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.
On 09/06/2011 03:43 PM, Thomas Holder wrote:
Try this:
cmd.save(kill.pdb, test)
sorry, forgot quotes, must be:
cmd.save(kill.pdb, test)
--
Thomas Holder
MPI for Developmental Biology
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Special Offer -- Download
So.
cmd.(something) ALWAYS has to be in string format.
So there is the cmd.frame wrong.
Then you dont quit the mutagenesis wizard
And you have a space in the cmd.save
*It total, try:*
#Initialize
fetch 1shr, async=0
create test, 1shr
cmd.wizard(mutagenesis)
cmd.do(refresh_wizard)
# Mutate
Hi Troels,
cmd.(something) ALWAYS has to be in string format.
So there is the cmd.frame wrong.
I'm sorry but this is not true, of course you can pass an integer to
cmd.frame
Then you dont quit the mutagenesis wizard
which is not a problem as well.
And you have a space in the cmd.save
Dear Rozaimi,
I'm sure people would bother to read your script and reply to your
question if you told us what your trying to achieve and what not
working properly looks like. Otherwise your wasting your time.
Andreas
On 02/09/2011 4:58, Rozaimi Razali wrote:
Can someone please explain to
Can someone please explain to me why my script is not working properly?
#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()
# Save
Hi all,
I'd like to use the Mutagenesis wizard in a Pymol/Python script! I'd
like to automate the following steps!
(1) Load a peptide pdb file with three residues. (easy)
(2) Mutate one residue, well actually I do not want to change a single
residue but change the rotamer of a residue. Unlike the
Hi Martin,
you can get hints about how to script wizard functions if you log your
activities while running the wizard.
A python script (mutate.py) that makes use of the mutagenesis wizard
could look like this:
## run through pymol, eg.:
## pymol -qc mutate.py 1god A/94/ ASN
from pymol
Hi there,
does anybody of you has an idea, if the mutagenesis stuff is available for use
inside scripts too?
I wanna load a pdb, mutate a resid and save the resulting pdb via commandline.
The only thing I found was modifying atoms, when I searched via help and
also checked the wiki, i hope
