Re: [PyMOL] One liner for getting amino acid sequence from pdb file
Hi Troels,
cmd.save("filename.fasta")
will save the sequence of your PDB file in a file in fasta format. Then you
could open the file and put the content in a list.
cheers,
Osvaldo
-- Forwarded message --
> From: "Troels Emtekær Linnet"
> To: "pymol-users@lists.sourceforge.net" >
> Cc:
> Date: Wed, 8 Feb 2012 15:24:37 +0100
> Subject: [PyMOL] One liner for getting amino acid sequence from pdb file
> Hi.
>
> I have a pdb file, which is a modelled structure from another sequence.
>
> I want to check the amino acid sequence in the structure.
> Does anyone know a one-liner in pymol which will extract the sequence
> in one-letter code?
>
> best
> Troels
>
>
--
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Re: [PyMOL] One liner for getting amino acid sequence from pdb file
Thanks!
I put it on the wiki:
http://pymolwiki.org/index.php/Get_fastastr
Cheers
2012/2/8 Thomas Holder
> print cmd.get_fastastr('all')
>
> Cheers,
> Thomas
>
>
> On 02/08/2012 03:24 PM, Troels Emtekær Linnet wrote:
>
>> Hi.
>>
>> I have a pdb file, which is a modelled structure from another sequence.
>>
>> I want to check the amino acid sequence in the structure.
>> Does anyone know a one-liner in pymol which will extract the sequence
>> in one-letter code?
>>
>> best
>> Troels
>>
>
> --
> Thomas Holder
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen
>
--
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Re: [PyMOL] One liner for getting amino acid sequence from pdb file
print cmd.get_fastastr('all')
Cheers,
Thomas
On 02/08/2012 03:24 PM, Troels Emtekær Linnet wrote:
> Hi.
>
> I have a pdb file, which is a modelled structure from another sequence.
>
> I want to check the amino acid sequence in the structure.
> Does anyone know a one-liner in pymol which will extract the sequence
> in one-letter code?
>
> best
> Troels
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
--
Keep Your Developer Skills Current with LearnDevNow!
The most comprehensive online learning library for Microsoft developers
is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
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[PyMOL] One liner for getting amino acid sequence from pdb file
Hi. I have a pdb file, which is a modelled structure from another sequence. I want to check the amino acid sequence in the structure. Does anyone know a one-liner in pymol which will extract the sequence in one-letter code? best Troels -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d___ 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
