[PyMOL] Iterating through all objects and calculate RMS

[Subha K <sub...@gm...>]

Hi There,

I am trying to calculate the rmsd of all ligands loaded in the pymol with
reference to a reference ligand using a script. My current script looks
like this,


myobjects = cmd.get_object_list()

print myobjects

cmd.select('sele', "F60_target_14 and resn UNK")

cmd.create('obj01', 'sele')

for i in myobjects:

    i = i.strip()

    cmd.sele('sele', i +'and resn UNK')

    cmd.create ('obj02', 'sele')

    cmd.rms_cur ('obj02', 'obj01')

    cmd.delete ('obj02')


obj01 will be my reference and I want to use rms_cur to all objects loaded.
The problems here are,
(1) My obj02 selection part is not working properly. I know I am not
calling the myobject list in the correct way. Could somebody help me fix
this?
(2) I want to write the rmsd values to a file. How can I do it?

Thanks for the help.

Regards,
Subha