id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15784 Unresponsive on Ubuntu 20.04 Dr. Michael F. Schmid Greg Couch "{{{ > Begin forwarded message: > > From: ""Dr. Michael F. Schmid"" > Subject: Re: showing all atoms > Date: August 19, 2024 at 11:31:49 AM PDT > To: Eric Pettersen > Cc: Tom Goddard > > Updating ChimeraX to be sure I have current functionality, I have run into the following. > I updated ubuntu on my workstation to 20.04. It ran a “partial upgrade”. > Downloaded chimeraX 1.8 for 20.04 > Sudo installed. > Running chimerax, I get on the command line > NOTE: available bundle cache has not been initialized yet > And an unresponsive chimerax window, with open 7k3v, the last command I previously ran before the upgrade, on the command line, and Welcome to ChimeraX under the command line. > Mike > > From: Tom Goddard > Date: Friday, August 16, 2024 at 9:40 PM > To: Dr. Michael F. Schmid > Cc: Eric Pettersen > Subject: Re: showing all atoms > > Hi Mike, > > ChimeraX handles alternate atom positions differently. I think the Log will say there are alternate locations and have a link to show the Altloc explorer panel to display them. Eric wrote this and can advise further. I am on vacation until Wednesday. > > Tom > > > On Aug 16, 2024, at 2:17 PM, Dr. Michael F. Schmid wrote: > >  > Hi- > In Chimera, if I open (fetch by PDB or by mmcif) 7k3v, and show atoms, I see all alternate conformations of the side chain of, ex. GLU 162 (of which there are 3). In ChimeraX, if I issue the command line open 7k3v, I only see one of the conformations. Waddupwidat? > Mike }}} " defect closed normal Platform limitation chimerax-programmers all ChimeraX