Hi,
Part of the structure that I am trying to find is a DNA sequence and not a
protein. I have pdb with the DNA part, and I create a fasta file (both
attached) but when I am running IMP, it's write this warning:
"BuildSystem.add_state: -------- domain 0 of molecule DNA_1 represented by
pdb file
/cs/labs/dina/meravb/CENP_new_cross_links_and_PDB_renumbered/pdb_files/Nuc_numbering_fixed_in_map.pdb
WARNING: Replacing sequence residue 1 "THR" with PDB type "DC"
WARNING: Replacing sequence residue 2 "GLY" with PDB type "DT"
WARNING: Replacing sequence residue 3 "CYS" with PDB type "DG"
WARNING: Replacing sequence residue 4 "ALA" with PDB type "DC"
WARNING: Replacing sequence residue 5 "GLY" with PDB type "DA"
WARNING: Replacing sequence residue 6 "ALA" with PDB type "DG"
WARNING: Replacing sequence residue 7 "THR" with PDB type "DA"
WARNING: Replacing sequence residue 8 "THR" with PDB type "DT"
WARNING: Replacing sequence residue 9 "CYS" with PDB type "DT"....."
How can I run in imp in a way that will recognize the DNA?
Thanks,
Merav
