I have successfully installed pymol on linux using instructions from this link on pymolwiki page and customized it to install to a path of my choice. Later I started to add pymol-script-repo to the same folder, after slightly tweaking instructions (to setup paths of my choice) from link

Whenever I use the plugins from the plugin list in pymol window its output are directed to some different paths. For example autodock-vina saves its results in "home" folder while cyspka in "results" folder of pymol-script-repo.

Is this happening because i have deviated from the instructions for installation or the plugins are predefined in the same format?
Is it possible that i can instruct the plugin to save the results in the current working directory or path of my choice?

Thank you

Best Regards