id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
5364	ChimeraX Molecular Dynamics Viewer	finnegan.73@…	Eric Pettersen	"{{{
Hi, my name is Tyler Finnegan and I'm a graduate student in the Badjic lab at Ohio State. I recently was trying to visualize an MD trajectory using your Molecular Dynamics Viewer (MDV). What I did was create a pdb file of the trajectory using VMD and upon trying to load this file into the MDV I received the following error:


IndexError: list index out of range

File ""C:\My\path\to\chimeral\UCSF\ChimeraX\1.2\site-packages\com\kdiller\dynamics\viewer\gui.py"", line 227, in openFile
self.atomStruct.atoms.coords = self.atomLocation[0]

See log for complete Python traceback.


I'm not sure if this error was with the python module, gui.py, or whether I need to format my input PDB differently. Currently it is formatted with AMBER TERs in-between molecules and ENDs between frames--I believe this is the issue. I've attached this PDB for your reference. When it was loaded in manually with the command line,


open 'D:/My/Path/To/File/CAR_traj_testing.pdb' coordset true

It gave an error in the log box which seemed to have issue with the 'END' in the PDB file. Is there another word I should use as a delimiter between frames in my pdb?



Thanks in advance for your help and I look forward to hearing back from you!


Best,

Tyler Finnegan



}}}

[attachment:""CAR_traj_testing.pdb""]
"	defect	closed	normal		MD/Ensemble Analysis		duplicate						all	ChimeraX