Re: [PyMOL] Iterating through all objects and calculate RMS

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

Oh yeah, thanks a lot Gabriel Marques.

I figured out the rms_cur part too.

On Tue, Oct 18, 2016 at 12:23 PM, Gabriel Marques <
gab...@sc...> wrote:

> Looks like you’re missing a space in the string ‘and resn UNK’, it should
> be: i + ‘ and resn UNK’
>
> Regards,
> Gabriel Marques
>
> On Oct 18, 2016, at 1:57 PM, Subha K <sub...@gm...> wrote:
>
> 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
>
>
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