In my first e-mail I made a mistake a protonated His is a charged His.

Thanks to the guidance of Jason I found that the more convenient way to solve my problem was modifying the file "/usr/lib/python2.7/dist-packages/pymol/editor.py", inside that file there is dictionary, relating the names of the pkl fragments (located in the "/usr/share/chempy/fragments" folder) with a One letter code. I use lowercase for the neutral Asp, Glu, Lys and Arg and also lowercase for the protonated His (the default His in PyMOL is the neutral NE2 tautomer).


_aa_codes =  {
    'A' : 'ala',
    'B' : 'ace',
    'C' : 'cys',
    'D' : 'asp',
    'd' : 'asph',
    'E' : 'glu',
    'e' : 'gluh',
    'F' : 'phe',
    'G' : 'gly',
    'H' : 'his',
    'h' : 'hip',
    'I' : 'ile',
    'K' : 'lys',
    'k' : 'lysn',
    'L' : 'leu',
    'M' : 'met',
    'N' : 'asn',
    'P' : 'pro',
    'Q' : 'gln',
    'R' : 'arg',
    'r' : 'argn',
    'S' : 'ser',
    'T' : 'thr',
    'V' : 'val',
    'W' : 'trp',
    'Y' : 'tyr',
    'Z' : 'nme',
    }


Cheers,

Osvaldo


On Fri, Oct 11, 2013 at 3:25 PM, Osvaldo Martin <aloctavodia@gmail.com> wrote:
Thanks for the tip!



On Fri, Oct 11, 2013 at 8:53 AM, Jason Vertrees <jason.vertrees@schrodinger.com> wrote:
Osvaldo,

To make PyMOL pick fragments from another location just edit the path
at the top of pymol/modules/chempy/fragments/__init__.py.

The fab command is in pymol/modules/pymol/editor.py.

Cheers,

-- Jason



On Thu, Oct 10, 2013 at 11:38 PM, Osvaldo Martin <aloctavodia@gmail.com> wrote:
> BTW, there is an easy option to make cmd.fab() to pick the fragments from an
> alternative location? (just to avoid modifying the original fragments files)
>
> thanks,
>
> Osvaldo.
>
> On Fri, Oct 11, 2013 at 12:32 AM, Osvaldo Martin <aloctavodia@gmail.com>
> wrote:
>>
>> Ok, I will try editing those files.
>>
>> Cheers,
>>
>> Osvaldo.
>>
>>
>>
>> On Fri, Oct 11, 2013 at 12:12 AM, Jason Vertrees
>> <jason.vertrees@schrodinger.com> wrote:
>>>
>>> Hi Osvaldo,
>>>
>>> This isn't built in yet. But, if you need to do that, you can edit the
>>> Python picked files found here:
>>>
>>> pymol/data/chempy/fragments
>>>
>>> Cheers
>>>
>>> -- Jason
>>>
>>> On Thu, Oct 10, 2013 at 2:41 PM, Osvaldo Martin <aloctavodia@gmail.com>
>>> wrote:
>>> >
>>> > I am using the comand cmd.fab() to create small peptides. There is an
>>> > easy
>>> > option to add neutral aminoacids? The default behaviour is to add
>>> > charged
>>> > amino acids with the charge of the free amino acid in solution at pH =
>>> > 7
>>> > i.e. Lys and Arg protonated and Glu, Asp and His unprotonated.
>>> >
>>> > Thanks in advance.
>>> >
>>> >
>>> > ------------------------------------------------------------------------------
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>>>
>>>
>>> --
>>> Jason Vertrees, PhD
>>> Director of Core Modeling Products
>>> Schrödinger, Inc.
>>>
>>> (e) Jason.Vertrees@schrodinger.com
>>> (o) +1 (603) 374-7120
>>
>>
>



--
Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.

(e) Jason.Vertrees@schrodinger.com
(o) +1 (603) 374-7120