Fix writeNMD residue number overflow for large systems (>9999 residues)

[Copilot]

NMWiz reads resids from NMD files and writes a temporary PDB for VMD to load. The PDB format allocates 4 characters (columns 23–26) for residue sequence numbers, so any value ≥ 10000 overflows into adjacent coordinate columns, causing VMD to misparse atom positions — manifesting as atoms "stretched along a line" or collapsed into a plane.

Change

• prody/dynamics/nmdfile.py — writeNMD: Before writing resids, check max(resnums) > 9999. If exceeded, renumber residues per-chain sequentially starting from 1 (wrapping modulo 9999), and emit a warning. Systems with all residue numbers ≤ 9999 are unaffected.

# Large phage system with 20,412 Cα atoms — residue numbers go up to 20412
writeNMD('anm_modes.nmd', anm[:5], phage.select('calpha'))
# @> WARNING Residue numbers exceed 9999. Renumbering residues in NMD output
#    to be compatible with NMWiz/VMD PDB format (max 9999 per chain).
# Previously: NMWiz would place ~half the atoms at wrong coordinates in VMD
# Now: all atoms render at their correct positions

The renumbering is per-chain so that multi-chain systems (e.g. viral capsids with many subunits, each ≤ 9999 residues) preserve intra-chain relative ordering. The original residue numbers are preserved in the in-memory AtomGroup; only the NMD file output is affected.

[karolamik13]

Checked. See below.

The old code:
$ python test.py
@> Connecting wwPDB FTP server RCSB PDB (USA).
@> Downloading PDB files via FTP failed, trying HTTP.
@> 1tqn downloaded (1tqn.pdb.gz)
@> PDB download via HTTP completed (1 downloaded, 0 failed).
@> 468 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> Hessian was built in 0.28s.
@> 5 modes were calculated in 0.15s.

$ grep '^resids' 1tqn_large_resids.nmd | head
resids 10028 10029 10030 10031 10032 10033 10034 10035 10036 10037 10038 10039 10040 10041 10042 10043 10044 10045 10046 10047

New code:
$ python test.py
@> PDB file is found in working directory (1tqn.pdb.gz).
@> 468 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Hessian was built in 0.21s.
@> 5 modes were calculated in 0.13s.

$ grep '^resids' 1tqn_large_resids.nmd | head
resids 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43

test.py looks like this:

from prody import *
ca = parsePDB('1tqn', subset='ca')
original_resnums = ca.getResnums()
ca.setResnums(original_resnums + 10000)
anm = calcANM(ca, n_modes=5)[0]
writeNMD('1tqn_large_resids.nmd', anm[:5], ca)

[jamesmkrieger]

What happens when you open the nmd file? Does the original give the strange behaviour of atoms on a line and the fixed one not?

[jamesmkrieger]

Yes, I confirm it works.

On main, your code gives this

On the fix branch, we get this