General description of the COMO program.
COMO is a new program for molecular replacement calculations, using the combined molecular replacement protocol (L. Tong (1996) Acta Cryst. A52, 782-784). It supports almost all the functionalities of my earlier TF program, which is part of the Replace package (L. Tong (1993) J. Appl. Cryst. 26, 748-751). In addition, COMO supports the calculation of cross rotation functions (by the Crowther fast rotation function) (R.A. Crowther (1972) The Molecular Replace Method, M.G. Rossmann Ed.) that was available as part of the GLRF program (L. Tong and M.G. Rossmann (1990) Acta Cryst. A46, 783-792). In summary, COMO is a complete program for the structure determination by the MR method, starting from a search atomic model. In this regard, COMO can replace the use of the TF program for most calculations.
However, COMO currently does not support the calculations of self rotation functions, locked (self and cross) rotation functions, locked translation functions (L. Tong (1996) Acta Cryst. A52, 476-479), or the contouring of the RF maps. These calculations are done very nicely in the GLRF program.
Combined molecular replacement is a protocol to carry out a limited six-dimensional search, covering both the rotational and translational degrees of freedom, for the solution to a MR problem (L. Tong (1996) Acta Cryst. A52, 782-784). The basic idea behind this is that the correct orientation for the search model will give a relatively high value in the rotation function. However, this orientation may not correspond to one of the peaks in the rotation function. Experiences suggest that this is oftentimes the case, where the correct orientation gives a high RF value, but is 510° away from the nearest peak in the RF. A traditional TF calculation using only the peaks in the RF will likely not succeed in finding the MR solution.
Some of the features that are supported by the COMO program include
Like the Replace package, the input to the COMO program are free-formatted and keyword-based. However, there are also significant differences to the input structure of the COMO program. The inputs are grouped into blocks, and currently the following blocks are supported
The program will perform the relevant calculations at the end of each input block (with the exception of the Model and RF blocks, see below). Consequently, the blocks can be repeated in the input file. For example, one could have the following sequence of blocks for input Model, TF, Model, RF, TF, Solution. The first Model-TF combination defines a molecule with known orientation and searches for its position by TF. The second Model-RF-TF defines a molecule with no known information and carries out both RF and TF calculations. Finally, the MR solutions from both calculations are output with the Solution block.
For the Model block, the calculations are performed immediately after each command, rather than at the end of the entire block. For the RF block, the calculation will generally not be done at the end of the input to this block (but also see the GO command in the RF block). The actual RF calculation will be initiated during the MR calculation as necessary.
The program will produce two kinds of error messages. A Warning error message is given to potential problems with either the user input or other parameters in the calculation. The calculation will continue, but the user should examine the Warning message with some care. A Fatal error message will stop the program execution.
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