Hey, (I sent the structure in the second e-mail as a zip file, but apparently, the Harvard mail system blocked it)
I also understood what was going on. The structure [2] is a very raw, early stage of our simulation, full of clashes (and the file has no CONECT in it). When I `set connect_mode, 1` [1] ( = CONECT records), I don’t see any bonds (which makes sense, as there is no CONECT in my PDB file) and PyMOL does not calculate bonds and loads the structure immediately! Thus, the fix is to `set connect_mode, 1` and use explicit CONECT in my file or load file without CONECT and use Surface representation to get insights into what’s going on (and calculate RMSD, etc.). Thanks, the issue is solved. Magnus [1] https://pymolwiki.org/index.php/Connect_mode [2] https://www.dropbox.com/t/kz4LISig75hlwCMj [sc 2024-10-31 at 12.58.22 2.jpg.jpeg]
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