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Using Atomic Constraints

Constraints are used in several modules in Simulate to select for structures that satisfy the required criterion from the user-supplied set of constraints. The constraints are listed in a text file. Constraints are a set of one or more binary pairs that define the conditions to be tested and used to accept structures that satisfy all supplied conditions.

There are several keywords that define the syntax to define constraints.


NOTES:

Format for constraints between two object definitions:

    (1)     :   (2) 

SEG RESID NAME  : SEG RESID NAME : DISTANCE : TYPE1 : TYPE2
    Example values:

    SEG RESID : SEG RESID NAME : DISTANCE : COM : ATM
    SEG : SEG RESID NAME : DISTANCE : ATM : ATM
    SEG : SEG : DISTANCE : ATM : ATM
    SEG RESID : SEG : DISTANCE : ATM : ATM

You can mix and match the granularity of each component of a distance constraint.

    SEG1 33-37 : SEG2 : 27.0 : ATM : ATM
    SEG1 21-28 : SEG2 1321-1359 CA : 8.0 : ATM : ATM

With the ATM ATM selection ALL atoms in residues 21-28 in SEG1 have to be within ALL CA atoms in residues 1321-1359.

    SEG1 21-28 : SEG2 1321-1359 CA : 8.0 : COM : COM

With the COM COM selection the center of mass of residues 21-28 in SEG1 have to be within the center of mass of ALL CA atoms in residues 1321-1359.

    SEG1 33-37 : SEG2 : 27.0 : ATM : COM
    SEG1 21-28 : SEG2 1321-1359 CA : 8.0 : COM : COM

    . . . etc.

NOTE: you can not have a RESID or RESID & NAME w/o SEG you can not have a NAME w/o SEG & RESID etc.

The key delineators are the hypen between resid numbers and the colons between selection 1, selection 2, distance, and the type definitions.

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