Linear morph between two PDB files

Quick start

This server takes two structures, finds equivalent pairs of atoms, and interpolates coordinates of intermediate structures on a line between equivalent atoms. The output is a single file containing the two original models and the intermediates. The header of the file contains information about the interpolations useful for validation and troubleshooting (such as how many atoms pairs were matched, how many atoms were ignored, what the maximum and average distance of atom pairs was).

File1:

File2:

# of intermediates:

How do you want to match equivalent pairs of atoms?
  1. Match chain ID, residue number and atom type:
  2. Match residue number and atom type, ignoring chain ID:
  3. Take atoms sequentially from each file
Please keep unmatched atoms from the first file

Test case

Input file 1: f1.pdb
Input file 2: f2.pdb
Intermediates: 8
Matching: by residuenumber, ignoring chain ID Result file: morph2.pdb

Input files

All remarks in the input file are ignored. The program only reads coordinates (i.e. all lines starting with "ATOM" or with "HETATM".

Matching atom pairs

Method 1:sequential

Each atom in the first file is matched up sequentially with each atom in the second file, regardless of the chain ID, residue number, atom type, and atom number. If file 1 has more atoms than file 2, the extra atoms are copied without interpolation into the output file. If file 2 has an excess of atoms, these are ignored. Statistics in the REMARK lines of the output give the details.

Method 2:residue number

Atoms are matched by residue number and atom type. Chain IDs are ignored in the matching process. If an input file has multiple atoms with the same residue number and atom type (but different chain ID, different model number, different alternate conformation), the atom read first in the file is used. Atoms in file 1 that have no match in file 2 are copied into the output without interpolation. Atoms in file 2 that have no match in file 2 are ignored.

Method 3:chain ID and residue number

Atoms are matched by chain ID, residue number and atom type. If an input file has multiple atoms with the same chain ID, residue number and atom type (but different model number, different alternate conformation), the atom read first in the file is used. Atoms in file 1 that have no match in file 2 are copied into the output without interpolation. Atoms in file 2 that have no match in file 2 are ignored.

Coordinates in output

Remarks in output file