[Chimera-users] Programmatic selection and minimisation

Miro Moman miromoman at gmail.com
Sun Dec 9 19:27:28 PST 2018


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,


Edelmiro Moman, PhD
South Ural State University - SUSU
Южно-Уральский государственный университет - ЮУрГУ
Phone: +7 902 614 73 77
E-mail: miromoman at gmail.com
<edelmiromoman at rcsi.ie>
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