Re: [PyMOL] Selecting subsequence in PyMol

[Keitaro Y. <yam...@ca...>]

Dear Jason,

I know there are many residue naming of RNA/DNA depending on what
software is used.
(for example, Adenine: ADE, A, Ar, Ad,... )

I hope PyMOL would support any naming!

Thanks,

Keitaro

2010/12/11 Jason Vertrees <jas...@sc...>:
> Hi Keitaro,
>
> Code has been started for "nucseq" and the shorthand "ns.".  I think
> it was not completed because at first glance it appears less than
> straightforward: "ps." searches for the one-letter residue names, but
> "ns." would have to map one-letter codes to those commonly used in the
> data, "DA" "DT", etc.
>
> Cheers,
>
> -- Jason
>
> On Fri, Dec 10, 2010 at 1:48 AM, Keitaro Yamashita
> <yam...@ca...> wrote:
>> It's very useful.
>> How about RNA/DNA sequence?
>>
>> Thanks in advance,
>>
>> Keitaro
>>
>> 2010/12/10 Jason Vertrees <jas...@sc...>:
>>> Hi Julio,
>>>
>>>> I'm using PyMOL 1.3 and I would like to select one specific part of the
>>>> molecule based on a peptide sequence that it is presented in protein. Is
>>>> there any way to select subsequences in PyMOL?
>>>>
>>>> Protein sequence:
>>>>
>>>> ...SMVADLTQATFTKEGKTQKVVDVLDHDYVFDTFFK...
>>>>
>>>> Peptide:
>>>>
>>>> GKTQKV
>>>
>>> Use the 'ps.' (peptide sequence) modifier:
>>>
>>> select targetSeq, ps. GKTQKV
>>>
>>> Cheers,
>>>
>>> -- Jason
>>>
>>> --
>>> Jason Vertrees, PhD
>>> PyMOL Product Manager
>>> Schrodinger, LLC
>>>
>>> (e) Jas...@sc...
>>> (o) +1 (603) 374-7120
>>>
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>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) Jas...@sc...
> (o) +1 (603) 374-7120
>