76111492  
  

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.04937, steps = 60  
shifted from previous position = 0.196  
rotated from previous position = 0.212 degrees  
atoms outside contour = 14824, contour level = 0.094923  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.76370634 0.62445747 0.16372378 -103.55460030  
-0.64042335 0.76479631 0.07031726 146.01767315  
-0.08130521 -0.15855427 0.98399695 35.77831553  
Axis -0.17490255 0.18725001 -0.96661602  
Axis point 144.90094906 217.61706829 0.00000000  
Rotation angle (degrees) 40.86530434  
Shift along axis 10.86988098  
  

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.04937, steps = 120  
shifted from previous position = 0.00102  
rotated from previous position = 0.00508 degrees  
atoms outside contour = 14829, contour level = 0.094923  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.76373357 0.62442510 0.16372022 -103.55334250  
-0.64038461 0.76483515 0.07024760 146.01638031  
-0.08135462 -0.15849436 0.98400252 35.77629638  
Axis -0.17481460 0.18729690 -0.96662285  
Axis point 144.91648940 217.62771115 0.00000000  
Rotation angle (degrees) 40.86216760  
Shift along axis 10.86886518  
  

> view matrix models
> #5,0.61404,0.78905,0.018953,-36.075,-0.77223,0.59565,0.22107,267.92,0.16314,-0.15038,0.97507,22.039

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.04705, steps = 100  
shifted from previous position = 2.14  
rotated from previous position = 3.03 degrees  
atoms outside contour = 14975, contour level = 0.094923  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.55318741 0.83087084 -0.06031020 -62.28392012  
-0.81365065 0.55441836 0.17490825 198.17853855  
0.17876325 -0.04768561 0.98273586 -30.96658984  
Axis -0.13276108 -0.14258996 -0.98083770  
Axis point 158.55090968 158.56603553 0.00000000  
Rotation angle (degrees) 56.96366239  
Shift along axis 10.38380984  
  

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.04705, steps = 44  
shifted from previous position = 0.00384  
rotated from previous position = 0.0109 degrees  
atoms outside contour = 14962, contour level = 0.094923  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.55316364 0.83089912 -0.06013839 -62.31902877  
-0.81369929 0.55436767 0.17484261 198.20804635  
0.17861535 -0.04778201 0.98275807 -30.92900970  
Axis -0.13277673 -0.14239639 -0.98086370  
Axis point 158.54539258 158.60366843 0.00000000  
Rotation angle (degrees) 56.96544785  
Shift along axis 10.38755031  
  

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.04706, steps = 64  
shifted from previous position = 0.0156  
rotated from previous position = 0.0138 degrees  
atoms outside contour = 14966, contour level = 0.094923  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.55324178 0.83083312 -0.06033100 -62.27653682  
-0.81360689 0.55447398 0.17493548 198.14519265  
0.17879416 -0.04769590 0.98272974 -30.98038513  
Axis -0.13278881 -0.14262654 -0.98082863  
Axis point 158.54215755 158.54707935 0.00000000  
Rotation angle (degrees) 56.96011250  
Shift along axis 10.39531189  
  

> ui mousemode right "translate selected models"

> view matrix models
> #5,0.60924,0.79289,0.012788,-32.973,-0.78276,0.59871,0.16981,279.26,0.12699,-0.11347,0.98539,16.696

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.04943, steps = 112  
shifted from previous position = 2.69  
rotated from previous position = 4.14 degrees  
atoms outside contour = 14755, contour level = 0.094923  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.60008751 0.79939790 -0.02929083 -67.29237264  
-0.78933349 0.59767941 0.14047045 190.51947152  
0.12979831 -0.06117433 0.98965150 -22.80609914  
Axis -0.12529507 -0.09885247 -0.98718252  
Axis point 160.11855629 162.38249245 0.00000000  
Rotation angle (degrees) 53.57933023  
Shift along axis 12.11186435  
  

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.04943, steps = 80  
shifted from previous position = 0.0154  
rotated from previous position = 0.00579 degrees  
atoms outside contour = 14747, contour level = 0.094923  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.60008433 0.79940329 -0.02920881 -67.31235876  
-0.78933624 0.59766203 0.14052891 190.50913025  
0.12979627 -0.06127363 0.98964562 -22.80086992  
Axis -0.12539157 -0.09879904 -0.98717562  
Axis point 160.09722776 162.39256974 0.00000000  
Rotation angle (degrees) 53.58027131  
Shift along axis 12.12674616  
  

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.04943, steps = 84  
shifted from previous position = 0.00576  
rotated from previous position = 0.011 degrees  
atoms outside contour = 14746, contour level = 0.094923  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.59999487 0.79946973 -0.02922823 -67.30530726  
-0.78942105 0.59758556 0.14037767 190.57159703  
0.12969406 -0.06115250 0.98966652 -22.80582466  
Axis -0.12521400 -0.09874103 -0.98720396  
Axis point 160.13362800 162.40945368 0.00000000  
Rotation angle (degrees) 53.58543486  
Shift along axis 12.12433083  
  

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.04943, steps = 80  
shifted from previous position = 0.00507  
rotated from previous position = 0.00948 degrees  
atoms outside contour = 14743, contour level = 0.094923  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.60006325 0.79942199 -0.02912987 -67.32914783  
-0.78936639 0.59763413 0.14047820 190.52990844  
0.12971037 -0.06130167 0.98965515 -22.77772661  
Axis -0.12537522 -0.09869483 -0.98718812  
Axis point 160.09806540 162.41524955 0.00000000  
Rotation angle (degrees) 53.58167592  
Shift along axis 12.12299131  
  

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.04943, steps = 64  
shifted from previous position = 0.00259  
rotated from previous position = 0.00547 degrees  
atoms outside contour = 14746, contour level = 0.094923  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.60006497 0.79941724 -0.02922482 -67.30914280  
-0.78935470 0.59764761 0.14048658 190.52393340  
0.12977354 -0.06123233 0.98965116 -22.80285397  
Axis -0.12533798 -0.09879358 -0.98718297  
Axis point 160.10725965 162.39578426 0.00000000  
Rotation angle (degrees) 53.58127689  
Shift along axis 12.12443897  
  

> view matrix models
> #5,0.65042,0.75817,0.046173,-43.325,-0.75592,0.64014,0.13709,275.07,0.074378,-0.12407,0.98948,23.174

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.04913, steps = 124  
shifted from previous position = 3.48  
rotated from previous position = 3.08 degrees  
atoms outside contour = 14857, contour level = 0.094923  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.63674954 0.76970765 -0.04582723 -65.95139547  
-0.76152057 0.63707649 0.11924742 184.99112153  
0.12098110 -0.04103236 0.99180639 -29.68268488  
Axis -0.10349953 -0.10771529 -0.98877968  
Axis point 167.70840781 162.64586238 0.00000000  
Rotation angle (degrees) 50.74179501  
Shift along axis 16.24920176  
  

