These are all great ideas--I'm glad I asked.
I updated the wiki page (http://www.pymolwiki.org/index.php/Aa_codes)
to reflect this discussion.
Cheers,
-- Jason
On Mon, Sep 13, 2010 at 4:17 AM, Tsjerk Wassenaar <tsje...@gmail.com> wrote:
> Hi Jason e.a.,
>
> I usually do the hashing like:
>
> aa1 = list("ACDEFGHIKLMNPQRSTVWY")
> aa3 = "ALA CYS ASP GLU PHE GLY HIS ILE LYS MET ASN PRO GLN ARG SER THR
> VAL TRP TYR".split()
> aa123 = dict(zip(aa1,aa3))
> aa321 = dict(zip(aa3,aa1))
>
> The real convenience in there is that you can easily construct any
> kind of hash by just adding a matching list, and zipping.
>
> Then to extract a sequence, I tend to go for a construction like:
>
> sequence = [ aa321[i.resn] for i in cmd.get_model(selection + " and n.
> ca").atom ]
>
> Cheers,
>
> Tsjerk
>
> On Mon, Sep 13, 2010 at 12:30 AM, Jason Vertrees
> <jason.vertr...@schrodinger.com> wrote:
>> 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
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>>>>>> _______________________________________________
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>>>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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>>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Start uncovering the many advantages of virtual appliances
>>>>> and start using them to simplify application deployment and
>>>>> accelerate your shift to cloud computing
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>>>>> _______________________________________________
>>>>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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>>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>>
>> --
>> Jason Vertrees, PhD
>> PyMOL Product Manager
>> Schrodinger, LLC
>>
>> (e) jason.vertr...@schrodinger.com
>> (o) +1 (603) 374-7120
>>
>> ------------------------------------------------------------------------------
>> 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
>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> Groningen Institute for Biomolecular Research and Biotechnology /
> University of Groningen
> The Netherlands
>
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
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