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

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

to close the wizard, you can also apply
cmd.set_wizard("done")

and you need to be carefull about the rotamer you're choosing. it 
happens that the first one ends up being in physically non-reasonable 
contact distance to other residues, so atoms become overlayed.
also, the mutagenesis wizard has the funny habit of sometimes not adding 
hydrogens to terminal -C or -N after mutating a residue, just for the 
record.
Martin





On 22.08.11 13:23, Troels Emtekær Linnet wrote:
> 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...@bl... <mailto: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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