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.04915, steps = 44  
shifted from previous position = 0.0171  
rotated from previous position = 0.0354 degrees  
atoms outside contour = 14842, contour level = 0.094923  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.63719625 0.76932755 -0.04600037 -65.93426432  
-0.76114740 0.63754419 0.11913031 184.84295904  
0.12097750 -0.04089633 0.99181244 -29.71034670  
Axis -0.10338631 -0.10787720 -0.98877388  
Axis point 167.71604322 162.61203032 0.00000000  
Rotation angle (degrees) 50.70773111  
Shift along axis 16.25317461  
  

> view matrix models
> #5,0.68511,0.72779,0.030811,-86.92,-0.72573,0.67832,0.11485,296.98,0.062687,-0.10105,0.9929,10.392

> view matrix models
> #5,0.68511,0.72779,0.030811,-39.88,-0.72573,0.67832,0.11485,293.72,0.062687,-0.10105,0.9929,17.451

> view matrix models
> #5,0.68511,0.72779,0.030811,-44.088,-0.72573,0.67832,0.11485,265.33,0.062687,-0.10105,0.9929,23.996

> view matrix models
> #5,0.68511,0.72779,0.030811,-40.252,-0.72573,0.67832,0.11485,261.52,0.062687,-0.10105,0.9929,25.078

> view matrix models
> #5,0.68511,0.72779,0.030811,-33.572,-0.72573,0.67832,0.11485,257.73,0.062687,-0.10105,0.9929,20.863

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.04749, steps = 60  
shifted from previous position = 0.879  
rotated from previous position = 2.08 degrees  
atoms outside contour = 14974, contour level = 0.094923  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.64432706 0.76467178 -0.01094037 -67.42162415  
-0.75805335 0.64050857 0.12289784 173.74044830  
0.10098391 -0.07089302 0.99235902 -22.76297843  
Axis -0.12591327 -0.07272145 -0.98937224  
Axis point 156.13692987 157.76907756 0.00000000  
Rotation angle (degrees) 50.31269494  
Shift along axis 18.37567906  
  

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.04748, steps = 44  
shifted from previous position = 0.017  
rotated from previous position = 0.0169 degrees  
atoms outside contour = 14962, contour level = 0.094923  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.64417427 0.76479936 -0.01101970 -67.38661546  
-0.75819476 0.64037927 0.12269915 173.82172322  
0.10089702 -0.07068456 0.99238273 -22.78573071  
Axis -0.12563123 -0.07270641 -0.98940920  
Axis point 156.19133275 157.76081645 0.00000000  
Rotation angle (degrees) 50.32231272  
Shift along axis 18.37232156  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #5,0.84162,0.53958,-0.023109,-17.475,-0.53902,0.83653,-0.098366,233.43,-0.033745,0.095242,0.99488,1.7843

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.04576, steps = 76  
shifted from previous position = 0.978  
rotated from previous position = 1.87 degrees  
atoms outside contour = 14995, contour level = 0.094923  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.81835256 0.56039169 -0.12751557 -40.20876921  
-0.57096249 0.81806127 -0.06911996 143.23045772  
0.06558130 0.12937110 0.98942519 -52.09784649  
Axis 0.17041485 -0.16578367 -0.97132618  
Axis point 210.15757425 145.95642372 0.00000000  
Rotation angle (degrees) 35.61783513  
Shift along axis 20.00655979  
  

> view matrix models
> #5,0.71153,0.70265,-0.0031216,-26.629,-0.70193,0.71059,-0.048622,278.23,-0.031946,0.036787,0.99881,11.572

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.04982, steps = 84  
shifted from previous position = 2.49  
rotated from previous position = 3.56 degrees  
atoms outside contour = 14721, contour level = 0.094923  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.64221819 0.76425179 -0.05894895 -58.45144700  
-0.76577958 0.64307982 -0.00547370 200.75520043  
0.03372560 0.04865721 0.99824598 -31.22693299  
Axis 0.03529224 -0.06042189 -0.99754882  
Axis point 186.73799129 164.68573731 0.00000000  
Rotation angle (degrees) 50.07591942  
Shift along axis 16.95749897  
  

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.04982, steps = 44  
shifted from previous position = 0.00309  
rotated from previous position = 0.00418 degrees  
atoms outside contour = 14721, contour level = 0.094923  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.64223376 0.76423872 -0.05894867 -58.45377002  
-0.76576416 0.64309876 -0.00540501 200.73462767  
0.03377910 0.04861206 0.99824638 -31.23037433  
Axis 0.03521868 -0.06045774 -0.99754925  
Axis point 186.72294180 164.67918843 0.00000000  
Rotation angle (degrees) 50.07461523  
Shift along axis 16.95920949  
  

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.0498, steps = 44  
shifted from previous position = 0.0125  
rotated from previous position = 0.017 degrees  
atoms outside contour = 14719, contour level = 0.094923  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.64211554 0.76433343 -0.05900863 -58.43257003  
-0.76586997 0.64297070 -0.00564332 200.82926682  
0.03362744 0.04881661 0.99824151 -31.23167453  
Axis 0.03550256 -0.06038968 -0.99754331  
Axis point 186.78399783 164.69450034 0.00000000  
Rotation angle (degrees) 50.08399679  
Shift along axis 16.95242655  
  

> ui mousemode right "translate selected models"

> view matrix models
> #5,0.68295,0.73003,0.025118,-38.743,-0.73004,0.68332,-0.010454,289.33,-0.024796,-0.011198,0.99963,25.888

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.05163, steps = 80  
shifted from previous position = 1.62  
rotated from previous position = 1.99 degrees  
atoms outside contour = 14559, contour level = 0.094923  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.66473153 0.74597274 -0.04070179 -68.85951574  
-0.74664245 0.66522274 -0.00193466 200.75760068  
0.02563255 0.03167571 0.99916946 -23.43096415  
Axis 0.02248988 -0.04438663 -0.99876125  
Axis point 189.83160607 178.01607057 0.00000000  
Rotation angle (degrees) 48.35127762  
Shift along axis 12.94234269  
  

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.05162, steps = 48  
shifted from previous position = 0.017  
rotated from previous position = 0.013 degrees  
atoms outside contour = 14550, contour level = 0.094923  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.66480394 0.74591595 -0.04055971 -68.90410727  
-0.74657736 0.66529620 -0.00178822 200.69875174  
0.02565035 0.03146977 0.99917551 -23.39568884  
Axis 0.02225611 -0.04430748 -0.99877000  
Axis point 189.77418006 178.04107232 0.00000000  
Rotation angle (degrees) 48.34545302  
Shift along axis 12.94091853  
  

> view matrix models
> #5,0.70382,0.70905,0.043347,-38.386,-0.70954,0.70465,-0.0056079,281.47,-0.03452,-0.026809,0.99904,30.477

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.05293, steps = 108  
shifted from previous position = 1.76  
rotated from previous position = 1.9 degrees  
atoms outside contour = 14561, contour level = 0.094923  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.66629089 0.74522692 -0.02632985 -67.32822190  
-0.74566675 0.66556282 -0.03173681 206.21011170  
-0.00612696 0.04077924 0.99914939 -16.77637077  
Axis 0.04857743 -0.01353362 -0.99872773  
Axis point 196.45023114 179.01248018 0.00000000  
Rotation angle (degrees) 48.27918526  
Shift along axis 10.69362560  
  

