How to quantify cross-linked data?

[Dmorgen]

what should be put in the base/full sequence?

Thanks!
D.

[rmillikin]

the full sequence can be whatever you want (it's just a label). the base sequence must be composed of only amino acids, and it's best if you can get as close to the real composition of the molecule as possible. though it will still work if you put in a dummy sequence (it will use mostly averagine). so you could just put something like "G" for every base sequence, or you could put in the alpha+beta peptide sequences mashed together. both would work reasonably well I think

[Dmorgen]

Will do, thanks!

D.