Dear all,

I have a molecule in PyMol which I want to open in ChimeraX. But after exporting the molecule as .pdb, some structural information seems to be lost  - regions that in the PyMol session file are embedded into helices are now loops (this regards to several residues only). If I open the .pdb in PyMol, it looks the same as in chimeraX. I have no idea what I keep doing wrong, any hints? The first 14 residues of the original protein (from PDB, corresponding to Histag) were removed with a custom PyMol script which changed residues enumeration so that it properly starts with 1 - that is why the molecule from PyMol is needed. I would be grateful for the help.

best,

maciek
For anyone who might be interested:
1 - open original .pdb in text editor
2 - remove all atoms (lines starting with ATOMS) corresponding to unwanted residues, save file
3 - go to https://wenmr.science.uu.nl/pdbtools/ and renumber your sequence (saved file) as desired
4 - go back to your original structure file and find all lines starting with HELIX or SHEET and copy them to the beginning of your corrected file (just before the first residue) and apply corrections to the secondary elements ranges (for example, I deleted 14 residues from the beginning, so need to shift back secondary elements ranges by 14)
5 - save the file and check if the structure adheres to what you expect

For me, it worked perfectly.