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.05293, steps = 124  
shifted from previous position = 0.00146  
rotated from previous position = 0.000742 degrees  
atoms outside contour = 14562, contour level = 0.094923  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.66628816 0.74522893 -0.02634186 -67.32542836  
-0.74566926 0.66556016 -0.03173327 206.21110667  
-0.00611646 0.04078582 0.99914918 -16.77824242  
Axis 0.04857931 -0.01354865 -0.99872743  
Axis point 196.45175227 179.00959388 0.00000000  
Rotation angle (degrees) 48.27939947  
Shift along axis 10.69238568  
  

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.05293, steps = 76  
shifted from previous position = 0.00337  
rotated from previous position = 0.0031 degrees  
atoms outside contour = 14566, contour level = 0.094923  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.66629184 0.74522566 -0.02634134 -67.32356894  
-0.74566630 0.66556604 -0.03167956 206.19815289  
-0.00607652 0.04074968 0.99915090 -16.78150644  
Axis 0.04851945 -0.01357515 -0.99872998  
Axis point 196.44072902 179.00125855 0.00000000  
Rotation angle (degrees) 48.27896664  
Shift along axis 10.69452040  
  

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.05295, steps = 100  
shifted from previous position = 0.00862  
rotated from previous position = 0.00788 degrees  
atoms outside contour = 14563, contour level = 0.094923  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.66634279 0.74517952 -0.02635797 -67.31296563  
-0.74562159 0.66562164 -0.03156350 206.15776573  
-0.00597604 0.04068518 0.99915414 -16.79051061  
Axis 0.04840167 -0.01365450 -0.99873462  
Axis point 196.42430073 178.97574744 0.00000000  
Rotation angle (degrees) 48.27475304  
Shift along axis 10.69622294  
  

> view matrix models
> #5,0.70266,0.70907,0.059078,-38.147,-0.70845,0.70492,-0.034571,289.73,-0.066158,-0.017562,0.99765,30.43

> ui mousemode right "rotate selected models"

> view matrix models
> #5,0.46174,0.86552,-0.19407,24.484,-0.87327,0.48194,0.07166,341.22,0.15555,0.13638,0.97837,-35.015

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.0458, steps = 120  
shifted from previous position = 2.53  
rotated from previous position = 1.5 degrees  
atoms outside contour = 14924, contour level = 0.094923  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.40725390 0.87849222 -0.24979121 0.05187453  
-0.89648350 0.43677221 0.07448053 255.73515864  
0.17453242 0.19360121 0.96543099 -76.89908453  
Axis 0.06513336 -0.23201363 -0.97052940  
Axis point 202.64592497 137.80700875 0.00000000  
Rotation angle (degrees) 66.12588202  
Shift along axis 15.30215929  
  

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.04582, steps = 60  
shifted from previous position = 0.0225  
rotated from previous position = 0.0309 degrees  
atoms outside contour = 14921, contour level = 0.094923  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.40735693 0.87846091 -0.24973333 0.03449552  
-0.89653352 0.43675995 0.07394847 255.83242932  
0.17403436 0.19377088 0.96548686 -76.86755158  
Axis 0.06551938 -0.23171787 -0.97057408  
Axis point 202.70962657 137.85948736 0.00000000  
Rotation angle (degrees) 66.12128781  
Shift along axis 15.32696674  
  

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.04582, steps = 80  
shifted from previous position = 0.00211  
rotated from previous position = 0.00274 degrees  
atoms outside contour = 14919, contour level = 0.094923  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.40734795 0.87845789 -0.24975861 0.04148921  
-0.89654237 0.43674803 0.07391159 255.84092201  
0.17400980 0.19381144 0.96548314 -76.86959361  
Axis 0.06556133 -0.23171689 -0.97057148  
Axis point 202.71571912 137.85895497 0.00000000  
Rotation angle (degrees) 66.12205920  
Shift along axis 15.32749279  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #5,0.9774,0.20328,-0.057944,25.46,-0.2113,0.94697,-0.24206,189.67,0.005665,0.24883,0.96853,-25.898

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.04445, steps = 100  
shifted from previous position = 3.11  
rotated from previous position = 2.78 degrees  
atoms outside contour = 15082, contour level = 0.094923  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.95402369 0.26143761 -0.14659178 -9.92615772  
-0.28666621 0.93868817 -0.19153846 101.92986545  
0.08752861 0.22475514 0.97047610 -67.61225414  
Axis 0.57261761 -0.32203584 -0.75392439  
Axis point 342.72278627 125.54155532 0.00000000  
Rotation angle (degrees) 21.31533158  
Shift along axis 12.46556469  
  

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.04445, steps = 48  
shifted from previous position = 0.0157  
rotated from previous position = 0.0137 degrees  
atoms outside contour = 15077, contour level = 0.094923  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.95401498 0.26156127 -0.14642781 -9.98165392  
-0.28673875 0.93869269 -0.19140767 101.91770256  
0.08738588 0.22459231 0.97052665 -67.55083199  
Axis 0.57230728 -0.32166654 -0.75431758  
Axis point 342.54964425 125.64552451 0.00000000  
Rotation angle (degrees) 21.31167745  
Shift along axis 12.45869180  
  

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.04446, steps = 60  
shifted from previous position = 0.0113  
rotated from previous position = 0.0201 degrees  
atoms outside contour = 15073, contour level = 0.094923  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.95400107 0.26145228 -0.14671278 -9.90093020  
-0.28671199 0.93866565 -0.19158027 101.95507435  
0.08762515 0.22483210 0.97044956 -67.63188853  
Axis 0.57263632 -0.32225366 -0.75381710  
Axis point 342.76406982 125.45717112 0.00000000  
Rotation angle (degrees) 21.32097970  
Shift along axis 12.45704583  
  

> lighting soft

> select clear

> lighting soft

> volume #3 level 0.16

> volume #2 level 0.16

> volume #2 step 1

> volume #3 step 1

> color bychain

> ui mousemode right "translate selected models"

> select add #5

19604 atoms, 20064 bonds, 8 pseudobonds, 2556 residues, 2 models selected  

> view matrix models
> #5,0.97203,0.22846,-0.054472,-8.836,-0.23479,0.95107,-0.20082,202.6,0.0059265,0.20799,0.97811,-18.213

> view matrix models
> #5,0.97203,0.22846,-0.054472,-9.3701,-0.23479,0.95107,-0.20082,203,0.0059265,0.20799,0.97811,-17.86

> view matrix models
> #5,0.97203,0.22846,-0.054472,16.749,-0.23479,0.95107,-0.20082,194.42,0.0059265,0.20799,0.97811,-7.1728

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.06237, steps = 104  
shifted from previous position = 3.11  
rotated from previous position = 3.72 degrees  
atoms outside contour = 15180, contour level = 0.16  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.96798135 0.23038877 -0.09966488 -17.68032132  
-0.24460972 0.95488898 -0.16838379 92.00008272  
0.05637516 0.18737137 0.98067007 -43.38246830  
Axis 0.57976130 -0.25429281 -0.77408785  
Axis point 352.87623451 125.62300712 0.00000000  
Rotation angle (degrees) 17.86719653  
Shift along axis -0.06348462  
  

