This input block defines the information on the atomic model, including atomic coordinates, rotation and translation operations on the coordinates, and flag (status) of the atomic coordinates.

        In contrast to other input blocks, the commands in this block are executed as soon as they are read in. Therefore, the order of the commands can be crucially important for this input block. For example, if an overall B need to be assigned to all the atoms, the boverall command must be given before the input command. Another consequence of this immediate action is that an individual command can be repeated in the input file.

        The maximum number of atomic models that can be saved by the program at one time is currently 8. However, different models that have been input to the program can be merged with the append command, thus freeing room to handle additional molecules. The different models can be defined with a single input block, by repeating the input command several times in the block for example. Alternatively, separate input blocks can be used, one for each input file.

        Most of the commands for this input block (add, center, chain, flag, input, rotate, translate and others) apply only to molecule #1. These commands are sufficient to completely define a molecule. If more than one molecules are involved in the calculation, each molecule should be individually defined and the information can then be stored into another molecule before the input of the next molecule.

        The commands in this input block are generally similar in definition to the options of the COORdinate command in the TF program. However, one significant difference is the copy command, which in the current program specifies the number of copies of a model in the asymmetric unit. The old copy command, which duplicates the information for a given molecule, is now called duplicate.

        Note that the orthogonalization convention and the unit cell parameters must have been defined before this block is input.

        Remember that the following general input commands can also be used in this input block - comment, echo, and title.

        This specifies a number by which the residue numbers in molecule #1 will be incremented. The residues must be numbered either numerically or with one heading or trailing letter. For example, adding 300 to the residue numbers 225, 225A, and A225 will produce 525, 525A, and A525, respectively. The maximum number that can be added at one time is 9000. To specify a larger number, for example 9500, repeat this command --

   add 9000
   add 500

   or

   add 5000
   add 4500

        This specifies whether the program will keep only a poly-alanine model for the search atomic model. The program will keep all atoms named N, CA, C, O, and CB, and rename the residue to ALA. The default is for full atomic models. Be sure to turn this off before reading the next full atomic model.

        This will append the information present for molecule #1 to molecule N. Molecule #1 is then initialized, ready for the input of the next molecule. The flag for the new molecule will be taken from that for molecule N. The center of the new molecule will be calculated over all the atoms.

        This specifies an increment value to the atomic temperature factors as they are read in.

        This defines an overall value that replaces the atomic temperature factor values as they are read in. BOVER defaults to 0, meaning the original B values from the input file will be kept.

        This defines a temperature factor value for those atoms with a temperature factor of 0 in the input file. BZERO defaults to 30.

        For rotation function calculation, the model is placed in a large P1 cell, normally cube-shaped. The input here defines the size of this cell, as the length of the edge of the cube. By default, the program will determine the optimal size of this unit cell automatically, based on the atomic model.

        This centers molecule #1 to the specified position. If no center position is given in the command, the program will place the center at (0, 0, 0). The interpretation of the center position depends on the parameter CORTYP, and see the type command for a definition of the supported types.

        The program saves the atomic positions in de-orthogonalized fractional coordinates.

        This assigns a chain name to the atoms in molecule #1.

        This defines how mnay copies of molecule #1 are expected in the asymmetric unit. This information is used only for the search of additional molecules.

        This duplicates the information for molecule number MOL1 to MOL2.

        This terminates the input to this block. As the commands are executed as soon as they are input, no additional calculations will be done at the termination of the input.

        This defines the name of the file that contains the coordinate file names of the family for molecule #1. If family information is input, the input command should not be given.

        This assigns a flag to molecule #1, which essentially defines the status of the atomic model. Currently supported flags are---

• T - The molecule has known orientation and position. This molecule will be stationary during the translation searches. Molecules with this flag are the solutions of the MR problem and will be output with the solution block.


• R - The molecule has known orientation but unknown position. The position of this molecule can be located during TF calculation (see flag command in TF input block). There can be more than one molecules that carry this flag. The program will locate them sequentially. Family information is not allowed for this type of molecules, neither is the specification of multiple copies.


• C - The molecule has known orientation but unknown position. However, unlike the R flag, the orientation information is given in the form of a rotation function map. The program will select rotation angles from this map and locate the molecule in the unit cell if requested. Therefore, only one molecule can carry the C flag at a time.


• U - The molecule has unknown orientation and unknown position. The program will calculate a rotation function for the model, and then use the RF information to locate it in the unit cell.


• X - The molecule will be ignored by the program. This is the default state for an input molecule.

        This specifies which HETATM residues in the input file will contribute to the calculation. The default will keep the seleno-Met residues, if they are called MSE. Additional residue names can be specified with this command. Those residues that are not included by the HETATM residues as defined this way will be assigned occupancies of 0, and will not contribute to structure factors. But they will be carried along during the calculation.

        This inputs the atomic coordinates in file CORFIL to molecule #1. If there are atoms already present in molecule #1, the input coordinates will be appended to the existing ones. The file is assumed to the in the PDB format, in orthogalized Angstrom coordinates.

        NOTE that in order for the program to automatically assign file names for the RF and TF output maps, it is best to have the coordinate input file names to end with '.pdb' or '.PDB'.

        This merges the information for molecule numbers MOL1 and MOL2. For residues that are common between MOL1 and MOL2 (same residue number and same residue type), atomic coordinates from MOL2 will be used. Chain name is ignored in this comparison, and the final chain name will be taken from MOL1. The merged molecule is stored in number 1. Therefore, neither MOL1 nor MOL2 can be 1.

        This retrieves the atomic parameters stored in molecule number N to number 1. Molecule number N is then initialized.

        This will rotate the atoms in molecule #1 around a certain position by the specified angles (A1, A2, A3). ANGTYP specifies how the rotation angles should be interpreted -- E for Eulerian or P for Polar angles. The rotation will be carried out around the center specified by X, Y, Z. If the center is not supplied, rotation will be carried out around the center-of-mass of the molecule. The interpretation of rotation center depends on the current definition of coordinate type.

        This stores the atomic parameters in molecule #1 in number N. Molecule #1 is then initialized, ready for the input of the next molecule.

        This swaps the information for molecule numbers MOL1 and MOL2.

        This will apply a crystallographic symmetry operation to molecule #1. The number of the symmetry operation (in the same order as that in the International Tables, but check the program print files to be sure) is given by ISYM. The lattice centering operation number is given by ICS. The translation vectors (full unit cell lengths) are given by IX, IY, IZ.

        Atoms in molecule #1 will be translated by the specified vector. The type of the vector is given by CORTYP.

        This specifies the type of the atomic coordinates. The supported types are ---

• DF - De-orthogonalized fractional coordinates. These are the traditional fractional coordinates.


• DA - De-orthogonalized Angstrom coordinates. The program will divide by the unit cell lengths to derive the fractional coordinates.


• OA - Orthogonalized Angstrom coordinates. The program will multiply by the de-orthogonalization matrix based on the crystal unit cell parameters to derive the fractional coordinates.

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