Endonuclease PvuII (1PVI) DNA - GATTACAGATTACA
CAP - Catabolite gene Activating Protein (1BER)
DNA - GATTACAGATTACAGATTACA Endonuclease PvuII bound to palindromic DNA recognition site CAGCTG (1PVI) DNA - GATTACAGATTACAGATTACA TBP - TATA box Binding Protein (1C9B)
CAP - Catabolite gene Activating Protein (1BER)
GCN4 - leucine zipper transcription factor bound to palindromic DNA recognition site ATGAC(G)TCAT (1YSA)
GCN4 - leucine zipper transcription factor bound to palindromic DNA recognition site ATGAC(G)TCAT (1YSA)
GCN4 - leucine zipper transcription factor bound to palindromic DNA recognition site ATGAC(G)TCAT (1YSA)
GCN4 - leucine zipper transcription factor bound to palindromic DNA recognition site ATGAC(G)TCAT (1YSA)
GCN4 - leucine zipper transcription factor bound to palindromic DNA recognition site ATGAC(G)TCAT (1YSA)
TBP - TATA box Binding Protein (1C9B)
 

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Analyze

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Analyze the soup

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Atom position - Calculate average positions and RMSFs

Get or set the position of selected atoms , sum up positions to calculate averages and root mean square fluctuations .

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AddPos<Atom|Res|Mol>

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Sum atom positions to calculate average and standard deviation

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AveragePos<Atom|Res|Mol>

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Average atom positions

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Pos<Atom|Res|Mol>

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Set/get atom positions

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RMSF<Atom|Res|Mol>

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Calculate root mean square fluctuations

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Superposition

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Align atoms and calculate RMSDs

Superpose objects based on a selected set of atoms and calculate the resulting RMSDs . Structures can be aligned automatically in the Twinset.

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AlignObj

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Align objects

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RMSD<Atom|Res|Mol|Obj>

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Calculate RMSDs

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Sup<Atom|Res|Mol|Obj>

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Superpose objects

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Contacts

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List contacts and hydrogen bonds

Search for contacts and hydrogen bonds between two selections.

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ListCon<Atom|Res|Mol|Obj>

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List contacts

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ListHBo<Atom|Res|Mol|Obj>

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List hydrogen bonds

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Energy

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Calculate energies

Analyze the overall energy including individual terms, binding energies, solvation energies or formation energies (i.e. heats of formation).

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BindEnergyObj

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Calculate binding energies

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Energy<Atom|Res|Mol|Obj|All>

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Calculate force field energies

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FormEnergy<Atom|Res|Mol|Obj|All>

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Calculate formation energies

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SolvEnergy

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Calculate solvation energy

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Electrostatics

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Calculate electrostatic potentials and charges

Display an electrostatic potential grid inside the periodic cell, sum up the charges in a selection of atoms or calculate the resulting dipole moment .

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Charge<Atom|Res|Mol|Obj|All>

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Set/get the summed up charge

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Dipole<Atom|Res|Mol|Obj>

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Calculate electric dipole moments

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ShowESP

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Show electrostatic potential

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Geometry

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Measure distances, angles, dihedrals and radii

For quick measurements, click on an atom, then hold down <Ctrl> and click on up to three more atoms. When analyzing a molecular dynamics simulation, distances, angles, dihedrals and radii can also be measured from within a macro. The same holds for distances between geometric centers , angles between regression lines and dihedrals between planes fit to groups of atoms.

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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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Rotamers

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Show rotamer distributions

Show the backbone-dependent rotamer distribution for selected residues , or put it directly in the soup.

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ShowRota<Res|Mol|Obj|All>

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Show side-chain rotamers

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Secondary structure - Calculate secondary structure content

List the secondary structure per residue and the overall secondary structure content .

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HideSecStr<Res|Mol|Obj|All>

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Hide secondary structure

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SecStrPar

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Set secondary structure display parameters

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SecStr<Res|Mol|Obj|All>

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Set/get secondary structure

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ShowSecStr<Res|Mol|Obj|All>

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Show secondary structure

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Surface areas - Calculate VdW, molecular and accessible surfaces

Calculations of surface areas are influenced by the current surface environment and the resolution of the surface grid. If a protein has cavities, they can be treated separately.

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FirstSurf<Atom|Res>

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Get first surface atom(s) or residue(s) and area(s)

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Surf<Atom|Res|Mol|Obj|All>

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Calculate surface areas

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Volumes

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Calculate VdW, molecular and solvent accessible volumes

Calculations of volumes are influenced by the resolution of the surface grid .

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Volume<Atom|Res|Mol|Obj|All>

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Calculate volumes

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Soup content - List, count and compare units, get boundaries

List the properties of atoms to objects, including names, numbers and secondary structure, count how many units are contained in a selection, find differences between selections , determine the first and last atom or object spanning a selection and sum up atom masses.

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Compare<Atom|Res>

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Compare selections

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Count<Atom|Res|Mol|Obj>

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Count selected units

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List<Atom|Res|Mol|Obj>

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List selection

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Mass<Atom|Res|Mol|Obj|All>

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Calculate mass

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Span<Atom|Res|Obj>

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Determine first and last unit spanning a selection

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Checks

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Search for errors

Check objects for cis-peptide bonds, wrong isomeres, deviations from naming conventions and incorrectly placed water molecules and calculate the current solvent density . If you have the Twinset installed, you can run over 20 additional checks.

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Check<Atom|Res|Obj|All>

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Check structure quality

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SolvDensity

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Get solvent density in simulation cell