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

You want to make a python block:

.... 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.

import propka
results = []
resis = [["1DSB","*","30"],["1ERT","*","32"]]
for p,c,r in resis:
	pkavalues = propka.propka(molecule=p,chain=c,resi=r,logtime="",makebonds="no")
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




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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