id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2926 Adding coord sets tony.schaefer@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.17763 ChimeraX Version: 0.92 (2020-03-03) Description I'm not sure if this is a bug or if I need to add something to my code. I've had issues adding coordsets to molecules. When I open 'freq.out', I'm adding coordsets to it using `mdl.add_coordsets`. I'm doing the same thing in my tool to reset the coordinate sets (again using `mdl.add_coordsets`). Each time I set the coordsets, I print the coordset array to the reply log. It looks the same both times. The issue is that the second time I add the coordsets, it doesn't seem to work. I can open the shell and grab the coordsets (using `mdl.coordsets(1).xyzs`). However, the atom coordinates do not match the coordset (`mdl.atoms[i].coord`). The molecule also appears very different. The only thing I've gotten to work to overwrite coordsets with my tool is ``` mdl.remove_coordsets() for i, coordset in enumerate(coordsets): mdl.add_coordset(i+1, coordsets) mdl.active_coordset_id = i + 1 for atom, coord in zip(mdl.atoms, coordset): atom.coord = coord ``` where mdl is the model and coordsets in the coordset array (equal to the one I used when opening the molecule). Like I said, I've tried using `mdl.add_coordsets` here. I've also tried just looping over the coordset array and doing `mdl.add_coordset`. I've tried both of these with and without mdl.remove_coordsets(). Without the `for atom, coord` loop, the coordinate sets don't do what I expect. The atom coordinates seem to all get set to zero, but never updated to what's in coordsets. I'm not sure why I wouldn't be able to just use mdl.add_coordsets(x, replace=True). I've attached a session with two models: a freshly-opened 'freq.out', and a 'freq.out' where I've tried to overwrite the coordsets with mdl.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: ChimeraX-Core>=0.1 in d:\chimerax\bin\lib\site-packages (from ChimAARON==0.1) (0.92) 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: numpy in d:\chimerax\bin\lib\site-packages (from ChimAARON==0.1) (1.17.4+mkl) 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 2950636499272 acquired on C:\Users\Tony Schaefer\AppData\Local\UCSF\ChimeraX\Cache\0.92\toolshed\bundle_info.cache.lock Lock 2950636499272 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 | there are 5 coordsets 0 float64 [[ 0. 0. 0.68769] [ 0. 0. -0.53966] [ 0. 0.93947 -1.1318 ] [ 0. -0.93947 -1.1318 ]] 1 float64 [[ 0. -0. 0.672927] [-0. 0. -0.532651] [ 0. 0.945975 -1.127923] [ 0. -0.945975 -1.127923]] 2 float64 [[ 0. 0. 0.670659] [-0. 0. -0.528855] [ 0. 0.947362 -1.128687] [ 0. -0.947362 -1.128687]] 3 float64 [[ 0. -0. 0.671777] [-0. -0. -0.527821] [ 0. 0.946536 -1.129763] [ 0. -0.946536 -1.129763]] 4 float64 [[-0. 0. 0.673041] [ 0. 0. -0.526642] [-0. 0.945072 -1.130984] [-0. -0.945072 -1.130984]] Opened C:\Users\Tony Schaefer\Desktop\freq.out as a out file > toolshed show ""Managed Models"" there are 5 coordsets 0 float64 [[ 0. 0. 0.68769] [ 0. 0. -0.53966] [ 0. 0.93947 -1.1318 ] [ 0. -0.93947 -1.1318 ]] 1 float64 [[ 0. -0. 0.672927] [-0. 0. -0.532651] [ 0. 0.945975 -1.127923] [ 0. -0.945975 -1.127923]] 2 float64 [[ 0. 0. 0.670659] [-0. 0. -0.528855] [ 0. 0.947362 -1.128687] [ 0. -0.947362 -1.128687]] 3 float64 [[ 0. -0. 0.671777] [-0. -0. -0.527821] [ 0. 0.946536 -1.129763] [ 0. -0.946536 -1.129763]] 4 float64 [[-0. 0. 0.673041] [ 0. 0. -0.526642] [-0. 0.945072 -1.130984] [-0. -0.945072 -1.130984]] > toolshed show Shell OpenGL version: 3.3.0 NVIDIA 441.87 OpenGL renderer: GeForce RTX 2070/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation File attachment: coordsets.cxs }}} [attachment:""coordsets.cxs""] " defect closed normal MD/Ensemble Analysis not a bug Eric Pettersen all ChimeraX