Hello, I am trying to use Chimera programmatically in order to automatise a number of tasks. I have tree questions: 1) When I select a zone around the ligand (for instance "runCommand(select #0:501.A zr<5)" the selection level is either atoms or, in this case, residues. Is there a way to select molecules? Because the problem I am finding is that if I run "runCommand(select up)", depending on the PDB file, sometimes I need to do it twice and sometimes three times in order to select the entire molecules (be them proteins or not). I would like to have more control over this function. The purpose being deleting molecules that are far away from the ligand. 2) Right now I am running "DockPrep" followed by "minimize" (without further "prep"). The reason is that "DockPrep" enables me to set options, whereas for "minimize" with "prep" this possibility, if it exists, does not seem to be documented. Is that the case? 3) Finally, in "DockPrep", is there a way to select the charge model explicitly? For instance, to choose Gasteiger charges in order to save time. Kind regards, Miro -- Edelmiro Moman, PhD South Ural State University - SUSU Южно-Уральский государственный университет - ЮУрГУ Phone: +7 902 614 73 77 E-mail: miromoman@gmail.com https://www.linkedin.com/in/edelmiro-moman-3a9979a/ <https://www.linkedin.com/in/edelmiro-moman-3a9979a/> <edelmiromoman@rcsi.ie>