Hi Martin,
PyMOL first searches the Dunbrack rotamer library for hits based upon
the amino acid type and it's original phi/psi angles. If it cannot
find a hit, it will then look for backbone independent positions. To
get the number of available rotamers given a residue, you need to
unpickle the library, create the lookup key into the library and then
count the results. It might look something like this:
# unpickle the library
import pickle
rot_lib =
pickle.load(open("$PYMOL_HOME/data/chempy/sidechains/sc_bb_dep.pkl",'r'))
# get residue name, you need to select the residue
# into "my_res"
from pymol import stored
stored.r = ''
iterate first my_res, stored.r = resn
# get residue info; prepare dictionary key
(phi,psi) = cmd.phi_psi("br. first my_res")
# warren also does 20 and 60 in place of 10--three possible lookups
key = ( stored.r, int(10*round(phi/10)), int(10*round(psi/10)))
if key in rot_lib.keys():
print "This rotamer has %s possible positions" % len(rot_lib[key])
Lookups in the independent library are easier--just provide a residue name.
Cheers,
-- Jason
On Sun, Sep 12, 2010 at 11:04 AM, Martin Hediger <ma....@bluewin.ch> wrote:
> Dear all, let me rephrase my question in a less confusing way.
> For a given mutant, I need a PDB file for every available rotamer. I
> guess thats the simplest way of putting it. How can I achieve that?
>
> Thanks for hints.
> Martin
>
>
>
>
>
> Am 12.09.10 00:08, schrieb Martin Hediger:
>> Hi all
>> I want to do some scripted mutations on a range of residues. Say I want
>> to mutate residue 189 to every rotamer of [Asp, His, Glu, Thr, Lys]
>> available in the PyMOL internal rotamer library. I'm seeing that PyMOL
>> issues cmd.get_wizard().do_state(i) to select rotamer 'i' for a
>> mutation. Now, if I want to iterate over all available rotamers, I need
>> the limit rotamer number. How can I obtain the maximum number of
>> rotamers available for every amino acid?
>>
>> Thanks for hints on this
>>
>> Martin
>>
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>
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--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
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