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 <tlinnet@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
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