Fig. 7 Preparing the IMP modeling script. (a) Content of the topology file topology.txt. (b) Definition of input
files. (c) Examples of rigid body groups
Table 1
Function of headings from the topology file
Heading
Function
component_name
Name of subunit
domain_name
Subunit identifier for modelling
fasta_fn
Fasta filename
fasta_id
References the subunit sequence listed in specified file
pdb_fn
References the PDB file containing all structures
Chain
References the chain belonging to the subunit in the PDB specified
residue_range
Obtains the atomic position of the residues within range from the PDB
pdb_offset
Offsets the PDB by the number specified
bead_size
Number of residues to represent using a single bead for coarse-graining
em_residues_per_gaussian
Number of components for GMM model generation
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Andy M. Lau and Argyris Politis