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 <tlin...@gmail.com> 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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--<------<---@
Abdullah Kahraman, PhD
Aebersold - Malmstroem Group
Institute of Molecular Systems Biology
ETH Zurich
HPT C75
Wolfgang-Pauli-Str. 16
8093 Zurich
Switzerland
http://www.imsb.ethz.ch/researchgroup/malars/people/abdullah_kahraman
abdul...@imsb.biol.ethz.ch
work: +41-(0)44-633 66 71
mobile: +41-(0)76-317 0305
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