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.06238, steps = 28  
shifted from previous position = 0.0221  
rotated from previous position = 0.0177 degrees  
atoms outside contour = 15172, contour level = 0.16  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.96798849 0.23048549 -0.09937154 -17.76638204  
-0.24464904 0.95488143 -0.16836948 92.01152447  
0.05608132 0.18729087 0.98070230 -43.30335768  
Axis 0.57970001 -0.25337666 -0.77443409  
Axis point 352.79967334 125.88777805 0.00000000  
Rotation angle (degrees) 17.86422619  
Shift along axis -0.07714771  
  

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.06237, steps = 40  
shifted from previous position = 0.00929  
rotated from previous position = 0.0111 degrees  
atoms outside contour = 15170, contour level = 0.16  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.96796508 0.23050747 -0.09954840 -17.72660193  
-0.24469956 0.95488225 -0.16829140 92.00007050  
0.05626457 0.18725965 0.98069777 -43.32870120  
Axis 0.57944239 -0.25392878 -0.77444605  
Axis point 352.70990969 125.72632876 0.00000000  
Rotation angle (degrees) 17.86675890  
Shift along axis -0.07726862  
  

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.06238, steps = 40  
shifted from previous position = 0.00349  
rotated from previous position = 0.00294 degrees  
atoms outside contour = 15173, contour level = 0.16  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.96795882 0.23053949 -0.09953509 -17.73542329  
-0.24472638 0.95488232 -0.16825195 91.99985854  
0.05625558 0.18721983 0.98070588 -43.32343274  
Axis 0.57931890 -0.25389493 -0.77454954  
Axis point 352.66632143 125.75232094 0.00000000  
Rotation angle (degrees) 17.86657798  
Shift along axis -0.07661827  
  

> view matrix models
> #5,0.98103,0.19368,-0.007925,10.836,-0.19206,0.96566,-0.17499,175.54,-0.02624,0.17319,0.98454,2.0903

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.06238, steps = 96  
shifted from previous position = 3.51  
rotated from previous position = 0.009 degrees  
atoms outside contour = 15167, contour level = 0.16  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.96798316 0.23049533 -0.09940061 -17.75949341  
-0.24466148 0.95488669 -0.16832156 92.00214860  
0.05611899 0.18725194 0.98070758 -43.30425449  
Axis 0.57957375 -0.25349211 -0.77449081  
Axis point 352.75292351 125.85708735 0.00000000  
Rotation angle (degrees) 17.86373954  
Shift along axis -0.07600783  
  

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.06238, steps = 48  
shifted from previous position = 0.00409  
rotated from previous position = 0.00921 degrees  
atoms outside contour = 15172, contour level = 0.16  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.96795578 0.23055650 -0.09952527 -17.73964625  
-0.24474054 0.95488108 -0.16823844 91.99944615  
0.05624633 0.18720524 0.98070920 -43.31952640  
Axis 0.57927025 -0.25386260 -0.77459652  
Axis point 352.64199822 125.76391617 0.00000000  
Rotation angle (degrees) 17.86666866  
Shift along axis -0.07611348  
  

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.06238, steps = 44  
shifted from previous position = 0.0106  
rotated from previous position = 0.0203 degrees  
atoms outside contour = 15186, contour level = 0.16  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.96802106 0.23036836 -0.09932590 -17.75342643  
-0.24453073 0.95489371 -0.16847166 92.00473371  
0.05603513 0.18737234 0.98068938 -43.31822109  
Axis 0.58009303 -0.25326787 -0.77417534  
Axis point 352.95981829 125.89941139 0.00000000  
Rotation angle (degrees) 17.86124443  
Shift along axis -0.06458278  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #5,0.99793,-0.038524,0.051583,41.379,0.053547,0.94147,-0.33281,164.57,-0.035742,0.33488,0.94158,-15.159

> view matrix models
> #5,0.79981,-0.1974,0.56686,11.667,0.237,0.9715,0.0039163,63.001,-0.55148,0.13122,0.8238,138.92

> view matrix models
> #5,0.66554,0.39935,0.63054,-84.409,-0.73053,0.52162,0.44073,242.84,-0.1529,-0.75395,0.63889,261.39

> view matrix models
> #5,0.9987,-2.5766e-05,0.051022,34.305,0.008663,0.98557,-0.16907,134.51,-0.050281,0.16929,0.98428,9.8883

> view matrix models
> #5,0.99311,-0.069414,0.094437,39.989,0.080444,0.98969,-0.11851,111.18,-0.085237,0.12529,0.98845,23.604

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.521, steps = 136  
shifted from previous position = 7.86  
rotated from previous position = 6.92 degrees  
atoms outside contour = 2002, contour level = 0.16  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.99999998 0.00005358 -0.00007640 0.01324976  
-0.00005357 0.99999998 0.00010882 -0.01975909  
0.00007640 -0.00010882 0.99999998 -0.00694491  
Axis -0.75912742 -0.53295449 -0.37374466  
Axis point 0.00000000 -53.29611542 166.53904150  
Rotation angle (degrees) 0.00821348  
Shift along axis 0.00306806  
  

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.521, steps = 44  
shifted from previous position = 0.0109  
rotated from previous position = 0.00668 degrees  
atoms outside contour = 2000, contour level = 0.16  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.99999998 0.00011331 -0.00000445 -0.00636527  
-0.00011331 0.99999998 0.00003914 0.00519207  
0.00000445 -0.00003914 0.99999999 0.00325331  
Axis -0.32628554 -0.03710988 -0.94454254  
Axis point 45.43018136 59.60289623 0.00000000  
Rotation angle (degrees) 0.00687315  
Shift along axis -0.00118867  
  

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.521, steps = 40  
shifted from previous position = 0.00705  
rotated from previous position = 0.00202 degrees  
atoms outside contour = 2006, contour level = 0.16  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.99999998 0.00013644 0.00000887 -0.00748202  
-0.00013644 0.99999998 0.00001606 0.01642198  
-0.00000887 -0.00001606 0.99999999 0.00479207  
Axis -0.11666189 0.06441733 -0.99108043  
Axis point 121.68525093 57.25494622 0.00000000  
Rotation angle (degrees) 0.00788792  
Shift along axis -0.00281860  
  

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.5209, steps = 40  
shifted from previous position = 0.0101  
rotated from previous position = 0.00962 degrees  
atoms outside contour = 2000, contour level = 0.16  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.99999998 0.00008109 -0.00011632 0.02838138  
-0.00008108 0.99999998 0.00011334 -0.01415472  
0.00011633 -0.00011334 0.99999998 -0.00960739  
Axis -0.62437786 -0.64080896 -0.44667233  
Axis point 99.35136883 0.00000000 220.59130185  
Rotation angle (degrees) 0.01040062  
Shift along axis -0.00435888  
  

