Molmap: divide by zero

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-08-07)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.91 (2019-08-07)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/maf2080/Documents/181/PP_59/postprocess_masked.mrc

Opened postprocess_masked.mrc, grid size 256,256,256, pixel 1.06, shown at
level 0.00633, step 1, values float32  

> surface dust #1

> set bgColor white

> lighting soft

> ui mousemode rightMode zoom

> ui mousemode rightMode translate

> ui mousemode rightMode zoom

> ui mousemode rightMode zoom

> ui mousemode rightMode translate

> ui mousemode rightMode rotate

> toolshed show "Segment Map"

Segmenting postprocess_masked.mrc, density threshold 0.017615  
Showing postprocess_masked.seg - 0 regions, 0 surfaces  
Only showing 1000 of 2159 regions.  
Showing 1000 of 2159 region surfaces  
4212 watershed regions, grouped to 2159 regions  

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #!2 models

> show #!1 models

Smoothing and grouping, standard deviation 2 voxels  
Showing 284 region surfaces  
Got 284 regions after smoothing 2 voxels.  

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> open /Users/maf2080/Documents/221/PP194/af_pdb_fit-coot-0.pdb

af_pdb_fit-coot-0.pdb title:  
PDB: AFTMEM16 reconstituted In nanodiscs In the presence of CA2+ [more
info...]  
  
Chain information for af_pdb_fit-coot-0.pdb #3  
---  
Chain | Description  
A B | plasma membrane channel protein (AQY1), putative  
  
Non-standard residues in af_pdb_fit-coot-0.pdb #3  
---  
CA — calcium ion  
  

> hide #!2 models

> toolshed show "Fit in Map"

Fit molecule af_pdb_fit-coot-0.pdb (#3) to map postprocess_masked.mrc (#1)
using 9524 atoms  
average map value = 0.006091, steps = 92  
shifted from previous position = 1.65  
rotated from previous position = 3.99 degrees  
atoms outside contour = 8095, contour level = 0.017615  
  
Position of af_pdb_fit-coot-0.pdb (#3) relative to postprocess_masked.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99973440 0.02260793 -0.00447308 -2.18243026  
-0.02226532 0.99758898 0.06573043 -5.48778840  
0.00594833 -0.06561338 0.99782739 10.53269811  
Axis -0.94364050 -0.07487271 -0.32239214  
Axis point 0.00000000 152.99474753 90.15527836  
Rotation angle (degrees) 3.99067973  
Shift along axis -0.92534392  
  

> select #3

9524 atoms, 9770 bonds, 30 pseudobonds, 3 models selected  

> ~select #3

Nothing selected  

> view #3 clip false

> view #3 clip false

> show #!2 models

> hide #!2 models

> hide #!3.1 models

> hide #!3.2 models

> select #3

9524 atoms, 9770 bonds, 30 pseudobonds, 3 models selected  

> ~select #3

Nothing selected  
Average map value = 0.006091 for 9524 atoms, 8095 outside contour  
Fit molecule af_pdb_fit-coot-0.pdb (#3) to map postprocess_masked.mrc (#1)
using 9524 atoms  
average map value = 0.006092, steps = 48  
shifted from previous position = 0.0161  
rotated from previous position = 0.00478 degrees  
atoms outside contour = 8093, contour level = 0.017615  
  
Position of af_pdb_fit-coot-0.pdb (#3) relative to postprocess_masked.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99973392 0.02262502 -0.00449389 -2.16723700  
-0.02228148 0.99759380 0.06565174 -5.47416678  
0.00596845 -0.06553414 0.99783248 10.52387010  
Axis -0.94342231 -0.07523978 -0.32294476  
Axis point 0.00000000 152.96436233 90.06791984  
Rotation angle (degrees) 3.98679707  
Shift along axis -0.94213388  
  
Average map value = 0.006092 for 9524 atoms, 8093 outside contour  
Fit molecule af_pdb_fit-coot-0.pdb (#3) to map postprocess_masked.mrc (#1)
using 9524 atoms  
average map value = 0.006092, steps = 44  
shifted from previous position = 0.00737  
rotated from previous position = 0.0112 degrees  
atoms outside contour = 8090, contour level = 0.017615  
  
