In case of an AlphaFold Uniprot Accession Id query, this viewer previews the AlphaFold model .cif file downloaded directly from the database. This enables the view of the Confidence Score provided by AlphaFold. Otherwise: The PDBeurope Mol* 3D viewer has issues at rendering non standard amino acids, so it loads the original PDB file from which were removed any non-standard amino acid listed below:

Code	Full name
ASX (B)	asparagine or aspartic acid
GLX (Z)	glutamine or glutamic acid
CSO (C)	S-hydroxycysteine
HIP (H)	ND1-phosphohistidine
HSD (H)	prototropic tautomer of histidine, H on ND1 (CHARMM)
HSE (H)	prototropic tautomer of histidine, H on NE2 (CHARMM)
HSP (H)	protonated histidine
MSE	selenomethionine
SEC (U)	selenocysteine
SEP (S)	phosphoserine
TPO (T)	phosphothreonine
PTR (Y)	O-phosphotyrosine
XLE (J)	leucine or isoleucine
XAA (X)	unspecified or unknown

We keep only the classical 20 amino acids (the 'protein' flag selection of ProDy): http://prody.csb.pitt.edu/manual/reference/atomic/flags.html#protein.
ALA, ARG, ASN, ASP, CYS, GLN, GLU, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, and VAL

This figure represents the number of times each SWORD partition is detected.
A partition represents a Protein Unit (PU), so the histogram essentially represents the number of times each PU is found among all SWORD alternative partitionings.
Bar tips are labelled by the PU size.
Bars follow the protein sequence numerotation, going from left (smallest delineation boundary / beginning of protein sequence) to right (highest boundary / end of the protein sequence).

The histogram represents the number of times each domain is found by SWORD among all alternative partitions.

Bars are ordered by frequency, from left to right, from most frequent to less frequent respectively.

start-end A black colored badge represents a Protein Unit that was not selected in SWORD2 output.

start-end A colored badge represents a Protein Unit that was selected in SWORD2 alternative partitionings. The same color is used for each PU accross the whole results page of SWORD2 for convenience.

This measure is similar to the Hirsch index (h-index) used in scientometrics, except that it is based on the decomposition quality.

The viewer displays several elements:

• Sequence: the amino acids sequence of the chain of the queried protein.
• Secondary structures: the secondary structures of the protein are assigned using DSSP program.
• SWORD2 partitions (Optimal & Alternatives): determined by SWORD2 and coloured in line with the other results of the page, meaning that all the Protein Units belonging to the same Domain share the same color.
• Protein Units: determined by SWORD2 and coloured in line with the other results of the page, meaning that all the same Protein Units share the same colour.
• Junctions: correspond to the hinges between either Protein Units or Domains determined by SWORD. They are defined as the boundary positions of Protein Units and Domains.
• Frequency: represents the raw frequency, standardized by the total number of domain delineations produced.
• Weights: represents the frequency weighted by delineation quality and standardised by the total number of domain delineations produced.

Z-score

The Z-score is calculated over 2000 random protein decoys and measures how much a Domain or Protein Unit deviates from the random mean value of foldability-likeliness in terms of standard deviation. For example, a Z-score of -3 means that the Domain or Protein Unit deviates from the random mean value by 3 standard deviations, which means that the structure is far from being random and therefore has an increased probability of being an autonomous structural unit.

AUL - Autonomous Units Likelihood

AUL is a percentage based on the Chebyshev's Theorem which estimates the minimum proportion of observed protein structures that fall within a specified number of standard deviations from the mean.
We calculate the percentage according to the following conditions: $$ \begin{cases} 0 & |k| \lt 1 \\ (1 - {1 \over k^2})\times100 & |k| \ge 1 \end{cases}$$ where k equals the number of standard deviations: Z-score.
For example, an AUL of 81% (Z-score of -2.3) means that at least 81% of the observed structures fall inside 2.3 standard deviations.