IMP-users February 2018

imp-users@salilab.org

2 participants
2 discussions

Rigid body from multiple chains
by Komjati Kornel 26 Feb '18

26 Feb '18

Hi, I would like to model a protein with multiple chains (A,B,C,D) as an entire rigid body. Unfortunately I cannot find a way to do this, it seems like that a rigid body can only contain one protein chain. Is there any method to create my desired model? Thanks in advance, Kornel

2 1

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

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IMP-users February 2018