Position of af_pdb_fit-coot-0.pdb (#3) relative to postprocess_masked.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99973572 0.02251936 -0.00462164 -2.13664003  
-0.02216704 0.99758950 0.06575567 -5.50871203  
0.00609127 -0.06563585 0.99782505 10.52363886  
Axis -0.94393548 -0.07696311 -0.32103346  
Axis point 0.00000000 152.74973201 90.47246001  
Rotation angle (degrees) 3.99088194  
Shift along axis -0.93762227  
  
Average map value = 0.006092 for 9524 atoms, 8090 outside contour  
Fit molecule af_pdb_fit-coot-0.pdb (#3) to map postprocess_masked.mrc (#1)
using 9524 atoms  
average map value = 0.006092, steps = 44  
shifted from previous position = 0.00737  
rotated from previous position = 0.0112 degrees  
atoms outside contour = 8090, contour level = 0.017615  
  
Position of af_pdb_fit-coot-0.pdb (#3) relative to postprocess_masked.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99973572 0.02251936 -0.00462164 -2.13664003  
-0.02216704 0.99758950 0.06575567 -5.50871203  
0.00609127 -0.06563585 0.99782505 10.52363886  
Axis -0.94393548 -0.07696311 -0.32103346  
Axis point 0.00000000 152.74973201 90.47246001  
Rotation angle (degrees) 3.99088194  
Shift along axis -0.93762227  
  
Fit molecule af_pdb_fit-coot-0.pdb (#3) to map postprocess_masked.mrc (#1)
using 9524 atoms  
average map value = 0.00609, steps = 48  
shifted from previous position = 0.02  
rotated from previous position = 0.01 degrees  
atoms outside contour = 8097, contour level = 0.017615  
  
Position of af_pdb_fit-coot-0.pdb (#3) relative to postprocess_masked.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99973563 0.02249392 -0.00476309 -2.13091967  
-0.02213300 0.99759685 0.06565551 -5.49799933  
0.00622850 -0.06553273 0.99783098 10.47954981  
Axis -0.94375801 -0.07907262 -0.32104258  
Axis point 0.00000000 152.42025768 90.42532378  
Rotation angle (degrees) 3.98544838  
Shift along axis -0.91856795  
  
Fit molecule af_pdb_fit-coot-0.pdb (#3) to map postprocess_masked.mrc (#1)
using 9524 atoms  
average map value = 0.006092, steps = 60  
shifted from previous position = 0.0214  
rotated from previous position = 0.0272 degrees  
atoms outside contour = 8097, contour level = 0.017615  
  
Position of af_pdb_fit-coot-0.pdb (#3) relative to postprocess_masked.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99973352 0.02267526 -0.00432740 -2.19753196  
-0.02234217 0.99758838 0.06571347 -5.47164016  
0.00580704 -0.06559927 0.99782915 10.55569592  
Axis -0.94344403 -0.07281303 -0.32343721  
Axis point 0.00000000 153.28885813 89.93495859  
Rotation angle (degrees) 3.99056629  
Shift along axis -0.94244973  
  
Fit molecule af_pdb_fit-coot-0.pdb (#3) to map postprocess_masked.mrc (#1)
using 9524 atoms  
average map value = 0.006092, steps = 76  
shifted from previous position = 0.00393  
rotated from previous position = 0.00698 degrees  
atoms outside contour = 8093, contour level = 0.017615  
  
Position of af_pdb_fit-coot-0.pdb (#3) relative to postprocess_masked.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99973368 0.02264708 -0.00443602 -2.18186523  
-0.02230720 0.99759229 0.06566584 -5.47177198  
0.00591248 -0.06554940 0.99783181 10.53212377  
Axis -0.94339859 -0.07440257 -0.32320792  
Axis point 0.00000000 153.06961263 90.00343463  
Rotation angle (degrees) 3.98779116  
Shift along axis -0.93858336  
  
Fit molecule af_pdb_fit-coot-0.pdb (#3) to map postprocess_masked.mrc (#1)
using 9524 atoms  
average map value = 0.006092, steps = 48  
shifted from previous position = 0.00553  
rotated from previous position = 0.00768 degrees  
atoms outside contour = 8096, contour level = 0.017615  
  
Position of af_pdb_fit-coot-0.pdb (#3) relative to postprocess_masked.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99973303 0.02269951 -0.00431262 -2.20140063  
-0.02236760 0.99759091 0.06566633 -5.46157412  
0.00579283 -0.06555234 0.99783232 10.55062953  
Axis -0.94327490 -0.07264377 -0.32396813  
Axis point 0.00000000 153.30955510 89.84122995  
Rotation angle (degrees) 3.98841908  
Shift along axis -0.94479246  
  
