Hi Alex, Unfortunately, there is no way to prevent Dock Prep from deleting the solvent in nogui mode without resorting to using Python instead of commands. Depending on what your structure is like, you could possibly use addh and addcharge instead of Dock Prep before minimization (and minimize with “prep false”), but that wouldn’t handle deleting excess alternate locations, changing MSE to MET, filling out missing side chains and so forth. Obviously, this process would be simple if you were using ChimeraX but I assume there is some reason you need to keep using Chimera here. If you want to try going the Python route in Chimera, let me know and I’ll try to provide some guidance. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Jul 27, 2026, at 11:09 AM, Alexander Hung Lee via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hello, I've been using the energy minimization protocol in Chimera via commandline, nogui. Recently, I've needed to keep the solvent from crystal structure when minimizing but the integrated Dock Prep deletes it. Is there a way to prevent Dock Prep from deleting solvent in Chimera?
I know in ChimeraX has the command line implementation of Dock Prep as "dockprep", but I didn't find a counterpart to it in the older Chimera program.
Thank you, Alex Lee _______________________________________________ Chimera-users mailing list -- chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu <mailto:chimera-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/