July 2026 - Chimera-users - RBVI Mailing Lists

Command line dock prep in Chimera
by Alexander Hung Lee 27 Jul '26

27 Jul '26

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

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adding residues to N-terminal
by Dilara KARAMAN 27 Jul '26

27 Jul '26

Good days, I'm new user of Chimera therefore I need help using build structure option of program. I want to add MRAE residues to N-terminal of enzyme as an alpha helix structure but I can not use the directions of tutorial such as: addaa tyr,30 :29.a - add tyrosine in an extended conformation as residue 30, after residue 29 in chain A (the new residue will also be in chain A) Where can I write this command? I'm trying to add four residues to N terminal but I'm adding them to another point. I'm sending the screen image. Please help me. Best regards Dilara Karaman

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I need older version
by Dilara KARAMAN 21 Jul '26

21 Jul '26

Good days, Thank you for your usefull protein preparation options. I have a problem when setting the Chimera in my Windows 7, 64 bit computer. Because of this old version of Windows Chimera can not be established. Is there any older version of Chimera to set on Windows7? Before 10 years, I used chimera on Windows7 but now it is not available. Please help me. Best regards Dilara Karaman

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