[PyMOL] regarding pymol-script-repo

[ccp4 p. <ccp...@gm...>]

Hi

 I have successfully installed pymol on linux using instructions from this
link <http://www.pymolwiki.org/index.php/User:Tlinnet/Linux_Install> 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<http://www.pymolwiki.org/index.php/Git_install_scripts>

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
Priyan