Re: [PyMOL] neutral aminoacids
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 wrote:
> Thanks for the tip!
>
>
>
> On Fri, Oct 11, 2013 at 8:53 AM, Jason Vertrees <
> jason.vertr...@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
>> 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 > >
>> > wrote:
>> >>
>> >> Ok, I will try editing those files.
>> >>
>> >> Cheers,
>> >>
>> >> Osvaldo.
>> >>
>> >>
>> >>
>> >> On Fri, Oct 11, 2013 at 12:12 AM, Jason Vertrees
>> >> 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 <
>> aloctavo...@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.
>> >>> >
>> >>> >
>> >>> >
>> --
>> >>> > October Webinars: Code for Performance
>> >>> > Free Intel webinars can help you accelerate application performance.
>> >>> > Explore tips for MPI, OpenMP, advanced profiling, and more. Get the
>> >>> > most
>> >>> > from
>> >>> > the latest Intel processors and coprocessors. See abstracts and
>> >>> > register >
>> >>> >
>> >>> >
>> http://pubads.g.doubleclick.net/gampad/clk?id=60134071&iu=/4140/ostg.clktrk
>> >>> > ___
>> >>> > 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
>> >>>
>> >>>
>> >>>
>> >>> --
>> >>> Jason Vertrees, PhD
>> >>> Director of Core Modeling Products
>> >>> Schrödinger, Inc.
>> >>>
>> >>> (e) jason.vertr...@schrodinger.com
>> >>> (o) +1 (603) 374-7120
>> >>
>> >>
>> >
>>
>>
>>
>> --
>> Jason Vertrees, PhD
>> Director of Core Modeling Products
>> Schrödinger, Inc.
>>
>> (e) jason.vertr...@schrodinger.com
>> (o) +1 (603) 374-7120
>>
>
>
--
October Webinars: Code for Performance
Free Intel webinars can help you accelerate application performance.
Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
the latest Intel processors and coprocessors. See abstracts and register >
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Re: [PyMOL] neutral aminoacids
Thanks for the tip! On Fri, Oct 11, 2013 at 8:53 AM, Jason Vertrees < jason.vertr...@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 > 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 > > wrote: > >> > >> Ok, I will try editing those files. > >> > >> Cheers, > >> > >> Osvaldo. > >> > >> > >> > >> On Fri, Oct 11, 2013 at 12:12 AM, Jason Vertrees > >> 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 > > >>> 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. > >>> > > >>> > > >>> > > -- > >>> > October Webinars: Code for Performance > >>> > Free Intel webinars can help you accelerate application performance. > >>> > Explore tips for MPI, OpenMP, advanced profiling, and more. Get the > >>> > most > >>> > from > >>> > the latest Intel processors and coprocessors. See abstracts and > >>> > register > > >>> > > >>> > > http://pubads.g.doubleclick.net/gampad/clk?id=60134071&iu=/4140/ostg.clktrk > >>> > ___ > >>> > 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 > >>> > >>> > >>> > >>> -- > >>> Jason Vertrees, PhD > >>> Director of Core Modeling Products > >>> Schrödinger, Inc. > >>> > >>> (e) jason.vertr...@schrodinger.com > >>> (o) +1 (603) 374-7120 > >> > >> > > > > > > -- > Jason Vertrees, PhD > Director of Core Modeling Products > Schrödinger, Inc. > > (e) jason.vertr...@schrodinger.com > (o) +1 (603) 374-7120 > -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60134071&iu=/4140/ostg.clktrk___ 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
Re: [PyMOL] neutral aminoacids
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 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 > wrote: >> >> Ok, I will try editing those files. >> >> Cheers, >> >> Osvaldo. >> >> >> >> On Fri, Oct 11, 2013 at 12:12 AM, Jason Vertrees >> 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 >>> 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. >>> > >>> > >>> > -- >>> > October Webinars: Code for Performance >>> > Free Intel webinars can help you accelerate application performance. >>> > Explore tips for MPI, OpenMP, advanced profiling, and more. Get the >>> > most >>> > from >>> > the latest Intel processors and coprocessors. See abstracts and >>> > register > >>> > >>> > http://pubads.g.doubleclick.net/gampad/clk?id=60134071&iu=/4140/ostg.clktrk >>> > ___ >>> > 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 >>> >>> >>> >>> -- >>> Jason Vertrees, PhD >>> Director of Core Modeling Products >>> Schrödinger, Inc. >>> >>> (e) jason.vertr...@schrodinger.com >>> (o) +1 (603) 374-7120 >> >> > -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60134071&iu=/4140/ostg.clktrk ___ 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
Re: [PyMOL] neutral aminoacids
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 wrote: > Ok, I will try editing those files. > > Cheers, > > Osvaldo. > > > > On Fri, Oct 11, 2013 at 12:12 AM, Jason Vertrees < > jason.vertr...@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 >> 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. >> > >> > >> -- >> > October Webinars: Code for Performance >> > Free Intel webinars can help you accelerate application performance. >> > Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most >> > from >> > the latest Intel processors and coprocessors. See abstracts and >> register > >> > >> http://pubads.g.doubleclick.net/gampad/clk?id=60134071&iu=/4140/ostg.clktrk >> > ___ >> > 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 >> >> >> >> -- >> Jason Vertrees, PhD >> Director of Core Modeling Products >> Schrödinger, Inc. >> >> (e) jason.vertr...@schrodinger.com >> (o) +1 (603) 374-7120 >> > > -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60134071&iu=/4140/ostg.clktrk___ 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
Re: [PyMOL] neutral aminoacids
Ok, I will try editing those files. Cheers, Osvaldo. On Fri, Oct 11, 2013 at 12:12 AM, Jason Vertrees < jason.vertr...@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 > 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. > > > > > -- > > October Webinars: Code for Performance > > Free Intel webinars can help you accelerate application performance. > > Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most > > from > > the latest Intel processors and coprocessors. See abstracts and register > > > > > http://pubads.g.doubleclick.net/gampad/clk?id=60134071&iu=/4140/ostg.clktrk > > ___ > > 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 > > > > -- > Jason Vertrees, PhD > Director of Core Modeling Products > Schrödinger, Inc. > > (e) jason.vertr...@schrodinger.com > (o) +1 (603) 374-7120 > -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60134071&iu=/4140/ostg.clktrk___ 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
Re: [PyMOL] neutral aminoacids
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 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. > > -- > October Webinars: Code for Performance > Free Intel webinars can help you accelerate application performance. > Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most > from > the latest Intel processors and coprocessors. See abstracts and register > > http://pubads.g.doubleclick.net/gampad/clk?id=60134071&iu=/4140/ostg.clktrk > ___ > 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 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60134071&iu=/4140/ostg.clktrk ___ 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
[PyMOL] neutral aminoacids
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. -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60134071&iu=/4140/ostg.clktrk___ 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
