[ccp4bb] A tool for MR that renumbers and replaces amino acids of your search model
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
Re: [ccp4bb] A tool for MR that renumbers and replaces amino acids of your search model
I believe FFAS03 will renumber aa's based on the sequence you plug into it, and then give you two choices - complete replacement of all residues, or just the exact matches and stub to serine for the others. cheers, On Thu, Feb 3, 2011 at 8:11 AM, Justin Hall hallj...@onid.orst.edu 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 -- Amy K. Wernimont, PhD Structural Genomics Consortium University of Toronto MaRS South Tower, Suite 705 101 College Street Toronto, Ontario Canada M5G 1L7 Tel: 416.978.1859
Re: [ccp4bb] A tool for MR that renumbers and replaces amino acids of your search model
CHAINSAW retains conserved amino acids but prunes nonconserved residues to the C-beta or C-gamma atom. PDBSET can renumber I think Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3, Campus Cantoblanco E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.researcherid.com/rid/B-3678-2009 On 3 Feb 2011, at 14:11, 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
Re: [ccp4bb] A tool for MR that renumbers and replaces amino acids of your search model
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
