MD Viewer: no ligand

[jeandidier.marechal@…]

The following bug report has been submitted:
Platform:        Darwin-18.6.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-07-16)
Description
Hi guys,

we are testing several things on ChimeraX. We have generated a single pdb file for a movie from chimera and loaded it in chimeraX. There is a diffusion of ligand happening but in chimeraX we can see nothing else than the protein...ligand is missing. Apparently there is some problem with the way chimeraX parses the pdb. 
Thank you

Log:
UCSF ChimeraX version: 0.91 (2019-07-16)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show "Molecular Dynamics Viewer"

Please register the custom scheme 'kmd' via
QWebEngineUrlScheme::registerScheme() before installing the custom scheme
handler.  

Chain information for structure #1  
---  
Chain | Description  
B | No description available  
  

> show

> show ligand




OpenGL version: 4.1 INTEL-12.9.22
OpenGL renderer: Intel HD Graphics 4000 OpenGL Engine
OpenGL vendor: Intel Inc.
File attachment: save_test.pdb

save_test.pdb​

[jeandidier.marechal@…]

Added by email2trac

[pett]

Hi JD,

This seems to be a limitation of the MD viewer on the toolshed (which wasn't written by us). If you open the file using ChimeraX's "built in" MD processing, namely: open /path/to/save_test.pdb coordset true, then the ligand is shown (and a playback slider appears). FYI, if you use "browse" instead of the filename in the command, then a file-system browser will be shown for you to choose the file with.

--Eric