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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>>> >
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>>> > _______________________________________________
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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