How to renumber a protein structure sequence based on a full length protein sequence?

[Andrew Orry]

Q.

How to renumber a protein structure sequence based on a  full length protein sequence?

A.

You need to make an alignment between the protein structure sequence and the full length sequence then use the command below - documentation is here:

http://www.molsoft.com/man/icm-commands.html#align-res-numbers

align number ms_chainsToBeRenumbered seq_master [ i_offset ] 

Here is an example:

seqmaster = Sequence("ACDEFGHIKLMNPQRST") 
 build string   "DEFGH-----PQRST"  # dashes are skipped    
 make sequence a_1 name="seqmodel"   # sequence is auto-linked 
 a = Align(seqmodel,seqmaster)       # linked alignment 
 align number a_1 seqmaster 
 # Info> residues of a_def.m renumbered by sequence 'seqmaster' from alignment 'a'    
 display residue label