Re: [PyMOL] My first script?

[Troels E. L. <tl...@gm...>]

If you have some name scheme for your molecules, you could figure it out
from this:

You want to make a python block:

python
.... do python code here
python end


Then define a loop, and figure out to call your naming scheme.
Do a calculation, and add the result to an array or something.


reinitializeimport propkacmd.bg_color("white")cmd.set("auto_zoom","off")

results = []
python
resis = [["1DSB","*","30"],["1ERT","*","32"]]
 for p,c,r in resis:
	cmd.fetch(p,async="0")
	cmd.refresh()
	pkavalues = propka.propka(molecule=p,chain=c,resi=r,logtime="",makebonds="no")
	results.append(pkavalues)
	cmd.refresh()
python end





2012/5/9 Joel Tyndall <joe...@ot...>

>  Hi folks,****
>
> ** **
>
> So I have no scripting skills in python but I can use pymol reasonably
> well. ****
>
> ** **
>
> I want to superimpose (pair_fit) 4 atoms (all the same) from a library of
> conformers onto a template molecule (similar to clustering after
> conformational searching). I could probably nut out how to do the
> pairfitting actually I could do this easily by command line but I have >
> 100 molecules so I’m not sure how to script this.****
>
> ** **
>
> Any help would be welcome****
>
> ** **
>
> Cheers****
>
>
> Joel****
>
> ** **
>
> _________________________________****
>
> Joel Tyndall, PhD
>
> Senior Lecturer in Medicinal Chemistry
> National School of Pharmacy
> University of Otago
> PO Box 56 Dunedin 9054
> New Zealand   ****
>
> Skype: jtyndall****
>
> ** **
>
> Ph: +64 3 479 7293****
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