Wonderful. I'm close to completing what I need, thanks a lot.
I have one other question here. Say I have a peptide:
N-Ala-Ala-Glu-COO (I'm just pointing out the terminal amide and carbonyl
groups). Then I protonate it with h_add
H2N-Ala-Ala-Glu-(C=O)H. Now I carry out a mutation on the last position
with the mutagenesis wizard to His. After this, the H's on the C=O is
missing:
H2N-Ala-Ala-His-(C=O).
This is a bit unfortunate, because it would screw up the protonation of
the whole system if I reissue h_add on the whole system after a
mutation. Is it possible to fix atoms on only a selection, e.g. the site
picked to mutate?
Thanks for any advise on this.
Martin
Am 20.09.10 16:59, schrieb Jason Vertrees:
> Hi Martin,
>
>> atoms within less than VdW distance. Is there an easy, very low-level, PyMOL
>> way of fixing this? Can the sculpting wizard be used for this?
>
> Yes, after you place the sidechain and have the new structure (via the
> "apply" function) you can then apply sculpting. It would look
> something like this:
>
> # pause the UI
> cmd.set("suspend_updates",1)
>
> # reset the sphere scale
> cmd.set("sphere_scale","1.0")
>
> # go back to frame 1 (if you changed it)
> cmd.frame(1)
>
> # enable sculpting
> cmd.set("sculpting",1)
>
> # sculpt for 100 cycles
> cmd.sculpt_activate("myProtein")
> cmd.set("sculpting_cycles",100)
>
> # resume the UI
> cmd.set("suspend_updates",0)
>
> # write coords
> cmd.sculpt_iterate("myProtein")
>
> #quit sculpting
> cmd.unset("sculpting")
>
>
> Load a small protein and call it "myProtein". Then, copy/paste the
> above code into PyMOL to see what happens.
>
> Cheers,
>
> -- Jason
>
>
>
> On Mon, Sep 20, 2010 at 5:35 AM, Martin Hediger<ma....@bluewin.ch> wrote:
>> Dear All
>> Just one little thing, say I obtain a couple of rotamers by mutating a
>> sidechain. It happens that some of them are sterically not favourable, i.e.
>> atoms within less than VdW distance. Is there an easy, very low-level, PyMOL
>> way of fixing this? Can the sculpting wizard be used for this?
>>
>> Thanks a lot for any suggestions.
>>
>> Martin
>>
>>
>>
>>
>>
>>
>>
>> Am 19.09.10 19:00, schrieb Jason Vertrees:
>>> Martin,
>>>
>>>> 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.
>>> I'm not aware of any. Some of our other seasoned PyMOLers might,
>>> though. If you need help w/the plugin there's a simple tutorial on
>>> the PyMOLWiki (http://www.pymolwiki.org/index.php/Plugins_Tutorial)
>>> and TKinter/PMW are very easy to develop with. Good luck!
>>>
>>> Cheers,
>>>
>>> -- Jason
>>>
>>> On Sat, Sep 18, 2010 at 6:48 PM, Martin Hediger<ma....@bluewin.ch> wrote:
>>>> 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
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>>>>>> Start uncovering the many advantages of virtual appliances
>>>>>>>>>>>>> and start using them to simplify application deployment and
>>>>>>>>>>>>> accelerate your shift to cloud computing
>>>>>>>>>>>>> http://p.sf.net/sfu/novell-sfdev2dev
>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>>>>>>>>>>>>> Info Page:
>>>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>>>>>>>>>>> Archives:
>>>>>>>>>>>>> http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>>>>> Start uncovering the many advantages of virtual appliances
>>>>>>>>>>>> and start using them to simplify application deployment and
>>>>>>>>>>>> accelerate your shift to cloud computing
>>>>>>>>>>>> http://p.sf.net/sfu/novell-sfdev2dev
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>>>>>>>>>>>> Info Page:
>>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>>>>>>>>>> Archives:
>>>>>>>>>>>> http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>>>>>>>>>>>>
>>>
>>
>
>
------------------------------------------------------------------------------
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
