[Chimera-users] Questions in ChimeraX comparing with Chimera

Long Gui Long.Gui at UTSouthwestern.edu
Wed Apr 27 11:25:58 PDT 2022

Dear Chimera users,

I have been recently transferring to ChimeraX from the conventional Chimera and I am currently struggling with two features existing in Chimera but not in ChimeraX.

  1.  How could I combine two or several different ChimeraX files? I have been doing in Chimera as I was opening new chimera files by "Files...Open...", this is a window pop-up as the following and if I click "No", the new Chimera will be added to the cold Chimera as the old one was not closed. However, when I performed the similar operation in ChimeraX, there is no such window and the new ChimeraX would REPLACE the old one. I wonder if there is a way (probably using command to open? but I did not find the correct open options.) to open the new ChimeraX without closing the old one?


  1.  I am also working with tomogram slices and cellular segmentation. Previously, in Chimera I can set this Transparency value to 0 and the Plane of the tomogram will be totally opaque. Now in ChimeraX I have used the command "transparency #2 0" (#2 is the tomogram files) but it still look quite different from my previous images in Chimera. Is there a way to set it up in ChimeraX so it could look similar as before?


Thanks again and I am very grateful if any advice or help could be provided.

Long Gui, Ph.D.

Postdoc Researcher, Nicastro Lab
University of Texas Southwestern Medical Center

Long.Gui at utsouthwestern.edu
Tel: (214)-645-1561


UT Southwestern

Medical Center

The future of medicine, today.
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