Hi Jesse, I am not aware of a structure file (i.e. PDB) which can store information such as color and thus when you load a PDB file pymol applies the default colors to it.
You can however make it so that all proteins loaded into pymol are automatically assigned the grey colour, this is done by editing the pymolrc. In the menu go: File -> Edit -> pymolrc (will create file) -> type “set cartoon_color, grey80” When you close and reopen pymol, this will ensure that all proteins loaded into pymol are given the grey80 colour, you can make any additional edits to the pymolrc file as you please i.e stick color is still default Cheers, Ali Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist Supervised by A/Prof Thomas Balle The University of Sydney School of Pharmacy | Faculty of Medicine and Health 424, Brain and Mind Centre | The University of Sydney | NSW 2050 From: "Sarameri, Jesse" <jesse.saram...@helsinki.fi> Date: Wednesday, 26 June 2019 at 6:34 pm To: "pymol-users@lists.sourceforge.net" <pymol-users@lists.sourceforge.net> Subject: [PyMOL] Export molecule does not keep changes Hello! (English is not my native language; please excuse typing errors.) Goal is to recolor molecule so it stays that way after the edit. This is how I thought it would work: Lets start by opening any molecule (like downloading 5jh0.cif from https://www.rcsb.org/structure/5jh0) Changed the color of the molecule to grey, save as session (.pse file), open it and still grey, great! But if I want to export to molecule (.pdb for example), open the molecule, no changes applied. Tried to change Saved state settings and different formats but no effect. No error messages either. I did RTFM and STFW not able to find answer. (If I missed it, feel free to send pics with red circles and arrows to highlight it.) Software and hardware used: Open source PyMOL version 2.1.0. Windows 10 Lenovo X280 Laptop Many thanks for help incase someone else might encounter this problem. Regards, Jesse Sarameri
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