Thanks Elaine Best Sasha -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Monday, September 29, 2025 19:10 To: Alexandra Zahradnikova Cc: ChimeraX Users Help Subject: Re: [chimerax-users] Orient many tetramers Hi Sasha, When you just rotate the whole view, the model is not transformed, only the point of view. To actually transform the model position, you'd have move it (or them, if multiple) using some model-specific mouse mode, not the usual mousemodes that move the whole view. At least according to my tests, if you move all the models in sync, it will always move the whole view instead of transforming the individual models. Soe what you could do is (1) open the structure(s) of interest and then open some other structure (doesn't matter what, you will ignore the latter, it's just there as an anchor (2) DO NOT move the scene as a whole, i.e. absolutely no rotation or translation after you open the models (3) use a model-specific mousemode to rotate only the model(s) of interest and leave the other unmoved - for example, in the Right Mouse tab of icons across the top, choose "rotate selected models," (icon looks like selected water molecule with curved arrows around it), Ctrl-click to select some part of your model of interest (if your tetramer is 4 separate models, you would have to select at least 1 atom in each), then use right mouse to rotate it/them. See Right Mouse help: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html> (4) then save your model(s) "relative" to the other model that you didn't move I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 29, 2025, at 4:46 AM, Alexandra Zahradnikova via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi I have a set of tetramers created by AlphaFold. They are randomly oriented. In order to measure their pore size in a third-party program, I need to orient them with their z axis pointing in the z direction. I can orient them with respect to the screen, but I don't know how to save this view orientation (i.e. so that the z axis in the pdb file goes vertically). Is there any way how to do it? The switch in the "save" command specifying whether to use transformed or untransformed coordinates does not make any difference, and the file is always saved in the original orientation. Best Sasha
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