Fit molecule af_pdb_fit-coot-0.pdb (#3) to map postprocess_masked.mrc (#1)
using 9524 atoms  
average map value = 0.006093, steps = 48  
shifted from previous position = 0.00463  
rotated from previous position = 0.00426 degrees  
atoms outside contour = 8093, contour level = 0.017615  
  
Position of af_pdb_fit-coot-0.pdb (#3) relative to postprocess_masked.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99973360 0.02266804 -0.00434581 -2.19061753  
-0.02233368 0.99758783 0.06572468 -5.47701238  
0.00582518 -0.06561011 0.99782833 10.55624686  
Axis -0.94347780 -0.07306592 -0.32328164  
Axis point 0.00000000 153.25478362 90.00857354  
Rotation angle (degrees) 3.99109468  
Shift along axis -0.94565888  
  
Fit molecule af_pdb_fit-coot-0.pdb (#3) to map postprocess_masked.mrc (#1)
using 9524 atoms  
average map value = 0.006092, steps = 44  
shifted from previous position = 0.00492  
rotated from previous position = 0.0145 degrees  
atoms outside contour = 8091, contour level = 0.017615  
  
Position of af_pdb_fit-coot-0.pdb (#3) relative to postprocess_masked.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99973454 0.02258115 -0.00457613 -2.15127535  
-0.02223225 0.99759416 0.06566292 -5.48354596  
0.00604786 -0.06554375 0.99783137 10.51435075  
Axis -0.94355935 -0.07640135 -0.32227097  
Axis point 0.00000000 152.81254199 90.20280892  
Rotation angle (degrees) 3.98684980  
Shift along axis -0.93966379  
  
Fit molecule af_pdb_fit-coot-0.pdb (#3) to map postprocess_masked.mrc (#1)
using 9524 atoms  
average map value = 0.00609, steps = 48  
shifted from previous position = 0.0173  
rotated from previous position = 0.00262 degrees  
atoms outside contour = 8095, contour level = 0.017615  
  
Position of af_pdb_fit-coot-0.pdb (#3) relative to postprocess_masked.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99973486 0.02255882 -0.00461598 -2.15839562  
-0.02220736 0.99759486 0.06566068 -5.48562447  
0.00608611 -0.06554076 0.99783133 10.50134227  
Axis -0.94361780 -0.07697082 -0.32196419  
Axis point 0.00000000 152.71099064 90.21977608  
Rotation angle (degrees) 3.98644328  
Shift along axis -0.92212264  
  
Fit molecule af_pdb_fit-coot-0.pdb (#3) to map postprocess_masked.mrc (#1)
using 9524 atoms  
average map value = 0.006092, steps = 60  
shifted from previous position = 0.0173  
rotated from previous position = 0.0203 degrees  
atoms outside contour = 8096, contour level = 0.017615  
  
Position of af_pdb_fit-coot-0.pdb (#3) relative to postprocess_masked.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99973333 0.02268977 -0.00429415 -2.20491328  
-0.02235875 0.99758714 0.06572653 -5.47238830  
0.00577511 -0.06561299 0.99782843 10.56158452  
Axis -0.94342907 -0.07232879 -0.32358946  
Axis point 0.00000000 153.34774639 89.92565086  
Rotation angle (degrees) 3.99144502  
Shift along axis -0.94162689  
  
Fit molecule af_pdb_fit-coot-0.pdb (#3) to map postprocess_masked.mrc (#1)
using 9524 atoms  
average map value = 0.00609, steps = 44  
shifted from previous position = 0.0229  
rotated from previous position = 0.0218 degrees  
atoms outside contour = 8097, contour level = 0.017615  
  
Position of af_pdb_fit-coot-0.pdb (#3) relative to postprocess_masked.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99973374 0.02261273 -0.00459517 -2.17129993  
-0.02226346 0.99760367 0.06550762 -5.45282995  
0.00606547 -0.06538787 0.99784149 10.47603579  
Axis -0.94315607 -0.07681434 -0.32335149  
Axis point 0.00000000 152.69287287 89.90490026  
Rotation angle (degrees) 3.97908209  
Shift along axis -0.92071152  
  
Fit molecule af_pdb_fit-coot-0.pdb (#3) to map postprocess_masked.mrc (#1)
using 9524 atoms  
average map value = 0.006092, steps = 48  
shifted from previous position = 0.0255  
rotated from previous position = 0.00886 degrees  
atoms outside contour = 8094, contour level = 0.017615  
  
