Re: [PyMOL] Getting surface residues

[Troels E. L. <tl...@gm...>]

Thanks!

Troels Emtekær Linnet
Ved kløvermarken 9, 1.th
2300 København S
Mobil: +45 60210234



2012/10/31 Abdullah Kahraman <abd...@im...>

> Dear Troels,
>
> Personally I don't use PyMol for this problem. Rather I use the
> application NACCESS (http://www.bioinf.manchester.ac.uk/naccess/) and
> choose a total relative solvent accessibility of at least 5% (Miller, S.
> et al, 1987, *J Mol Biol* 196, 641–656) to assess whether a residue is at
> the protein surface or not. The relative solvent accessibilities are listed
> in 5th column of the NACCESS .rsa output file.
>
> Best
> Abdullah
>
>
> On 31 Oct 2012, at 07:11, Troels Emtekær Linnet <tl...@gm...> wrote:
>
> Hi Pymolers.
>
> How would you get a list of surface residues the fastest way?
>
> Like:
>  [3-10], [14-18]
>
> I have a rough structure from crystallography, and have made
> a trypsin digest and mass spec analysis.
>
> And I see fragments which have been post-trans modified.
>
> Now I am interested in matching if those fragments are surface exposed or
> internal.
>
> What tools does pymol have to find out if the residues are surface exposed?
> Or is there another "easy" tool?
>
> Best
> Troels Emtekær Linnet
> Ved kløvermarken 9, 1.th
> 2300 København S
> Mobil: +45 60210234
>
>
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> Aebersold - Malmstroem Group
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