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.5209, steps = 48  
shifted from previous position = 0.0111  
rotated from previous position = 0.00521 degrees  
atoms outside contour = 2005, contour level = 0.16  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.99999997 0.00004856 -0.00016090 0.04043632  
-0.00004853 0.99999997 0.00018572 -0.03825918  
0.00016091 -0.00018571 0.99999996 -0.01424211  
Axis -0.74145657 -0.64239818 -0.19382139  
Axis point 0.00000000 -79.48459257 215.14483294  
Rotation angle (degrees) 0.01435090  
Shift along axis -0.00264372  
  

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.521, steps = 44  
shifted from previous position = 0.0211  
rotated from previous position = 0.00719 degrees  
atoms outside contour = 2002, contour level = 0.16  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.99999998 0.00006713 -0.00006421 0.01145597  
-0.00006713 0.99999998 0.00010801 -0.01415889  
0.00006422 -0.00010801 0.99999998 0.00775095  
Axis -0.75816663 -0.45073187 -0.47119438  
Axis point 0.00000000 45.76796116 155.94165450  
Rotation angle (degrees) 0.00816256  
Shift along axis -0.00595588  
  

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.521, steps = 44  
shifted from previous position = 0.0161  
rotated from previous position = 0.00823 degrees  
atoms outside contour = 2002, contour level = 0.16  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.99999998 0.00014144 -0.00005248 0.00647961  
-0.00014144 0.99999998 -0.00001439 0.02406762  
0.00005248 0.00001440 0.99999999 -0.02418116  
Axis 0.09499591 -0.34629014 -0.93330537  
Axis point 206.52337077 -35.82232803 0.00000000  
Rotation angle (degrees) 0.00868288  
Shift along axis 0.01484956  
  

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.521, steps = 48  
shifted from previous position = 0.00594  
rotated from previous position = 0.00615 degrees  
atoms outside contour = 2000, contour level = 0.16  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.99999997 0.00020087 0.00003626 -0.02141021  
-0.00020087 0.99999997 -0.00002554 0.04256824  
-0.00003627 0.00002553 0.99999999 -0.00834882  
Axis 0.12413731 0.17629612 -0.97647817  
Axis point 200.49652555 114.63994069 0.00000000  
Rotation angle (degrees) 0.01178639  
Shift along axis 0.01299925  
  

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.521, steps = 60  
shifted from previous position = 0.00492  
rotated from previous position = 0.0106 degrees  
atoms outside contour = 1997, contour level = 0.16  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.99999998 0.00010067 -0.00010245 0.01778115  
-0.00010067 0.99999998 0.00004404 0.01110089  
0.00010245 -0.00004403 0.99999998 -0.01946003  
Axis -0.29311006 -0.68194670 -0.67010088  
Axis point 188.26378801 0.00000000 174.28183173  
Rotation angle (degrees) 0.00860768  
Shift along axis 0.00025813  
  

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.521, steps = 40  
shifted from previous position = 0.00299  
rotated from previous position = 0.0051 degrees  
atoms outside contour = 2000, contour level = 0.16  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.99999998 0.00008716 -0.00010045 0.01717731  
-0.00008715 0.99999998 0.00013205 -0.00862388  
0.00010046 -0.00013204 0.99999998 -0.00227282  
Axis -0.70457003 -0.53601065 -0.46505232  
Axis point 0.00000000 -39.84537210 91.37736101  
Rotation angle (degrees) 0.01073787  
Shift along axis -0.00642314  
  

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.521, steps = 44  
shifted from previous position = 0.0147  
rotated from previous position = 0.00274 degrees  
atoms outside contour = 1997, contour level = 0.16  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.99999998 0.00004562 -0.00007693 0.02192144  
-0.00004561 0.99999998 0.00012901 -0.02961066  
0.00007693 -0.00012901 0.99999998 0.00570799  
Axis -0.82181651 -0.49007420 -0.29059406  
Axis point 0.00000000 32.59450198 249.13445628  
Rotation angle (degrees) 0.00899432  
Shift along axis -0.00516269  
  

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.521, steps = 48  
shifted from previous position = 0.00271  
rotated from previous position = 0.00082 degrees  
atoms outside contour = 1996, contour level = 0.16  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.99999998 0.00005113 -0.00008636 0.02020634  
-0.00005112 0.99999998 0.00011976 -0.02756756  
0.00008636 -0.00011975 0.99999998 0.00135247  
Axis -0.76644130 -0.55272324 -0.32720751  
Axis point 0.00000000 9.38108872 233.39310419  
Rotation angle (degrees) 0.00895228  
Shift along axis -0.00069228  
  

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.5209, steps = 48  
shifted from previous position = 0.0091  
rotated from previous position = 0.0145 degrees  
atoms outside contour = 2004, contour level = 0.16  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.99999997 0.00013781 0.00006891 -0.01536638  
-0.00013780 0.99999998 -0.00006086 0.01988692  
-0.00006892 0.00006085 0.99999999 -0.00250563  
Axis 0.36737168 0.41599397 -0.83185760  
Axis point 130.07984739 124.07931334 0.00000000  
Rotation angle (degrees) 0.00949157  
Shift along axis 0.00471199  
  

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.521, steps = 40  
shifted from previous position = 0.00882  
rotated from previous position = 0.0032 degrees  
atoms outside contour = 2005, contour level = 0.16  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.99999998 0.00013763 0.00004619 -0.01668564  
-0.00013763 0.99999998 -0.00000979 0.01727444  
-0.00004619 0.00000978 0.99999999 0.00308773  
Axis 0.06723722 0.31744387 -0.94589034  
Axis point 122.18120152 121.94841553 0.00000000  
Rotation angle (degrees) 0.00833673  
Shift along axis 0.00144111  
  

> fitmap #5 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#5) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = 0.521, steps = 28  
shifted from previous position = 0.0113  
rotated from previous position = 0.00218 degrees  
atoms outside contour = 2002, contour level = 0.16  
  
Position of 494apo_J437_2.42-coot-0.pdb (#5) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
0.99999997 0.00016044 0.00004499 -0.01904373  
-0.00016045 0.99999998 0.00002059 0.02519844  
-0.00004498 -0.00002060 0.99999999 0.00232504  
Axis -0.12266423 0.26793324 -0.95559681  
Axis point 145.57876224 113.45734230 0.00000000  
Rotation angle (degrees) 0.00961996  
Shift along axis 0.00686568  
  

> select clear

> hide #!3 models

> ui mousemode right "translate selected models"

> select add #4

19604 atoms, 20064 bonds, 8 pseudobonds, 2556 residues, 2 models selected  

> view matrix models #4,1,0,0,24.202,0,1,0,13.797,0,0,1,36.326

> view matrix models #4,1,0,0,26.45,0,1,0,3.8983,0,0,1,37.965

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.99968,-0.024288,-0.0072954,32.297,0.024245,0.99969,-0.0058915,0.57446,0.0074363,0.0057127,0.99996,35.558

> view matrix models
> #4,-0.45842,-0.78189,0.42249,360.11,0.88397,-0.45031,0.12577,82.716,0.091914,0.43112,0.8976,-38.836

> view matrix models
> #4,-0.51598,-0.84063,0.16464,429.13,0.85656,-0.50811,0.090121,104.92,0.0079001,0.18753,0.98223,5.5229

