Absolutely fantastic! :-)
I got this to work with the pymol propka script.
fetch 1ohr, async=0
create 1ohrB3C, 1ohr
hide everything, all
show cartoon, 1ohrB3C
cmd.wizard("mutagenesis")
cmd.do("refresh_wizard")
# To get an overview over the wizard API:
#for i in dir(cmd.get_wizard()): print i
# lets mutate chain B residue 3 to CYS. (1ohrB3C)
cmd.get_wizard().set_mode("CYS")
cmd.get_wizard().do_select("/1ohrB3C//B/3")
# Select the first rotamer, which is most probable
cmd.frame(1)
# Apply the mutation
cmd.get_wizard().apply()
# Close wiard
cmd.wizard(None)
# Find the new pka value
import propka
propka
Troels Emtekær Linnet
Karl-Liebknecht-Straße 53, 2 RE <http://maps.google.dk/>
04107 Leipzig, Tyskland
Mobil: +49 1577-8944752
2011/8/22 Martin Hediger <ma....@bluewin.ch>
> **
> Hi Troels
> It's indeed possible.
> The wizards are available through the cmd module.
>
> # Initialize
> load yourProtein
> cmd.wizard("mutagenesis")
> cmd.do("refresh_wizard")
>
> # To get an overview over the wizard API:
> for i in dir(cmd.get_wizard(): print i
>
> # lets mutate residue 104 to GLN
> cmd.get_wizard().set_mode("GLN")
> cmd.get_wizard().do_select("104/")
>
> # Select the rotamer
> cmd.frame(11)
>
> # Apply the mutation
> cmd.get_wizard().apply()
>
> There is alot more you could do inbetween these lines, but this is what I
> use it like.
> Martin
>
>
>
>
> On 21.08.11 15:56, Troels Emtekær Linnet wrote:
>
> Hi.
>
> I wonder if it is possible to interact with the mutagenesis wizard from the
> command line?
>
> I am trying to determine best mutants for FRET labelling, by predicting the
> pka value/reactivity for a possible cysteine.
>
> I would like to make a script that loops over the residues in my protein,
> change the residue to a cysteine, save the molecule and then initiate
> propka <http://pymolwiki.org/index.php/Propka> to get the pka for the
> cysteine.
>
> I have googled myself to:
>
> fetch 4ins, async=0
> wizard mutagenesis
> cmd.get_wizard().do_select("/4ins//A/ASN`18/CB")
> cmd.get_wizard().do_pick("/4ins//A/ASN`18/CB")
>
> But I get:
> Error: please select an atom, not a bond.
>
> Can someone help here?
>
> Best
> Troels
>
>
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