Edit - Change content and properties of the soup

CAP - Catabolite gene Activating Protein (1BER)

Endonuclease PvuII bound to palindromic DNA recognition site CAGCTG (1PVI)

GCN4 - leucine zipper transcription factor bound to palindromic DNA recognition site ATGAC(G)TCAT (1YSA)

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Change content and properties of the soup

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Undo and redo changes

Undo and redo a number of changes up to the maximum undo-level.

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Redo
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Redo changes

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Undo
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Undo changes

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UndoLevels
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Set number of undo levels

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Objects
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Center, transform, transfer, remove, add and delete

Center objects for more intuitive mouse rotations, transfer them on top of another object , transform the atom coordinates, remove them temporarily from the soup (e.g. to exclude them from simulations), bring them back and delete them partly or entirely.

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Add<Obj|All>
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Add objects to the soup

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Center<Atom|Res|Mol|Obj|All>
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Center atoms

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Del<Atom|Res|Mol|Obj|All>
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Delete atoms

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Remove<Obj|All>
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Remove objects from the soup

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Transfer<Obj|All>
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Transfer objects into another coordinate system

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Transform<Obj|All>

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Transform objects

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Split points - Edit split points, split and join entire objects

Split points correspond to 'TER' entries in PDB files. Add or delete them , or split entire objects into multiple child objects, joining them again later.

Add bonds between certain atoms, change the order of existing bonds, find bonds automatically , assign the bond orders automatically, change bond orders to the Kekule or resonance form , and delete them again.

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AddBond
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Add covalent bonds

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DelBond
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Delete covalent bonds

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KekulizeBond
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Remove fractional bond orders

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Link<Atom|Res|Mol|Obj|All>
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Find bonds automatically

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ResonateBond
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Introduce fractional bond orders

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SwapBond
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Swap order of covalent bonds

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TypeBond
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Assign bond orders automatically

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Building
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Build atoms to molecules, oligomers, crystals and loops

Swap chemical elements , atom positions, residue side-chains and entire objects. Create individual atoms , or residues, build loops (including the loop database) or entire proteins, extending them at the C-terminus , possibly adding missing oxygens and protection caps. To prepare a molecular dynamics simulation, clean the structures. When looking at oligomers, duplicate objects, use the BIOMT transformations in the PDB file to create the biological oligomeric state or add the crystal symmetry related copies .

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AddCap<Obj|All>
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Add N/C-terminal capping groups

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AddRes
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Add terminal residue

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AddTer<Obj|All>
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Add C-terminal oxygens

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BuildAtom
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Build single atom

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BuildLoop
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Build central or terminal loop

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BuildLoopDB
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Build loop data base

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BuildMol
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Build peptide chain

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BuildRes
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Build single residue

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Clean<Obj|All>
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Clean objects for molecular dynamics simulation

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Crystallize<Obj|All>
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Crystallize objects to fill the unit cell

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Duplicate<Obj|All>

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Duplicate objects

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Oligomerize<Obj|All>
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Oligomerize objects to generate the biologically active form

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SwapAtom
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Swap chemical element of atoms

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SwapObj
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Swap two objects in the list

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SwapPosAtom
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Swap atom positions

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SwapRes
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Swap residue side-chains

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Geometry
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Set or optimize distances, angles and dihedrals

The quickest way of setting distances, angles and dihedrals is to mark up to four atoms with the mouse and click on Geometry in the atom context menu. It is always the last atom (marked with red fireflies) that moves. The geometry of small molecules can be optimized using semi-empirical quantum chemistry . In the Twinset, you can also regularize the covalent geometry.

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Angle
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Set/get angle between atoms

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Dihedral
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Set/get dihedral angle between atoms

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Distance
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Set/get distance between atoms

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GroupAngle
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Get angle between two atom groups

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GroupDihedral
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Get dihedral angle between two atom groups

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GroupDistance
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Get distance between two atom groups

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Optimize<Res|Mol|Obj|All>
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Optimize molecular geometry

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Radius<Atom|Res|Mol|Obj|All>
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Calculate the VdW radius

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Regularize<Obj|All>
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Regularize covalent geometry

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Sampling
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Search conformational space

Possible side-chain rotamers or domain movements can be analyzed by sampling dihedral angles (internal coordinates), while protein flexibility is best looked at in cartesian space by sampling loops or using Bert de Groot's CONCOORD plugin (currently Linux only). Apply CONCOORD only to energy-minimized structures without bumps, otherwise you may run into convergence problems.

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SampleDih
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Sample dihedral angles

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SampleLoop
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Sample central or terminal loop

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Surface environments - Define the context of surface analysis

To show or calculate partial surfaces, add or remove atoms to/from the surface environment.

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AddEnv<Atom|Res|Mol|Obj|All>
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Add to environment for surface calculations

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RemoveEnv<Atom|Res|Mol|Obj|All>
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Remove from environment for surface calculations

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Hydrogens
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Add, swap and delete

Add missing hydrogens at default positions and use an energy minimization to place them correctly. Change their order within the residue and delete them when needed. In the Twinset, you can also optimize the hydrogen bonding network .

Quickly delete all water molecules in an object.

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DelWater<Obj|All>

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Delete all water molecules

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Names and numbers - Set or get properties of atoms to objects

Change or retrieve names of atoms, residues, molecules, segments and objects, reorder objects in the scene and change the residue numbers, including insertion codes. You can also change the Occupancy and B-factor of individual atoms.

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BFactor<Atom|Res|Mol|Obj|All>
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Set/get the B-factor

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Name<Atom|Res|Seg|Mol|Obj>
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Set/get names of objects, segments, molecules, residues and atoms

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Occup<Atom|Res|Mol|Obj|All>
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Set/get the occupancy

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Prop<Atom|Res|Mol|Obj|All>
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Set/get the property value

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Renumber<Obj|All>

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Renumber objects

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RenumberRes
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Renumber residues