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.51598,-0.84063,0.16464,424.45,0.85656,-0.50811,0.090121,97.711,0.0079001,0.18753,0.98223,-13.7

> fitmap #4 inMap #3

Fit molecule 494apo_J437_2.42-coot-0.pdb (#4) to map 494apo_J423_2.43_flip.mrc
(#3) using 19604 atoms  
average map value = -0.0004024, steps = 80  
shifted from previous position = 2.42  
rotated from previous position = 1.46 degrees  
atoms outside contour = 19587, contour level = 0.16  
  
Position of 494apo_J437_2.42-coot-0.pdb (#4) relative to
494apo_J423_2.43_flip.mrc (#3) coordinates:  
Matrix rotation and translation  
-0.47550387 -0.87316941 0.10710397 384.87511981  
0.87955685 -0.46958398 0.07662014 -3.77887991  
-0.01660806 0.13063721 0.99129113 -30.73274718  
Axis 0.03072788 0.07037422 0.99704727  
Axis point 193.63816859 114.23623797 0.00000000  
Rotation angle (degrees) 118.48302432  
Shift along axis -19.08154074  
  

> fitmap #4 inMap #2

Fit molecule 494apo_J437_2.42-coot-0.pdb (#4) to map 494apo_J437_2.42_flip.mrc
(#2) using 19604 atoms  
average map value = 0.04108, steps = 140  
shifted from previous position = 2.66  
rotated from previous position = 4.02 degrees  
atoms outside contour = 16368, contour level = 0.16  
  
Position of 494apo_J437_2.42-coot-0.pdb (#4) relative to
494apo_J437_2.42_flip.mrc (#2) coordinates:  
Matrix rotation and translation  
0.66700842 0.74163409 0.07126466 -72.63068468  
-0.73609809 0.67075558 -0.09081061 209.94378347  
-0.11514942 0.00811366 0.99331505 7.98721235  
Axis 0.06627092 0.12488171 -0.98995592  
Axis point 198.67801372 188.34531508 0.00000000  
Rotation angle (degrees) 48.27627078  
Shift along axis 13.49784852  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.5604,-0.75277,0.34538,384.58,0.73574,-0.64396,-0.20976,200.75,0.38031,0.13656,0.91472,-60.063

> fitmap #4 inMap #2

Fit molecule 494apo_J437_2.42-coot-0.pdb (#4) to map 494apo_J437_2.42_flip.mrc
(#2) using 19604 atoms  
average map value = 0.04522, steps = 92  
shifted from previous position = 0.668  
rotated from previous position = 3.98 degrees  
atoms outside contour = 16206, contour level = 0.16  
  
Position of 494apo_J437_2.42-coot-0.pdb (#4) relative to
494apo_J437_2.42_flip.mrc (#2) coordinates:  
Matrix rotation and translation  
0.74967737 0.65259183 -0.11003528 -38.60296144  
-0.65175403 0.75688210 0.04843746 152.58152696  
0.11489362 0.03540347 0.99274672 -39.20481033  
Axis -0.00984692 -0.16992926 -0.98540707  
Axis point 188.55026440 131.28040088 0.00000000  
Rotation angle (degrees) 41.43966356  
Shift along axis 13.08475124  
  

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.57538,-0.75339,0.31834,401.41,0.75408,-0.63937,-0.15019,181,0.31669,0.15364,0.936,-57.485

> fitmap #4 inMap #2

Fit molecule 494apo_J437_2.42-coot-0.pdb (#4) to map 494apo_J437_2.42_flip.mrc
(#2) using 19604 atoms  
average map value = 0.0518, steps = 168  
shifted from previous position = 3.26  
rotated from previous position = 3.73 degrees  
atoms outside contour = 15867, contour level = 0.16  
  
Position of 494apo_J437_2.42-coot-0.pdb (#4) relative to
494apo_J437_2.42_flip.mrc (#2) coordinates:  
Matrix rotation and translation  
0.78499508 0.61329665 -0.08746399 -51.29838714  
-0.60885440 0.78983865 0.07383249 134.10097081  
0.11436366 -0.00470531 0.99342782 -32.11670920  
Axis -0.06327614 -0.16260801 -0.98465972  
Axis point 174.24830241 143.38246292 0.00000000  
Rotation angle (degrees) 38.35964385  
Shift along axis 13.06410180  
  

> fitmap #4 inMap #2

Fit molecule 494apo_J437_2.42-coot-0.pdb (#4) to map 494apo_J437_2.42_flip.mrc
(#2) using 19604 atoms  
average map value = 0.0518, steps = 40  
shifted from previous position = 0.00274  
rotated from previous position = 0.00378 degrees  
atoms outside contour = 15863, contour level = 0.16  
  
Position of 494apo_J437_2.42-coot-0.pdb (#4) relative to
494apo_J437_2.42_flip.mrc (#2) coordinates:  
Matrix rotation and translation  
0.78502343 0.61325589 -0.08749541 -51.29151169  
-0.60881032 0.78987026 0.07385779 134.08128281  
0.11440375 -0.00471199 0.99342317 -32.12403727  
Axis -0.06330548 -0.16267479 -0.98464680  
Axis point 174.24239072 143.36981266 0.00000000  
Rotation angle (degrees) 38.35709053  
Shift along axis 13.06622013  
  

> fitmap #4 inMap #2

Fit molecule 494apo_J437_2.42-coot-0.pdb (#4) to map 494apo_J437_2.42_flip.mrc
(#2) using 19604 atoms  
average map value = 0.0518, steps = 40  
shifted from previous position = 0.00115  
rotated from previous position = 0.000279 degrees  
atoms outside contour = 15862, contour level = 0.16  
  
Position of 494apo_J437_2.42-coot-0.pdb (#4) relative to
494apo_J437_2.42_flip.mrc (#2) coordinates:  
Matrix rotation and translation  
0.78502229 0.61325750 -0.08749433 -51.29161794  
-0.60881144 0.78986898 0.07386226 134.08141281  
0.11440565 -0.00471598 0.99342293 -32.12259804  
Axis -0.06331212 -0.16267501 -0.98464634  
Axis point 174.24173253 143.36967756 0.00000000  
Rotation angle (degrees) 38.35721312  
Shift along axis 13.06508502  
  

> view matrix models
> #4,-0.61707,-0.73059,0.29232,376.6,0.71774,-0.67485,-0.17153,124.49,0.32259,0.10397,0.94081,-48.399

> view matrix models
> #4,-0.61707,-0.73059,0.29232,392.36,0.71774,-0.67485,-0.17153,191.33,0.32259,0.10397,0.94081,-35.569

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.92892,-0.28785,0.23293,379.92,0.17022,-0.8906,-0.42174,377.97,0.32884,-0.35211,0.87629,58.558

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.92892,-0.28785,0.23293,394.38,0.17022,-0.8906,-0.42174,376.96,0.32884,-0.35211,0.87629,57.587

> view matrix models
> #4,-0.92892,-0.28785,0.23293,402.73,0.17022,-0.8906,-0.42174,384.74,0.32884,-0.35211,0.87629,48.353