Position of af_pdb_fit-coot-0.pdb (#3) relative to postprocess_masked.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99973435 0.02259406 -0.00455306 -2.15395539  
-0.02224669 0.99759437 0.06565482 -5.48012511  
0.00602552 -0.06553608 0.99783201 10.51723924  
Axis -0.94351057 -0.07607998 -0.32248975  
Axis point 0.00000000 152.85967269 90.16175829  
Rotation angle (degrees) 3.98657607  
Shift along axis -0.94249438  
  
Fit molecule af_pdb_fit-coot-0.pdb (#3) to map postprocess_masked.mrc (#1)
using 9524 atoms  
average map value = 0.006092, steps = 44  
shifted from previous position = 0.00617  
rotated from previous position = 0.0117 degrees  
atoms outside contour = 8094, contour level = 0.017615  
  
Position of af_pdb_fit-coot-0.pdb (#3) relative to postprocess_masked.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99973317 0.02268246 -0.00437054 -2.19420043  
-0.02234695 0.99759320 0.06563851 -5.46060720  
0.00584886 -0.06552333 0.99783390 10.53710270  
Axis -0.94325618 -0.07349329 -0.32383100  
Axis point 0.00000000 153.19201639 89.86315043  
Rotation angle (degrees) 3.98676811  
Shift along axis -0.94122942  
  
Fit molecule af_pdb_fit-coot-0.pdb (#3) to map postprocess_masked.mrc (#1)
using 9524 atoms  
average map value = 0.006092, steps = 48  
shifted from previous position = 0.0119  
rotated from previous position = 0.0246 degrees  
atoms outside contour = 8092, contour level = 0.017615  
  
Position of af_pdb_fit-coot-0.pdb (#3) relative to postprocess_masked.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99973592 0.02248868 -0.00472688 -2.12197480  
-0.02212940 0.99758904 0.06577540 -5.51640782  
0.00619468 -0.06565342 0.99782326 10.51003004  
Axis -0.94400332 -0.07844540 -0.32047472  
Axis point 0.00000000 152.52974473 90.57013892  
Rotation angle (degrees) 3.99172958  
Shift along axis -0.93231092  
  
Fit molecule af_pdb_fit-coot-0.pdb (#3) to map postprocess_masked.mrc (#1)
using 9524 atoms  
average map value = 0.00609, steps = 44  
shifted from previous position = 0.0159  
rotated from previous position = 0.00886 degrees  
atoms outside contour = 8096, contour level = 0.017615  
  
Position of af_pdb_fit-coot-0.pdb (#3) relative to postprocess_masked.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99973492 0.02254583 -0.00466607 -2.15095722  
-0.02219121 0.99759620 0.06564574 -5.48683784  
0.00613489 -0.06552479 0.99783208 10.49116824  
Axis -0.94360518 -0.07769921 -0.32182618  
Axis point 0.00000000 152.60328418 90.25987373  
Rotation angle (degrees) 3.98555555  
Shift along axis -0.92035526  
  
Fit molecule af_pdb_fit-coot-0.pdb (#3) to map postprocess_masked.mrc (#1)
using 9524 atoms  
average map value = 0.006092, steps = 64  
shifted from previous position = 0.0158  
rotated from previous position = 0.0116 degrees  
atoms outside contour = 8094, contour level = 0.017615  
  
Position of af_pdb_fit-coot-0.pdb (#3) relative to postprocess_masked.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99973371 0.02263595 -0.00448556 -2.17390497  
-0.02229297 0.99759403 0.06564424 -5.47143349  
0.00596069 -0.06552676 0.99783301 10.52175846  
Axis -0.94336960 -0.07512844 -0.32312461  
Axis point 0.00000000 152.96924048 90.02985591  
Rotation angle (degrees) 3.98656704  
Shift along axis -0.93798303  
  
Fit molecule af_pdb_fit-coot-0.pdb (#3) to map postprocess_masked.mrc (#1)
using 9524 atoms  
average map value = 0.00609, steps = 60  
shifted from previous position = 0.0148  
rotated from previous position = 0.0081 degrees  
atoms outside contour = 8097, contour level = 0.017615  
  
