id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2934 Adding coord sets tony.schaefer@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.17763 ChimeraX Version: 0.92 (2020-03-03) Description more stuff on #2926 I've played around with it some more, and it looks like the problem happens when one or more atoms on the molecule have been deleted. My tool might delete some atoms, but it does replace them before trying to add coordsets. Log: > cd ""C:\Users\Tony Schaefer/Desktop"" Current working directory is: C:\Users\Tony Schaefer\Desktop UCSF ChimeraX version: 0.92 (2020-03-03) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Successfully installed 'ChimAARON-0.1-py3-none-any.whl' Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing c:\users\tony schaefer\appdata\local\ucsf\chimerax\cache\0.92\installers\chimaaron-0.1-py3-none- any.whl Requirement already satisfied, skipping upgrade: numpy in d:\chimerax\bin\lib\site-packages (from ChimAARON==0.1) (1.17.4+mkl) Requirement already satisfied, skipping upgrade: scipy in d:\chimerax\bin\lib\site-packages (from ChimAARON==0.1) (1.4.1) Requirement already satisfied, skipping upgrade: ChimeraX-Core>=0.1 in d:\chimerax\bin\lib\site-packages (from ChimAARON==0.1) (0.92) Installing collected packages: ChimAARON Attempting uninstall: ChimAARON Found existing installation: ChimAARON 0.1 Uninstalling ChimAARON-0.1: Successfully uninstalled ChimAARON-0.1 Successfully installed ChimAARON-0.1 Lock 2730295765320 acquired on C:\Users\Tony Schaefer\AppData\Local\UCSF\ChimeraX\Cache\0.92\toolshed\bundle_info.cache.lock Lock 2730295765320 released on C:\Users\Tony Schaefer\AppData\Local\UCSF\ChimeraX\Cache\0.92\toolshed\bundle_info.cache.lock > open ""C:\Users\Tony Schaefer\Desktop\freq.out"" Summary of feedback from opening C:\Users\Tony Schaefer\Desktop\freq.out --- notes | no chix atom O 0.00000000 -0.00000000 0.67304000 0 1 no chix atom C -0.00000000 -0.00000000 -0.52664300 0 2 no chix atom H 0.00000000 0.94502100 -1.13098300 0 3 no chix atom H 0.00000000 -0.94502100 -1.13098300 0 4 Opened C:\Users\Tony Schaefer\Desktop\freq.out as a out file > toolshed show ""Structure Modification"" > select /a:1@H2 1 atom, 1 model selected no chix atom C -0.00000000 -1.30280961 -1.36080988 0 -1 no chix atom H 0.21803884 -1.07908437 -2.42655254 0 -1.2 no chix atom H -0.99312523 -1.79493271 -1.29082032 0 -1.3 no chix atom H 0.77509507 -1.99630487 -0.97133357 0 -1.4 > toolshed show ""Managed Models"" chix_atom deleted H 0.00000000 -0.94502100 -1.13098300 0 4 > toolshed show ""Visualize Normal Modes"" D:\ChimeraX\bin\lib\site-packages\chimerax\core\graphics\view.py:866: RuntimeWarning: invalid value encountered in double_scalars return (d-r, d+r) D:\ChimeraX\bin\lib\site-packages\chimerax\core\geometry\vector.py:57: RuntimeWarning: invalid value encountered in double_scalars return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] D:\ChimeraX\bin\lib\site-packages\chimerax\core\geometry\matrix.py:166: RuntimeWarning: invalid value encountered in double_scalars \+ m1[r][2] * m2[2][c]) D:\ChimeraX\bin\lib\site-packages\chimerax\core\graphics\view.py:744: RuntimeWarning: invalid value encountered in less_equal if vw is None or vw >= b.width(): > close > open 6t20 format mmCIF fromDatabase pdb 6t20 title: Cryo-EM structure of phalloidin-stabilized F-actin (aged) [more info...] Chain