> fitmap #4 inMap #2

Fit molecule 494apo_J437_2.42-coot-0.pdb (#4) to map 494apo_J437_2.42_flip.mrc
(#2) using 19604 atoms  
average map value = 0.4934, steps = 224  
shifted from previous position = 7.19  
rotated from previous position = 20.2 degrees  
atoms outside contour = 2075, contour level = 0.16  
  
Position of 494apo_J437_2.42-coot-0.pdb (#4) relative to
494apo_J437_2.42_flip.mrc (#2) coordinates:  
Matrix rotation and translation  
1.00000001 -0.00001950 -0.00007302 0.02743556  
0.00001951 1.00000000 0.00012582 -0.02524303  
0.00007302 -0.00012583 1.00000000 0.00568501  
Axis -0.85723332 -0.49748558 0.13288764  
Axis point 0.00000000 55.93872938 240.97186534  
Rotation angle (degrees) 0.00840998  
Shift along axis -0.01020516  
  

> fitmap #4 inMap #2

Fit molecule 494apo_J437_2.42-coot-0.pdb (#4) to map 494apo_J437_2.42_flip.mrc
(#2) using 19604 atoms  
average map value = 0.4934, steps = 48  
shifted from previous position = 0.0053  
rotated from previous position = 0.0112 degrees  
atoms outside contour = 2075, contour level = 0.16  
  
Position of 494apo_J437_2.42-coot-0.pdb (#4) relative to
494apo_J437_2.42_flip.mrc (#2) coordinates:  
Matrix rotation and translation  
1.00000001 0.00005556 0.00006590 -0.01641438  
-0.00005556 1.00000001 0.00000922 0.01267001  
-0.00006590 -0.00000922 1.00000001 0.01020578  
Axis -0.10636966 0.76019520 -0.64092804  
Axis point 201.89024670 0.00000000 241.27352147  
Rotation angle (degrees) 0.00496709  
Shift along axis 0.00483650  
  

> fitmap #4 inMap #2

Fit molecule 494apo_J437_2.42-coot-0.pdb (#4) to map 494apo_J437_2.42_flip.mrc
(#2) using 19604 atoms  
average map value = 0.4934, steps = 44  
shifted from previous position = 0.0158  
rotated from previous position = 0.0113 degrees  
atoms outside contour = 2067, contour level = 0.16  
  
Position of 494apo_J437_2.42-coot-0.pdb (#4) relative to
494apo_J437_2.42_flip.mrc (#2) coordinates:  
Matrix rotation and translation  
1.00000001 -0.00002995 0.00001455 0.00602463  
0.00002995 0.99999999 0.00017878 -0.04482435  
-0.00001456 -0.00017878 0.99999999 0.04321386  
Axis -0.98309044 0.08003920 0.16470250  
Axis point 0.00000000 243.90136645 249.67803954  
Rotation angle (degrees) 0.01041937  
Shift along axis -0.00239303  
  

> fitmap #4 inMap #2

Fit molecule 494apo_J437_2.42-coot-0.pdb (#4) to map 494apo_J437_2.42_flip.mrc
(#2) using 19604 atoms  
average map value = 0.4934, steps = 40  
shifted from previous position = 0.0153  
rotated from previous position = 0.00879 degrees  
atoms outside contour = 2076, contour level = 0.16  
  
Position of 494apo_J437_2.42-coot-0.pdb (#4) relative to
494apo_J437_2.42_flip.mrc (#2) coordinates:  
Matrix rotation and translation  
1.00000001 0.00003122 0.00004502 -0.01075847  
-0.00003122 1.00000001 0.00004139 0.00400732  
-0.00004501 -0.00004140 1.00000001 0.01461604  
Axis -0.60288414 0.65557432 -0.45470102  
Axis point 349.61943661 0.00000000 205.96673339  
Rotation angle (degrees) 0.00393412  
Shift along axis 0.00246728  
  

> fitmap #4 inMap #2

Fit molecule 494apo_J437_2.42-coot-0.pdb (#4) to map 494apo_J437_2.42_flip.mrc
(#2) using 19604 atoms  
average map value = 0.4934, steps = 44  
shifted from previous position = 0.00357  
rotated from previous position = 0.00365 degrees  
atoms outside contour = 2075, contour level = 0.16  
  
Position of 494apo_J437_2.42-coot-0.pdb (#4) relative to
494apo_J437_2.42_flip.mrc (#2) coordinates:  
Matrix rotation and translation  
1.00000000 0.00007100 0.00009331 -0.02773075  
-0.00007100 1.00000001 0.00002928 0.01325803  
-0.00009330 -0.00002929 1.00000000 0.01771492  
Axis -0.24230391 0.77209583 -0.58750051  
Axis point 231.08067617 0.00000000 280.21529792  
Rotation angle (degrees) 0.00692396  
Shift along axis 0.00654821  
  

> fitmap #4 inMap #2

Fit molecule 494apo_J437_2.42-coot-0.pdb (#4) to map 494apo_J437_2.42_flip.mrc
(#2) using 19604 atoms  
average map value = 0.4934, steps = 48  
shifted from previous position = 0.0156  
rotated from previous position = 0.0041 degrees  
atoms outside contour = 2074, contour level = 0.16  
  
Position of 494apo_J437_2.42-coot-0.pdb (#4) relative to
494apo_J437_2.42_flip.mrc (#2) coordinates:  
Matrix rotation and translation  
1.00000000 0.00008967 0.00011478 -0.03154168  
-0.00008967 1.00000001 -0.00003629 0.02557483  
-0.00011478 0.00003628 1.00000000 0.02454407  
Axis 0.24175096 0.76464174 -0.59739390  
Axis point 199.60306361 0.00000000 269.07844678  
Rotation angle (degrees) 0.00860034  
Shift along axis -0.00273213  
  

> fitmap #4 inMap #2

Fit molecule 494apo_J437_2.42-coot-0.pdb (#4) to map 494apo_J437_2.42_flip.mrc
(#2) using 19604 atoms  
average map value = 0.4934, steps = 40  
shifted from previous position = 0.0181  
rotated from previous position = 0.0178 degrees  
atoms outside contour = 2072, contour level = 0.16  
  
Position of 494apo_J437_2.42-coot-0.pdb (#4) relative to
494apo_J437_2.42_flip.mrc (#2) coordinates:  
Matrix rotation and translation  
1.00000001 -0.00005324 -0.00008054 0.02958015  
0.00005326 1.00000000 0.00015723 -0.04314534  
0.00008053 -0.00015724 0.99999999 0.00771334  
Axis -0.85216723 -0.43649132 0.28859371  
Axis point 0.00000000 56.64163828 285.92650272  
Rotation angle (degrees) 0.01057174  
Shift along axis -0.00414865  
  

> fitmap #4 inMap #2

Fit molecule 494apo_J437_2.42-coot-0.pdb (#4) to map 494apo_J437_2.42_flip.mrc
(#2) using 19604 atoms  
average map value = 0.4934, steps = 40  
shifted from previous position = 0.00737  
rotated from previous position = 0.00452 degrees  
atoms outside contour = 2072, contour level = 0.16  
  
