Hi Tom Many thanks! Actually, since my channels have a C4 symmetry, they are correctly aligned with respect to the z axis even if the numbering of chains is random (I have tried 5 variants with different chain sequence). This simplifies things a lot. Best Sasha -----Original Message----- From: Tom Goddard [mailto:goddard@sonic.net] Sent: Monday, September 29, 2025 20:39 To: Alexandra Zahradnikova Cc: ChimeraX Users Help Subject: Re: [chimerax-users] Orient many tetramers Hi Sasha, Here's another idea about how to align a tetramer with symmetry axis along z and save it. The idea is to create 4 atoms in the aligned arrangement using the ChimeraX sym command, and then align the tetramer model to those 4 atoms. Here's an example using PDB 9r3i which is a tetramer with D2 symmetry. open 9r3i del ~/A:94@CA sym #1 D2 hide ribbon ; show atoms ; style sphere ; view orient open 9r3i color bychain align #3/A,B,D,C:94@CA to #2.1,3,2,4 save aligned_9r3i.cif model #3 I chose the CA atom of residue 94 chain A arbitrarily just picking one on the periphery of the tetramer. The align command is a bit tricky. I had to put the chains A,B,C,D and symmetric 4 atoms I made in the same clockwise order. Mousing over the 4 chains of 9r3i to see the popup window with the chain names shows they are in order A,B,D,C as I go clockwise, and my 4 atoms placed with D2 symmetry are in clockwise order #2.1, #2.3, #2.2, #2.4. So I used these orders in the align command. If you make tetramer predictions with AlphaFold, the 4 chains will ikely end up in different orders for different predictions. If you are comparing tetramers I would align one along z with the above procedure and then align each of the others to this one by choosing 4 atoms in each and using the align command. Tom PDB 9r3i original and z aligned.