Hi Rozaimi,
the only problem seems to be your last line, you save two objects (test,
1shr) to the same PDB file.
Try this:
cmd.save("kill.pdb", test)
Cheers,
Thomas
On 09/06/2011 03:25 PM, Rozaimi Razali wrote:
> Dear All,
>
> Sorry for the late reply and thank you for helping me out.
>
> Originally the wild residue (for 1shr) at position 36:B is a Proline. I
> want to mutate it to Histidine.
>
> I have tried the suggestion in this thread but the output file
> (kill.pdb) still gives PRO at position 36:B
>
> #Initialize
> fetch 1shr, async=0
> create test, 1shr
> cmd.wizard("mutagenesis")
> cmd.do("refresh_wizard")
>
> # Mutate
> cmd.get_wizard().set_mode("HIS")
> cmd.get_wizard().do_select("/test//B/36")
>
> cmd.frame("1")
> cmd.get_wizard().apply()
> cmd.set_wizard("done")
>
> # Save
> cmd.save("kill.pdb")
>
> I am not sure what is the problem here. I have also tried running the
> script on other machines and still the same problem is happening. FYI i
> am using Pymol version 1.3. Could this be the problem?
>
> I have tried using the log function + mutagenesis wizard in Pymol GUI
> but something strange is happening. The position 36:B did changed to His
> but....
>
> e.g.
>
> input file - 1shr.pdb -> atom number for 36:B:CA is 1334
> output file - kill.pdb -> atom number 36:B:CA 1380
>
> log.pml -> ...byresi((1shr`1380))...
>
> Why does it tag the atom number from the output file? Shouldn't it tag
> the atom number from the input file (1shr)?
--
Thomas Holder
MPI for Developmental Biology
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