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Select all structures that have exactly one C₅O ring

Enter Current().Count(Rings(5 * ["C"] + ["O"])) == 1 into the Structure Selection panel.

Explanation:

1. Current() returns the structure being tested.
2. Count() function counts occurrences of a specific motif.
3. Rings(5 * ["C"] + ["O"]) is a "Python" shortcut for Rings(["C", "C", "C", "C", "C", "O"]) which represents a ring with 5 C and 1 O atoms.
4. == 1 checks for equality. Other relation operators can be used as well ( >, >=, <, <=, !=).

Select all structures that satisfy multiple conditions

In the Structure Selection panel use the expression (c1) & (c2). For example, all structures that contain more than one C₅O ring and no more than 3 ASP residues is represented by the expression (Current().Count(Rings(5 * ["C"] + ["O"])) > 1) & (Current().Count(Residues("HIS")) <= 3). Due to the associativity rules of the operator &, each condition must be enclosed in the ( ). Or condition is represented by using | operator instead of &.

Select all backbone C atoms that are within 6 angstroms of MAN residue

Enter AtomNames("CA", "CB").Inside(Residues("MAN").AmbientAtoms(6)) into the Atom Selection panel.

Explanation:

1. AtomNames("CA", "CB") represents all atoms names "CA" or "CB".
2. .Inside(...) function says that the motive on the left should be looked for inside another one.
3. Residues("MAN").AmbientAtoms(6) represents all atoms on a MAN residue and all atoms within 6 angstroms around it.

Cluster loaded structures by their common residues

Enter Utils.ResidueHierarchialClustering("name") to the script panel. This will create several descriptors for the loaded structures with these properties:

• For each cluster, two descriptors are added:
  • name_N – all motifs that share at least N residues. If a motif has less than N residues, large cluster index will be displayed (2^31).
  • name_NFP – a list of the common residues. If a motif has less than N residues, “n/a” is displayed.
• Descriptors can be changed using the Structure Descriptors panel.
• There is also an export button in the Structure Descriptors panel.
• Use Group by Descriptor and Sort by Descriptor functions for added effect.

Create a descriptor with residue count

Enter Current().Count(Residues()) and select an appropriate name (say "resCount") in the Descpriptors panel.

Explanation:

1. Current() returns the structure we are computing the descriptor for.
2. .Count(Residues()) counts the residues.

It is possible to count all sorts of things:

• Atoms("C", "N") counts C and N atoms.
• AtomNames("CA", "CB") counts atoms named CA and CB.
• Residues("HIS", "ASP") counts HIS and ASP residues.
• Rings(5 * ["C"] + ["O"]) counts C₅O rings.

This descriptor can also be expanded and further analyzed for example in Excel using the Export menu in the Descriptors panel.

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