Syntax

NOE { <noe-statement> } END

is invoked from the main level of X-PLOR.

<noe-statement>:==

ASSIgn

<selection> <selection> <real> <real> <real> adds a distance restraint between the two selected sets of atoms to the NOE database. The interpretation of the real numbers depends on the particular type of restraining function (see Section 18.3). For the POTEntial=BIHA, SQUA, and SOFT options the <real> numbers are d, , and (see also Section 18.4) (default: none).

ASYMptote

<*class*> <real> is the slope c of the asymptote of the soft-square function (Eq. 18.10) (default: 0).

AVERaging

<*class*> R-6 | R-3 | SUM | CENTer specifies the averaging method (Section 18.2) (default: R-6).

BHIG <*class*> <real>

specifies the height of the potential barriers in the high dimensional restraining function (Eq. 18.15), only for POTEntial=HIGH (default: 0.01).

CEILing=<real>

specifies the ceiling value for energy constants; it applies to most restraining functions (Section 18.3) (default: 30).

CLASsification <class-name>

partitions the distance restraints database; it applies to all subsequent ASSIgn entries until another CLASS entry is issued (default: NIL).

COUNtviol <class>

counts violations in class and stores the smallest violation in the symbol ``$RESULT"; action is taken when this statement is issued.

DISTribute <class1> <class2> <real>

distributes distance restraints between two classes: the restraint will be put in <class1> if the distance is less than r (the specified real number); it will be put in <class2> if the distance is greater than or equal to r. Action is taken only when this statement is issued.

MONOmers

<*class*> <integer> specifies the number of monomers for the AVERage=SUM option (Section 18.2) (default: 1).

NCOUnt

<*class*> <integer> specifies number of assign statements for the high dimensional restraining function (Eq. 18.15); only even values are allowed (default: 2).

NREStraints=<integer>

is a required parameter that specifies the maximum expected number of distance restraints. It has to be greater than or equal to the actual number of restraints. The parameter is used to allocate space dynamically for the restraint list (default: 200).

POTEntial

<*class*> BIHArmonic | SQUAre | SOFTsquare | SYMMetry | HIGH | 3DPO specifies the restraining function (Section 18.3) (default: BIHArmonic).

PREDict

{ <predict-statement> } END can be used to predict interproton distances based on the Cartesian coordinates in the MAIN coordinate set. It lists all distances between the FROM and the TO selections of atoms that are within the range CUTOn ... CUTOff. Distances are averaged over the GROUps that are defined in the topology file for each residue (see Section 3.1.1). Current distance restraint information is overwritten by this statement.

PRINt THREshold=<real>

prints distance violations greater than the specified real number. This statement also declares two symbols, $RESULT and $VIOLATIONS, which correspond to the rms deviation of the distances and the number of violations greater than the THREshold value, respectively. The definition of the deviation depends on which restraining function is specified: in the case of the SQUAre-well and SOFTsquare functions, the deviation refers to the difference between the actual distance and the upper or lower bound if the distance is outside the error range; in the case of the BIHArmonic function, the deviation refers to the difference between the actual distance and the target distance. (A more precise definition is given by in Section 18.3.)

RAVErage

<*class*> { <raverage-statement> } END This statement is used to compute a running-average of each interproton distance. When the running average is turned on, an average distance is accumulated for each interatomic distance defined within the class of noe restraints. This running-average is updated at each time-step in molecular dynamics, and at each step in energy minimization. This facility is described in more detail in Section 18.11.

RESEt

erases the current NOE database.

RSWItch <*class*> <real>

is the switch parameter between the square-well and the asymptote (Eq. 18.10) (default: 10).

SCALe <*class*> <real>

scales the restraint class (Section 18.3) (default: 1).

SOEXponent <*class*> <real>

is an exponent; it is for the soft-square function (Eq. 18.10) (default: 2).

SQCOnstant <*class*> <real>

is an additional scale factor; it is for the square-well or soft-square function (Eqs. 18.8 and 18.10) (default: 20).

SQEXponent <*class*> <real>

is an exponent; it is for the square-well or soft-square function (Eqs. 18.8 and 18.10) (default: 2).

SQOFfset <*class*> <real>

applies a negative offset value to all upper bounds of the specified class(es). This offset is applied to the square-well or soft-square functions (Eqs. 18.8 and 18.10) and to the bounds used by distance geometry (see Chapter 19) (default: 0).

TAVErage

<*class*> { <taverage-statement> } END This statement is used to turn on or off time-averaged noe restraints. This facility is described in more detail in Section 18.11.

TEMPerature=<real>

is the temperature in K; it is only for the biharmonic function (Eq. 18.6) (default: 300).

<predict-statement>:==

CUTOff=<real>

specifies an upper limit for acceptable interproton distances (default: 10.0 Å).

CUTOn=<real>

specifies a lower limit for acceptable interproton distances (default: 0.0 Å).

FROM=<selection>

specifies an atom selection (default: none).

TO=<selection>

specifies an atom selection (default: none).

<raverage-statement>:==

ON

Turns on the running-average.

OFF

Turns off the running-average.

EXPOnent=<integer>

Specifies the exponent used in distance--averaging (default: 3).

RESEt=<CURRent,CONStraint>

Resets the distance running-averages setting the new initial values to either the current distances (CURRent) or the target distances in the NOE database (CONStraint).

<taverage-statement>:==

ON

Turns on time-averaged restraints.

OFF

Turns off time-averaged restraints.

TAU=<integer>

Specifies the exponential decay constant (in number of time steps) used in the averaging (default: 1000 time steps).

EXPOnent=<integer>

Specifies the exponent used in distance--averaging (default: 3).

FORCe=<CONServative,NONConservative>

Specifies whether a conservative or non-conservative force is used in time-averaging (default: CONServative).

RESEt=<CURRent,CONStraint>

Resets the distance time-averages setting the new initial values to either the current distances (CURRent) or the target distances in the NOE database (CONStraint).

• Requirements