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.


reinitialize
import propka
cmd.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 <joel.tyndall@otago.ac.nz>

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 Iím 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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