Hi Eric Sorry, I have sent the unfinished mail by mistake, but you got the problem perfectly. Since I need to analyze e.g. RMSD/RMSF or H-bonds per chain, I need to have different names for the four chains. I can do it in old Chimera, because it requires a combination of a TPR and an XTC file, which will produce the correct chain names. However ChimeraX reads only the GRO file but not the TPR file, and the GRO file does not seem to have this information. I attach a sample .gro file with the following .xtc trajectory. In the .gro file, everything including protein, ions, lipids, and water is one "principal chain" without a name. I have also added the .tpr file so you can compare the result in ChimeraX and Chimera. Best Sasha -----Original Message----- From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] Sent: Tuesday, April 22, 2025 7:12 PM To: Alexandra Zahradnikova Cc: ChimeraX Users Help Subject: Re: [chimerax-users] Labeling chains in MD simulation trajectories of a multimer Hi Alexandra, I don't actually have access to any .gro files that have multiple chains. If you could send me an example I might be able to improve ChimeraX's behavior in that situation. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Apr 22, 2025, at 7:23 AM, Alexandra Zahradnikova via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi All, I am interested in MD simulations of homomultimeric ion channels, which I do in GROMACS. I would like to analyze my output files with ChimeraX but I run into the following problem: The .gro output of the simulation consists of a single chain named /? in ChimeraX. When I open the file in old Chimera, it shows every chain of the original protein separately but with the same name ()
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