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Moloc: Molecular Modelling on UNIX Workstations: 12 Protein and C-alpha Utilities [pca]

Protein and C-alpha Utilities [pca]

Special tools are provided to handle peptides and proteins. This can be done on two levels of complexity. On the coarser level entire amino acids are treated as units. These are represented as single points, but also carry information about torsional angles. Such entries must be handled with a separate set of tools which are provided in the Calf building module (option c). On the finer level, all atoms are included and the normal modelling tools apply. In addition special testing and refinement utilities are provided (option p). These two types of structures can be mutually generated from each other (options k, q, a and b).
Furthermore, dedicated tools for structure building in protein crystallography are implemented, such as real space refinement, structure scanning etc.

C a Building [cab]

When building Calf structures one uses a similar repertoire of activities as in small-molecule building, at least for the basic steps. However, a couple of possibilities have no small-molecule counterpart. In addition to the pure building facilities, a couple of auxiliary options are placed within this menu.

Secondary structure search

For a set of consecutive residues a database can be searched for conformations fitting the given positions optimally. Optionally the agreement of the backbone dihedral angles can also be included in the score function.

Build Database for Backbone Conformations

The database is built up by reading in protein structures from disc files. Only coordinates of the Calfs and the values for the backbone dihedrals are kept.

Homology Building [bhm]

From a known protein structure a structural model for a homologous protein can be built, provided a sequence alignment is given. The alignment must be given in a file in which each line is interpreted as single letter code sequence of the original protein or of the homologous one, provided the line starts with either #1 or #2 respectively. All other lines are interpreted as comments. In case of deletions or insertions, missing residues must be indicated by a dot. For deletions the program simply connects the two ends of the last and first residues present. Insertions are positioned near a circle of appropriate size. It is understood that these regions are subjected to subsequent energy minimization within the Calf force field to generate acceptable geometries. The program automatically generates a user set which contains the residues in the homologous structure, which may be kept fixed under a subsequent minimization. This set must be activated (definition of fixed residues) prior to minimization.

Moving a C a Structure [camv]

A selection of options useful in positioning a Calf structure into a electron density map.

Real Space Refinement [rsr]

Real space refinement to fit segments of all-atom (protein) structures to a given electron density map can be performed here.

Protein refinement, tests etc. [prp]

This tool offers a set of options which are specific to biopolymer molecules (mostly proteins). Structures can be tested, refined, forged and displayed in color coded fashion.

Mend and Modify Proteins

Proteins in all atom form can be modified here with respect to side chains. Incomplete side chains can be completed. Side chains can be replaced by others.

Add Isolated Atoms (Water)

New water molecules can be inserted by picking anything with the left mouse button. The new atoms appear in the center of the visibility volume. If an other atom is nearby, no water is inserted and a corresponding message is issued. Picking with the middle button removes the picked atom, if it is an isolated oxygen. Insertion is silenced if the move option a is activated!

Scan Isolated Atoms, Residues

There are two similar menus for scanning through isolated atoms or residues. For atoms:

There is always a currently selected atom, which carries its label. All other isolated atoms are only marked. Picking an isolated atom makes it the selected one. Pressing the shift key and operating the mouse moves the currently selected atom about.

For residues:

There is always a currently selected residue, which carries its label at the Calf atom. By default the average B- factor is calculated. If a map is specified, the user can have map-gradient and RSCC (real space correlation coefficient) values evaluated as well.

Refinement of Protein or DNA

This menu facilitates the setup of an energy optimization calculation for large polymeric systems. Automatic sets on proteins and nucleic acid can be held fixed (stationary) or be subjected to positional constraints as a whole. Upon entering this option, the entries to be refined together must all be in the active state.

Protein Tests [tst]

Measured or modelled protein structures can be checked here for various stereochemical and energetic properties. Checks are performed entry-wise. Written results can be output to a file.

Energy tests for proteins [etst]

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