Re: [PyMOL] Interacting with Mutagenesis wizard in command line.

[Martin H. <ma...@bl...>]

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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