Position of 494apo_J437_2.42-coot-0.pdb (#4) relative to
494apo_J437_2.42_flip.mrc (#2) coordinates:  
Matrix rotation and translation  
1.00000001 -0.00001312 -0.00005887 0.02102950  
0.00001313 1.00000001 0.00009278 -0.01949995  
0.00005887 -0.00009278 1.00000000 0.00507204  
Axis -0.83839960 -0.53199561 0.11860344  
Axis point 0.00000000 63.15830151 248.33840849  
Rotation angle (degrees) 0.00634061  
Shift along axis -0.00665567  
  

> fitmap #4 inMap #2

Fit molecule 494apo_J437_2.42-coot-0.pdb (#4) to map 494apo_J437_2.42_flip.mrc
(#2) using 19604 atoms  
average map value = 0.4934, steps = 44  
shifted from previous position = 0.00255  
rotated from previous position = 0.00271 degrees  
atoms outside contour = 2074, contour level = 0.16  
  
Position of 494apo_J437_2.42-coot-0.pdb (#4) relative to
494apo_J437_2.42_flip.mrc (#2) coordinates:  
Matrix rotation and translation  
1.00000001 -0.00001962 -0.00007675 0.02593880  
0.00001963 1.00000000 0.00013611 -0.02769666  
0.00007675 -0.00013611 1.00000000 0.00740888  
Axis -0.86425522 -0.48737246 0.12462345  
Axis point 0.00000000 61.73393684 232.12760976  
Rotation angle (degrees) 0.00902326  
Shift along axis -0.00799583  
  

> fitmap #4 inMap #2

Fit molecule 494apo_J437_2.42-coot-0.pdb (#4) to map 494apo_J437_2.42_flip.mrc
(#2) using 19604 atoms  
average map value = 0.4934, steps = 48  
shifted from previous position = 0.00489  
rotated from previous position = 0.013 degrees  
atoms outside contour = 2077, contour level = 0.16  
  
Position of 494apo_J437_2.42-coot-0.pdb (#4) relative to
494apo_J437_2.42_flip.mrc (#2) coordinates:  
Matrix rotation and translation  
1.00000000 0.00006472 0.00008261 -0.02326723  
-0.00006472 1.00000001 -0.00000233 0.01516828  
-0.00008261 0.00000232 1.00000001 0.01194644  
Axis 0.02214288 0.78698649 -0.61657276  
Axis point 174.87586380 0.00000000 282.75259790  
Rotation angle (degrees) 0.00601430  
Shift along axis 0.00405618  
  

> select subtract #4

Nothing selected  

> save "D:/My Documents/Projects/494/494apo/494apo_double_fit.cxs" includeMaps
> true

> combine #4-5

Remapping chain ID 'A' in 494apo_J437_2.42-coot-0.pdb #5 to 'I'  
Remapping chain ID 'B' in 494apo_J437_2.42-coot-0.pdb #5 to 'J'  
Remapping chain ID 'C' in 494apo_J437_2.42-coot-0.pdb #5 to 'K'  
Remapping chain ID 'D' in 494apo_J437_2.42-coot-0.pdb #5 to 'L'  
Remapping chain ID 'E' in 494apo_J437_2.42-coot-0.pdb #5 to 'M'  
Remapping chain ID 'F' in 494apo_J437_2.42-coot-0.pdb #5 to 'N'  
Remapping chain ID 'G' in 494apo_J437_2.42-coot-0.pdb #5 to 'O'  
Remapping chain ID 'H' in 494apo_J437_2.42-coot-0.pdb #5 to 'P'  

> save "D:/My Documents/Projects/494/494apo/494apo_double.pdb" models #6
> relModel #1




OpenGL version: 3.3.0 NVIDIA 581.60
OpenGL renderer: NVIDIA RTX A1000 6GB Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.9
Locale: zh_CN.cp936
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: windows

Manufacturer: LENOVO
Model: 21FVA001CD
OS: Microsoft Windows 11 家庭中文版 (Build 26200)
Memory: 34,016,272,384
MaxProcessMemory: 137,438,953,344
CPU: 20 13th Gen Intel(R) Core(TM) i7-13700H
OSLanguage: zh-CN

Installed Packages:
    aiohappyeyeballs: 2.6.1
    aiohttp: 3.13.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.12.0
    appdirs: 1.4.4
    asttokens: 3.0.1
    attrs: 25.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 3.12.2
    build: 1.3.0
    certifi: 2025.11.12
    cftime: 1.6.5
    charset-normalizer: 3.4.4
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.1.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Animations: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.61.4
    ChimeraX-AtomicLibrary: 14.2.1
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.1
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.6.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-clix: 0.2.4
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.0
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.11
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5.3
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.7.3
    ChimeraX-Label: 1.2
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.2
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.1.0
    ChimeraX-MDcrds: 2.17.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.2
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.22
    ChimeraX-ModelPanel: 1.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0.1
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.15.2
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.11
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PhenixUI: 1.3.9
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.4
    ChimeraX-ProfileGrids: 1.4.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.5
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.3
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.3.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.10
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.3
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.49.1
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.5.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.5
    ChimeraX-Zone: 1.0.1
    click: 8.3.1
    colorama: 0.4.6
    comm: 0.2.3
    comtypes: 1.4.11
    contourpy: 1.3.3
    coverage: 7.13.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.1.4
    debugpy: 1.8.19
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.61.1
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.15.1
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.11
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.3.0
    ipykernel: 6.30.1
    ipython: 9.5.0
    ipython_pygments_lexers: 1.1.1
    ipywidgets: 8.1.8
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.25.1
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.6.3
    jupyter_core: 5.9.1
    jupyterlab_widgets: 3.0.16
    kiwisolver: 1.4.9
    line_profiler: 5.0.0
    lxml: 6.0.2
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.3
    matplotlib: 3.10.7
    matplotlib-inline: 0.2.1
    mcp: 1.18.0
    msgpack: 1.1.1
    multidict: 6.7.0
    ndindex: 1.10.1
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.14.1
    numpy: 1.26.4
    nvidia-nvjitlink-cu12: 12.9.86
    OpenMM: 8.2.0
    OpenMM-CUDA-12: 8.2.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.5
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.5.1
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.4.1
    psutil: 7.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.12.5
    pydantic-settings: 2.12.0
    pydantic_core: 2.41.5
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.6
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.2.5
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.9.1
    PyQt6-Qt6: 6.9.2
    PyQt6-WebEngine-commercial: 6.9.0
    PyQt6-WebEngine-Qt6: 6.9.2
    PyQt6_sip: 13.10.2
    pytest: 9.0.2
    pytest-cov: 7.0.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.1
    python-multipart: 0.0.21
    pytz: 2025.2
    pywin32: 311
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 4.0.0
    roman-numerals-py: 4.0.0
    rpds-py: 0.30.0
    scipy: 1.14.0
    Send2Trash: 1.8.3
    SEQCROW: 1.9.4
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.2.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    sse-starlette: 3.0.4
    stack-data: 0.6.3
    starlette: 0.50.0
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.4
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    tzdata: 2025.3
    urllib3: 2.6.2
    uvicorn: 0.38.0
    wcwidth: 0.2.14
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.15
    WMI: 1.5.1
    yarl: 1.22.0