This is great. Thanks a lot.
I am wondering, are there any scripts/ plugins for PyMOL out there that
facilitate the generation of a large amount of rotamers for different
mutants? I might take the effort and start building this into a plugin.
Martin
Am 16.09.10 19:51, schrieb Jason Vertrees:
> Hi Martin,
>
> This took a bit of work to figure out, but the following code solves
> your problem (above). It will download a PDB (I coded "1RSY") and
> select a residue (I coded 236). I will then mutate that residue to
> all possible residues given what the rotamer library knows about, and
> write that out to N-files called "stateXYZ.pdb", where XYZ is the
> mutation number. Instead of rewriting the code, it turns out you can
> hack the wizard through the API to do what you want:
>
> # begin a python block of code;
> python
> org = "1rsy"
> cpy = "1rsy_cpy"
>
> # fetch a PDB
> cmd.fetch(org, async=0)
>
> # make a copy on which to operate
> cmd.create(cpy,org)
> res = cpy + " and i. 236"
>
> # focus no the residue, if you want
> cmd.zoom(res, 3)
>
> # start the wizard to count the number of rotamers for this residue
> cmd.wizard("mutagenesis")
>
> # this was the painful part: if you just write "res" instead of "(res)"
> # pymol will delete your residue. "(res)" make it an anonymous selection
> cmd.get_wizard().do_select("("+res+")")
> nStates = cmd.count_states("mutation")
>
> # foreach state, make the change and write to disk
> for i in range(1,nStates+1):
> print "State ", i, "/", nStates
> cmd.get_wizard().do_select("("+res+")")
> cmd.frame(i)
> cmd.get_wizard().apply()
> cmd.save("state" + str(i) + ".pdb", cpy)
> cmd.delete(cpy)
> cmd.create(cpy,org)
>
> # end the python block
> python end
>
> # quit the wizard
> cmd.set_wizard()
>
> Cheers,
>
> -- Jason
>
> On Tue, Sep 14, 2010 at 6:33 PM, Martin Hediger<ma....@bluewin.ch> wrote:
>> I'm beginning to see things.
>> When I issue:
>>
>> for value in rot_lib[('ASP', 40, -100)]:
>> rl.write(str(value) + '\n')
>>
>> rot_lib is being initiated by
>>
>> rot_lib =
>> pickle.load(open("/Applications/PyMOLX11Hybrid.app/pymol/data/chempy/sidechains/sc_bb_dep.pkl",'r'))
>>
>>
>> I get the following output:
>> {('N', 'CA', 'CB', 'CG'): -169.69999999999999, 'FREQ': 0.47735699999999998,
>> ('CA', 'CB', 'CG', 'OD1'): 3.6000000000000001}
>> {('N', 'CA', 'CB', 'CG'): -173.5, 'FREQ': 0.19134399999999999, ('CA', 'CB',
>> 'CG', 'OD1'): 56.799999999999997}
>> {('N', 'CA', 'CB', 'CG'): -72.099999999999994, 'FREQ': 0.11949799999999999,
>> ('CA', 'CB', 'CG', 'OD1'): -12.9}
>> {('N', 'CA', 'CB', 'CG'): -167.80000000000001, 'FREQ': 0.108205, ('CA',
>> 'CB', 'CG', 'OD1'): -55.5}
>> {('N', 'CA', 'CB', 'CG'): -64.599999999999994, 'FREQ': 0.075302999999999995,
>> ('CA', 'CB', 'CG', 'OD1'): -50.0}
>> {('N', 'CA', 'CB', 'CG'): 62.399999999999999, 'FREQ': 0.013899, ('CA', 'CB',
>> 'CG', 'OD1'): 1.3}
>>
>> I understand these are dictionaries containing the phi, psi values for a
>> rotamer. Now this would mean in this case there are six rotamers for this
>> situation. Starting to get closer to what i want.
>> Still, if there is a easy way to get PDB files of every rotamer, that would
>> solve my problem.
>> So the thing left to figure out is how to find the right key for the rot_lib
>> to give me the rotamers of the residue i am actually interested in.
>>
>> Thanks again for the support.
>>
>> Martin
>>
>>
>>
>>
>>
>>
>> Am 14.09.10 01:01, schrieb Jason Vertrees:
>>> Hi Martin,
>>>
>>> Try replacing
>>>
>>>> (phi, psi) = cmd.phi_psi("br. first my_res")
>>> with
>>>
>>> (phi, psi) = cmd.phi_psi("br. first my_res").values()[0]
>>>
>>>
>>> Here's what I have now, for the script (I fixed one more bug):
>>> 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").values()[0]
>>> key = (stored.r, int(10*round(phi/10)), int(10*round(psi/10)))
>>>
>>> if key in rot_lib.keys():
>>> print "This rot has %s possible positions" % len(rot_lib[key])
>>>
>>>
>>>
>>> Cheers,
>>>
>>> -- Jason
>>>
>>> On Mon, Sep 13, 2010 at 5:04 PM, Martin Hediger<ma....@bluewin.ch> wrote:
>>>> 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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