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 <subhal...@gmail.com> 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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