information for 6t20 #1 --- Chain | Description A B C D E | Actin, α skeletal muscle F G H I J | phalloidin Non-standard residues in 6t20 #1 --- ADP — adenosine-5'-diphosphate EEP — (2S,4R)-2-amino-4,5-dihydroxy-4-methylpentanoic acid MG — magnesium ion > select /F:3@CB 1 atom, 1 model selected > toolshed show ""Structure Modification"" no chix atom C 144.89718478 155.50216630 203.40393904 0 14529 no chix atom C 144.28987881 156.55183295 204.10115029 0 14529.2 no chix atom C 145.51374191 154.46082570 204.10550242 0 14529.3 no chix atom C 144.91568709 155.51881838 206.20148830 0 14529.4 no chix atom C 145.52299306 154.46915174 205.50427705 0 14529.5 no chix atom C 144.29912996 156.56015899 205.49992491 0 14529.6 no chix atom H 143.81063218 157.36126151 203.55582936 0 14529.7 no chix atom H 143.82707420 157.37605933 206.04186295 0 14529.8 no chix atom H 144.92287796 155.52529016 207.28874726 0 14529.9 no chix atom H 146.00223970 153.65972317 206.04959798 0 14529.10 no chix atom H 145.98579768 153.64492535 203.56356439 0 14529.11 > close #1 > open ""C:\Users\Tony Schaefer\Desktop\freq.out"" Summary of feedback from opening C:\Users\Tony Schaefer\Desktop\freq.out --- notes | no chix atom O 0.00000000 -0.00000000 0.67304000 0 1 no chix atom C -0.00000000 -0.00000000 -0.52664300 0 2 no chix atom H 0.00000000 0.94502100 -1.13098300 0 3 no chix atom H 0.00000000 -0.94502100 -1.13098300 0 4 Opened C:\Users\Tony Schaefer\Desktop\freq.out as a out file > select /a:1@H2 1 atom, 1 model selected no chix atom C -0.00000000 -1.30280961 -1.36080988 0 -1 no chix atom C 1.21051022 -1.86944665 -1.77349815 0 -1.2 no chix atom C -1.21051022 -1.91955514 -1.69399765 0 -1.3 no chix atom C -0.00000000 -3.66957475 -2.85256195 0 -1.4 no chix atom C -1.21051022 -3.10293771 -2.43987368 0 -1.5 no chix atom C 1.21051022 -3.05282922 -2.51937418 0 -1.6 no chix atom H 2.15143345 -1.39005411 -1.51451335 0 -1.7 no chix atom H 2.15143345 -3.49327272 -2.84015425 0 -1.8 no chix atom H -0.00000000 -4.58941078 -3.43232682 0 -1.9 no chix atom H -2.15143345 -3.58233025 -2.69885849 0 -1.10 no chix atom H -2.15143345 -1.47911164 -1.37321758 0 -1.11 > toolshed show ""Managed Models"" > preset chimaaron ""index labels"" Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset chimaaron ball-stick-endcap Preset implemented in Python; no expansion to individual ChimeraX commands available. chix_atom deleted H 0.00000000 -0.94502100 -1.13098300 0 4 > preset chimaaron ""index labels"" Preset implemented in Python; no expansion to individual ChimeraX commands available. > toolshed show ""Visualize Normal Modes"" D:\ChimeraX\bin\lib\site-packages\chimerax\core\geometry\bounds.py:53: RuntimeWarning: overflow encountered in multiply r = 0.5*sqrt((size*size).sum()) > close #1 > open ""C:\Users\Tony Schaefer\Desktop\freq.out"" Summary of feedback from opening C:\Users\Tony Schaefer\Desktop\freq.out --- notes | no chix atom O 0.00000000 -0.00000000 0.67304000 0 1 no chix atom C -0.00000000 -0.00000000 -0.52664300 0 2 no chix atom H 0.00000000 0.94502100 -1.13098300 0 3 no chix atom H 0.00000000 -0.94502100 -1.13098300 0 4 Opened C:\Users\Tony Schaefer\Desktop\freq.out as a out file OpenGL version: 3.3.0 NVIDIA 441.87 OpenGL renderer: GeForce RTX 2070/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal MD/Ensemble Analysis fixed Tom Goddard all ChimeraX