U.S. flag

An official website of the United States government
  next up previous contents index  Xplor-NIH home Documentation

Next: Refinement Using Time-Averaged Distance Up: Distance Restraints Previous: 3D NOE-NOE Example

Example for a High Dimensional Restraining Function

The following example shows how to set up the high dimensional restraining function (Eq. 20.17) as described by Habazettl et al. (1990). For one NOE pair per unassigned proton pair, one should specify two ASSIgn statements along with NCOUnt set to 2; for two NOE pairs per unassigned proton pair, one should specify four ASSIgn statements along with NCOUnt set to 4, and so on. In the first pair of assignment statements below involving residue 17, the lower distance bound $l_a^1$ is set to 2 Å, the upper distance bound $u_a^1$ is set to 2.9 Å, the lower distance bound $l_b^1$ is set to 2.8 Å, and the upper distance bound $u_b^1$ is set to 3.7 Å. The lower distance difference bound $L_1$ is set to 0.6 Å while the upper distance difference bound $U_1$ is set to 1.0 Å. 

  class     2dim  
  assign (resid 17 and name hn)  (resid 17 and name hb1)   2.0  2.9  0.6  
  assign (resid 17 and name hn)  (resid 17 and name hb2)   2.8  3.7  1.0 
 
  assign (resid 2 and name hn)   (resid 1 and name hg1)    3.2  4.7 -0.3
  assign (resid 2 and name hn)   (resid 1 and name hg2)    3.2  4.7  0.3
  potential 2dim highdim 
  average   2dim center
  ncount    2dim 2 
  bhig      2dim 0.01 

  class     4dim 
  assign (resid 11 and name hn)  (resid 11 and name hb1)   3.2  4.7 -1.1
  assign (resid 11 and name hn)  (resid 11 and name hb2)   2.5  3.4 -0.5
  assign (resid 12 and name hn)  (resid 11 and name hb1)   3.0  5.5 -1.5
  assign (resid 12 and name hn)  (resid 11 and name hb2)   2.5  5.1 -0.7
  potential 4dim highdim 
  average   4dim center
  ncount    4dim 4 
  bhig      4dim 0.01 

  class     6dim  
  assign (resid 29 and name hn)  (resid 23 and name hd1#)   2.8  4.7 -1.5
  assign (resid 29 and name hn)  (resid 23 and name hd2#)   3.2  6.9  4.1
  assign (resid 29 and name ha1) (resid 23 and name hd1#)   2.1  4.3 -1.3
  assign (resid 29 and name ha1) (resid 23 and name hd2#)   3.0  6.5  4.4
  assign (resid 29 and name ha2) (resid 23 and name hd1#)   2.1  4.0 -1.3
  assign (resid 29 and name ha2) (resid 23 and name hd2#)   3.0  6.5  4.4
  potential 6dim highdim 
  average   6dim center
  ncount    6dim 6 
  bhig      6dim 0.01
The high dimensional restraints can be combined with other restraining classes and used in all of the protocols described in section 38.

next up previous contents index
Next: Refinement Using Time-Averaged Distance Up: Distance Restraints Previous: 3D NOE-NOE Example   Contents   Index
Xplor-NIH 2024-09-13