Position of af_pdb_fit-coot-0.pdb (#3) relative to postprocess_masked.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99973463 0.02257036 -0.00461064 -2.16110781  
-0.02221929 0.99759527 0.06565040 -5.48300306  
0.00608130 -0.06553054 0.99783203 10.49973747  
Axis -0.94355563 -0.07690475 -0.32216212  
Axis point 0.00000000 152.71091522 90.19173473  
Rotation angle (degrees) 3.98608225  
Shift along axis -0.92182327  
  
Fit molecule af_pdb_fit-coot-0.pdb (#3) to map postprocess_masked.mrc (#1)
using 9524 atoms  
average map value = 0.00609, steps = 48  
shifted from previous position = 0.00371  
rotated from previous position = 0.00482 degrees  
atoms outside contour = 8098, contour level = 0.017615  
  
Position of af_pdb_fit-coot-0.pdb (#3) relative to postprocess_masked.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99973509 0.02253414 -0.00468654 -2.14864722  
-0.02217818 0.99759625 0.06564940 -5.48979056  
0.00615463 -0.06552807 0.99783175 10.48796889  
Axis -0.94364339 -0.07798745 -0.32164438  
Axis point 0.00000000 152.56063156 90.29903498  
Rotation angle (degrees) 3.98560505  
Shift along axis -0.91770470  
  
Fit molecule af_pdb_fit-coot-0.pdb (#3) to map postprocess_masked.mrc (#1)
using 9524 atoms  
average map value = 0.006092, steps = 72  
shifted from previous position = 0.0196  
rotated from previous position = 0.0197 degrees  
atoms outside contour = 8093, contour level = 0.017615  
  
Position of af_pdb_fit-coot-0.pdb (#3) relative to postprocess_masked.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99973374 0.02265621 -0.00437472 -2.19094658  
-0.02231995 0.99758780 0.06572980 -5.47910968  
0.00585336 -0.06561466 0.99782787 10.55080002  
Axis -0.94351305 -0.07347344 -0.32308634  
Axis point 0.00000000 153.19511372 90.02984257  
Rotation angle (degrees) 3.99123935  
Shift along axis -0.93906368  
  
Fit molecule af_pdb_fit-coot-0.pdb (#3) to map postprocess_masked.mrc (#1)
using 9524 atoms  
average map value = 0.006089, steps = 48  
shifted from previous position = 0.0268  
rotated from previous position = 0.0304 degrees  
atoms outside contour = 8092, contour level = 0.017615  
  
Position of af_pdb_fit-coot-0.pdb (#3) relative to postprocess_masked.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99973501 0.02250728 -0.00483102 -2.12826364  
-0.02214282 0.99760654 0.06550491 -5.47209513  
0.00629379 -0.06538058 0.99784055 10.44015312  
Axis -0.94339624 -0.08018540 -0.32182890  
Axis point 0.00000000 152.20708352 90.21668007  
Rotation angle (degrees) 3.97776335  
Shift along axis -0.91336492  
  
Fit molecule af_pdb_fit-coot-0.pdb (#3) to map postprocess_masked.mrc (#1)
using 9524 atoms  
average map value = 0.00609, steps = 48  
shifted from previous position = 0.0156  
rotated from previous position = 0.0279 degrees  
atoms outside contour = 8092, contour level = 0.017615  
  
Position of af_pdb_fit-coot-0.pdb (#3) relative to postprocess_masked.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99973424 0.02262670 -0.00441345 -2.19427466  
-0.02228800 0.99758890 0.06572397 -5.48257605  
0.00588992 -0.06560814 0.99782808 10.53976703  
Axis -0.94360023 -0.07402804 -0.32270492  
Axis point 0.00000000 153.11626081 90.07703298  
Rotation angle (degrees) 3.99049420  
Shift along axis -0.92485227  
  
Fit molecule af_pdb_fit-coot-0.pdb (#3) to map postprocess_masked.mrc (#1)
using 9524 atoms  
average map value = 0.00609, steps = 56  
shifted from previous position = 0.00341  
rotated from previous position = 0.00904 degrees  
atoms outside contour = 8096, contour level = 0.017615  
  
Position of af_pdb_fit-coot-0.pdb (#3) relative to postprocess_masked.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99973429 0.02259768 -0.00455005 -2.17211606  
-0.02225052 0.99759456 0.06565072 -5.47804952  
0.00602266 -0.06553204 0.99783229 10.50823780  
Axis -0.94349088 -0.07604092 -0.32255657  
Axis point 0.00000000 152.82597207 90.11162521  
Rotation angle (degrees) 3.98641162  
Shift along axis -0.92357348  
  
