Hi,
I am trying to use multiple PDB files using the PMI multiscale modelling protocol. I'm doing it by creating different PMI.states within the main system. Is this the IMP.pmi way to do it?
My script:
data_directory = "../input/" pict_pdb = data_directory + "path/to/pdb1" hg_pdb_model = data_directory + "path/to/pdb2" hg_fasta = data_directory + "path/to/pdb2.fasta"
# Initialize model m = IMP.Model()
# HEMOGLOBIN hg_fasta_seqs = IMP.pmi.topology.Sequences(hg_fasta) hg_pdb_seqs = IMP.pmi.topology.PDBSequences(m, hg_pdb_model)
# PICT PDB pict_pdb_seqs = IMP.pmi.topology.PDBSequences(m, pict_pdb)
# Create System and State s = IMP.pmi.topology.System(m) # defining the root of a hierarchy st_1 = s.create_state() st_2 = s.create_state()
Thanks!
Best,
Altair
On 11/4/20 5:38 AM, Altair Hernández wrote: > I am trying to use multiple PDB files using the PMI multiscale modelling > protocol. I'm doing it by creating different PMI.states within the main > system. Is this the IMP.pmi way to do it?
What are you trying to achieve here? Multistate modeling is used when you have multiple conformations and/or compositions present in your sample, such that your experimental data can only be satisfied by multiple models (e.g. closed/open form, see https://salilab.org/phoq for an example).
You can, of course, use multiple PDB files as input for regular single-state modeling (a typical application would use a separate PDB file for each subunit in a complex). Just list them all in your topology file or Python script.
Ben
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Altair Hernández -
Ben Webb