id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
2951	Adding coord sets	tony.schaefer@…	Eric Pettersen	"{{{
The following bug report has been submitted:
Platform:        Windows-10-10.0.17763
ChimeraX Version: 0.93 (2020-03-12)
Description
follow up to #2934 (I don't know how to post comments here)

My issues do seem to be related to the issue with the position of atoms in the coordset array. Understanding where this comes from is helpful. My tools that touch coordinate sets are aimed at systems much smaller than classical MD trajectories, so I don't really notice any performance hit from my ""for atom, coord in zip(model.atoms, coordset)"" workaround. 

I did take a look at the code for the add_coordsets function, and it looks like it checks to see if one of the coordset's dimensions matches the model's num_atoms. Given that the number of atoms might not be the same as the coordset size, could that be changed to check against the corresponding current coordset dimension?

Log:
> cd ""C:\Users\Tony Schaefer/Desktop""

Current working directory is: C:\Users\Tony Schaefer\Desktop  
UCSF ChimeraX version: 0.93 (2020-03-12)  
© 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\0.93\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: ChimeraX-Core>=0.1 in
d:\chimerax\bin\lib\site-packages (from ChimAARON==0.1) (0.93)  
Requirement already satisfied, skipping upgrade: scipy in
d:\chimerax\bin\lib\site-packages (from ChimAARON==0.1) (1.4.1)  
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 2092432641544 acquired on C:\Users\Tony
Schaefer\AppData\Local\UCSF\ChimeraX\Cache\0.93\toolshed\bundle_info.cache.lock  
Lock 2092432641544 released on C:\Users\Tony
Schaefer\AppData\Local\UCSF\ChimeraX\Cache\0.93\toolshed\bundle_info.cache.lock  
  

> open ""C:\Users\Tony Schaefer\Desktop\freq.out""

Opened C:\Users\Tony Schaefer\Desktop\freq.out as a out file  

> select /a:1@H1

1 atom, 1 model selected  

> toolshed show ""Structure Modification""

> toolshed show ""Managed Models""

0  
1  
8  
9  

> toolshed show Shell




OpenGL version: 3.3.0 NVIDIA 441.87
OpenGL renderer: GeForce RTX 2070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: To Be Filled By O.E.M.
Model: To Be Filled By O.E.M.
OS: Microsoft Windows 10 Education (Build 17763)
Memory: 17,107,648,512
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 2700X Eight-Core Processor         ""

}}}
"	defect	closed	normal		MD/Ensemble Analysis		duplicate						all	ChimeraX