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
04107 Leipzig, Tyskland
Mobil:
+49 1577-8944752



2011/8/22 Martin Hediger <ma.hed@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 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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