IMP-users December 2017

imp-users@salilab.org

2 participants
2 discussions

running imp with DNA sequence
by מירב בריטברד 05 Feb '18

05 Feb '18

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

2 1

Floppy bodies
by Komjati Kornel 30 Nov '17

30 Nov '17

Hi all, My name is Kornel and I am trying to define a protein as a chain of rigid and floppy bodies. With the help of the online manual I worked out how to define rigid bodies, but for floppy bodies I have not found a solution. My sample topology looks like this: |component_name|domain_name|fasta_fn|fasta_id|pdb_fn|chain|residue_range|pdb_offset|bead_size|em_residues_per_gaussian| |CHAIN_A| RIGID_1 |fasta.txt| ID:A |protein.pdb |A| 121,150| 0| 30|0| |CHAIN_A| FLOPPY_1 |fasta.txt| ID:A |protein.pdb |A| 151,180| 0| 5|0| |CHAIN_A| RIGID_2 |fasta.txt| ID:A |protein.pdb |A| 181,220| 0| 30|0| |CHAIN_A| FLOPPY_2 |fasta.txt| ID:A |protein.pdb |A| 221,280| 0| 5|0| And the modeling.py looks like this: m = IMP.Model() topology = IMP.pmi.topology.TopologyReader(topology_file) domains = topology.get_components() rigid_bodies = [["RIGID_1"],["RIGID_2"]] bm = IMP.pmi.macros.BuildModel(m, component_topologies=domains, list_of_rigid_bodies=rigid_bodies) So my question is: what is the correct way to define domains as floppy bodies? Thanks, Kornel

2 1

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IMP-users December 2017