extracted PDB structure have broken peptide bonds

[anamika2501]

Dear Authors and team
I have used deeptime and pyemma both for constructing MSM, after PCCA I fetched the representative structure, but somehow the peptide bond between two of the residues is broken in all three structures.

here is the code

frame_set = set()

for i in range(nstates):
frames = np.where(metastable_traj == i)[0]
if len(frames) > 0:
frame_set.add(frames[0])

frame_set = sorted(frame_set)

current_index = 0
global_index = 0

for chunk in md.iterload('md_com.xtc', top='protein_only_com.pdb', chunk=100):

for frame in chunk:

    if global_index in frame_set:
        frame.save_pdb(f"pcca_state_{current_index+1}.pdb")
        print(f"Saved representative structure: pcca_state_{current_index+1}.pdb")
        current_index += 1

    global_index += 1

[clonker]

Hi @anamika2501,

The broken peptide bonds are most likely caused by periodic boundary conditions in your trajectory.
You should fix this before running any analysis.

MDTraj has an image_molecules utility:

traj = md.load('md_com.xtc', top='protein_only_com.pdb')
traj.image_molecules(inplace=True)

Then use the corrected trajectory for both your MSM/PCCA analysis and structure extraction. Also worth checking that protein_only_com.pdb has the correct topology (matching atom count and ordering) for md_com.xtc.