running imp with DNA sequence
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
On 12/10/17 1:17 AM, מירב בריטברד wrote: > 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"
1. Looks like you have an offset between your FASTA and PDB files. Your FASTA file reads "TGCA..." but your PDB is "CTGC...". Either fix the FASTA sequence to match or use the pdb_offset field in your topology file (assuming you're using one).
2. PMI assumes all sequences are of proteins by default. If you're calling the API directly, add is_nucleic=True when you call create_molecule(). If you're using a topology file, it doesn't seem to be documented anywhere, but add ',DNA' to the FASTA id in that file (you presumably have "DNA1" right now - just change it to "DNA1,DNA").
BTW, to my knowledge no DNA or RNA modeling has been done with IMP, so you may need to fix some bugs in the code here and there as you proceed.
Ben
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Ben Webb -
מירב בריטברד