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
