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13.2 XCONF — Extract Conformation

13.2.1 Syntax

     XCONf {[UNIT] unit} { [ BEST ]     } [ESURF real]
                         { [ WORSt] int }
                         { [NUMBer]     }

13.2.2 Function

The XCONF command reads a conformation from a conformation file, see Conformation File. The conformation can be specified by number, by evaluation ranking, or by accessible surface ranking. Accessible surface ranking was the method used in the paper, R. E. Bruccoleri, E. Haber, J. Novotny, “Structure of Antibody Hypervariable Loops Reproduced by a Conformational Search Algorithm”, Nature 335, 564-568 (1988); Nature 336, 1266 (1988).

The three possible ways of selecting conformations from the file are controlled by the BEST, WORST, NUMBER, ESURF options. If NUMBER is specified, or if neither BEST. WORST, nor NUMBER is specified, then the integer is used as the sequential conformation number in the file. This number may be specified as 0, which means that the reference coordinate set in the conformation file should be used (see Conformation File, for a description). If BEST or WORST is specified and ESURF is not specified, then the integer which follows BEST or WORST gives the rank ordering in evaluation terms. BEST directs the program to use the ordering with the lowest energy first, and WORST directs the program to use the highest energy first. If BEST or WORST is specified and ESURF is specified, then the accessible surfaces of the conformations within ESURF of the minimum will be calculated (regardless of the settings of BEST or WORST, and the selection will be based on the rank order of the accessible surfaces of this subset. This latter selection is controlled by the BEST or WORST keywords. The surfaces are calculated in the context of the entire system.

The conformation file is specified by UNIT operand. unit number. Only those atoms which were constructed in the search are read.

N.B. Make sure that the coordinates of the atoms outside of the constructed atoms are exactly the same as they were when CONGEN was run. Otherwise, the connections between the constructed atoms and their surroundings will be distorted. Also, the program will die if the conformation number is too large.


In these examples, let's assume that the evaluation used in the conformational search was ENERGY.

To select the ninth conformation from a conformation file on unit 60:


To select the second lowest energy conformation from the conformation file on unit 50:


To select the conformation which has the lowest surface area among the conformations within 3 kcal/mole of the lowest energy conformations in the file on unit 43: