Home > Libraries > Loaders > read_pdb.m

iFit/read_pdb

PURPOSE ^

result = PDB_Geometry(fname) read a PDB file

SYNOPSIS ^

function result = read_pdb(name)

DESCRIPTION ^

 result = PDB_Geometry(fname) read a PDB file

       Compute SAXS characteristics of molecule described in file fname.
       Input -     fname --> valid PDB file.
       Output      result --> structure with fields describing SAXS profile.

       result.Rg_charge = Radius of gyration of molecule weighting
           each residue by its charge.
       result.Rg_volume = Rg weighting residues by their volume.
       result.Rg_contrast = Rg weighting by their contrast above the
       solvent density (eg. charge - volume * rho_water).
       result.Rg_sphere = Rg if protein were densely packed into a sphere;
       result.Ne = Total charge of protein.
       result.Ne_excess =  Excess charge relative to solvent. 
       result.Protein_Density= Density of protein relative to solvent.
       result.Protein_Volume= Total volume of protein.

       result.pofr = Pair correlation function of protein p(r)
                       p(|r|) = integral of rho(r+r')rho(r') for all r' and averaged over 
                           all diretions r.  Normalized so integral of
                           p(|r|) is one.
                           r  - pofr(:,1)
                           p(r) - pofr(:,2)

       result.Ivq = Intensity versus q for protein I(q)
                       q = Ivq(:,1); I = Ivq(:,2)
 See also: read_xyz, read_poscar, read_mrc

CROSS-REFERENCE INFORMATION ^

This function calls: This function is called by:
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