I believe ccp4 "chainsaw" will do all three: truncate nonconserved AA
(to gly, ala, or all atoms in common), rename residue type, and renumber
(if you use clustalw alignment which has residue numbers for query and target).
It even renumbers around gaps and insertions in an intelligent way.
nedit $CDOC/chainsaw.doc
eab
Justin Hall wrote:
> Dear Community,
>
> I am looking for a tool that can convert a potential MR search model
> to match the residue number and a.a. type of my actual protein.
> Specifically, I have a homolog structure, with slightly different
> start and stop residues, and several non identical a.a.s relative to
> my protein. Can anyone direct me to a tool that can renumber the a.a.s
> in my search model, and stub nonidentical a.a.s to Ala? I recall there
> is a program in CCP4 that will renumber, leaving the user to change
> a.a. type, but this problem seams like such a common one that I am
> surprised there is not a utility that would perform both functions.
> Cheers~
>
> ~Justin
>
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