Hi Jason, thanks for the comprehensive answer.
One question though, is the line
iterate first my_res, stored.r = resn
correct this way? Are there no braces or quotation marks needed? Its not
perfectly clear to me if 'first' and 'my_res' are selections (indicated
by braces) or objects (name without braces in the main window).
I understand 'resn' is something like 'GLU', if I want to know how many
GLU rotamers are in the library.
Thanks again
Martin
Am 12.09.10 22:00, schrieb Jason Vertrees:
> 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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