Fit molecule af_pdb_fit-coot-0.pdb (#3) to map postprocess_masked.mrc (#1)
using 9524 atoms  
average map value = 0.006092, steps = 48  
shifted from previous position = 0.018  
rotated from previous position = 0.0125 degrees  
atoms outside contour = 8468, contour level = 0.026337  
  
Position of af_pdb_fit-coot-0.pdb (#3) relative to postprocess_masked.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99973368 0.02266250 -0.00435641 -2.19149740  
-0.02232744 0.99758778 0.06572745 -5.47962363  
0.00583545 -0.06561268 0.99782810 10.55376984  
Axis -0.94349749 -0.07321446 -0.32319056  
Axis point 0.00000000 153.22887431 90.04174111  
Rotation angle (degrees) 3.99117357  
Shift along axis -0.94201881  
  

> hide #1 target m

> show #!1 models

> show #1 target m

> volume selMaps projectionMode 2d-xyz

> volume selMaps appearance CT_Skin

> volume selMaps appearance CT_Skin

> view #1 clip false

> open /Users/maf2080/Documents/181/PP_59/af_fit.pdb

af_fit.pdb title:  
PDB: AFTMEM16 reconstituted In nanodiscs In the presence of CA2+ [more
info...]  
  
Chain information for af_fit.pdb #4  
---  
Chain | Description  
A B | plasma membrane channel protein (AQY1), putative  
  
Non-standard residues in af_fit.pdb #4  
---  
CA — calcium ion  
  

> hide #!3 models

Segmenting postprocess_masked.mrc, density threshold 0.010489  
Showing postprocess_masked.seg - 0 regions, 0 surfaces  
Only showing 1000 of 2722 regions.  
Showing 1000 of 2722 region surfaces  
6599 watershed regions, grouped to 2722 regions  
Segmenting postprocess_masked.mrc, density threshold 0.010489  
Showing postprocess_masked.seg - 0 regions, 0 surfaces  
Only showing 1000 of 2717 regions.  
Showing 1000 of 2717 region surfaces  
6599 watershed regions, grouped to 2717 regions  

> hide #!2 models

> show #!2 models

> molmap #4 0.000000 sigmaFactor 0.187 gridSpacing 0.000000 replace false

/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/molmap.py:214: RuntimeWarning: divide by zero
encountered in double_scalars  
for a in (2,1,0)]  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/segger/fit_dialog.py", line 3529, in GroupRegionsByMols  
mv = self._run_command ( cmd )  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/segger/fit_dialog.py", line 1629, in _run_command  
result = run ( self.session, command )  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2655, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/molmap.py", line 130, in molmap  
display_threshold, model_id, replace, show_dialog, name, session)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/molmap.py", line 145, in make_molecule_map  
transforms, name)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/molmap.py", line 193, in molecule_grid_data  
grid = bounding_grid(xyz, step, pad, transforms)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/molmap.py", line 214, in bounding_grid  
for a in (2,1,0)]  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/molmap.py", line 214, in <listcomp>  
for a in (2,1,0)]  
OverflowError: cannot convert float infinity to integer  
  
OverflowError: cannot convert float infinity to integer  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/molmap.py", line 214, in  
for a in (2,1,0)]  
  
See log for complete Python traceback.  
  

> molmap #4 0.000000 sigmaFactor 0.187 gridSpacing 0.000000 replace false

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/segger/fit_dialog.py", line 3529, in GroupRegionsByMols  
mv = self._run_command ( cmd )  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/segger/fit_dialog.py", line 1629, in _run_command  
result = run ( self.session, command )  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2655, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/molmap.py", line 130, in molmap  
display_threshold, model_id, replace, show_dialog, name, session)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/molmap.py", line 145, in make_molecule_map  
transforms, name)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/molmap.py", line 193, in molecule_grid_data  
grid = bounding_grid(xyz, step, pad, transforms)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/molmap.py", line 214, in bounding_grid  
for a in (2,1,0)]  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/molmap.py", line 214, in <listcomp>  
for a in (2,1,0)]  
OverflowError: cannot convert float infinity to integer  
  
OverflowError: cannot convert float infinity to integer  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/molmap.py", line 214, in  
for a in (2,1,0)]  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-10.36.25
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.

[Tom Goddard]

Fixed.

User tried 0 resolution and 0 grid spacing in molmap. Not sure what they were thinking. Require those to be positive now.