Hi Jason and PyMOL users
I tried to run the script to get the number of rotamers, but I seem to
have something missing.
The script looks as follows:
import pickle
rot_lib =
pickle.load(open("/Applications/PyMOLX11Hybrid.app/pymol/data/chempy/sidechains/sc_bb_dep.pkl",'r'))
from pymol import stored
from pymol import cmd
stored.r = ''
# What are we doing here? What is 'first'?
cmd.iterate("first my_res", "stored.r = resn")
(phi, psi) = cmd.phi_psi("br. first my_res")
key = (stored.r, int(10*round(ph/10)), int(10*round(psi/10)))
if key in rot_lib.keys():
print "This rot has %s possible positions" % len(rot_lib[key])
Now, I save this into rotlib.py, 'cd' PyMOL into the directory where
this script lies, select a residue from the GUI, rename the selection to
'my_res' and then 'run rotlib.py' the script. This returns the following
ERROR message in PyMOL:
Traceback ...
(phi, psi) = cmd.phi_psi("br. first my_res")
ValueError: need more than 0 values to unpack
Unfortunately, I dont understand what this is trying to tell me right
now, ok, some Argument seems to be missing, but I cant tell what
exactly. Also, could you possibly extend your explanation on what the
'iterate' method is used for. I think this would help me a lot.
As I said, all I want is a PDB file for every rotamer itself. If there
is a simpler way to achieve this, that is fine with me. The number of
rotamers is only important to me, since I need to know how many times i
should issue 'cmd.forward()' and save.
Thanks for the help.
Martin
Am 13.09.10 00:30, schrieb Jason Vertrees:
> Hi Martin,
>
>> iterate first my_res, stored.r = resn
> is syntactically correct, but could also be written,
>
> cmd.iterate("first my_res", "stored.r = resn");
>
> The command could be read as, "iterate over just first atom from the
> selection called 'my_res' and place the residue name in which that
> atom resides into 'stored.r'." So, "first" is a new-ish selection
> modifier that takes just the first atom from a selection. It's _very_
> handy: why iterate through all atoms in a residue to get a residue
> name, when just the first will do? "resn" indeed returns the 3-letter
> residue code.
>
> A more efficient way might be:
>
> # select a residue, here #50 (or use the mouse)
> select mySelection, i. 50
>
> # get it's one-letter residue id
> print string.split(cmd.get_fastastr("mySelection"),'\n')[1]
> # get it's three-letter residue id
> print three_letter[string.split(cmd.get_fastastr("mySelection"),'\n')[1]]
>
> I just posted this on http://www.pymolwiki.org/index.php/Aa_codes.
> (You will need the two dictionaries found there.)
>
> There really should be a much easier way to do that... Maybe someone
> has a far easier command?
>
> Cheers,
>
> -- Jason
>
>
>
>
> On Sun, Sep 12, 2010 at 4:25 PM, Martin Hediger<ma....@bluewin.ch> wrote:
>> 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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>>>>
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>>
>
>
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