NMR Restraints Grid

Result table
 (Save to zip file containing files for each block)

image	mrblock_id	pdb_id	bmrb_id	cing	stage	position	type
	551427	2lx5	18659	cing	1-original	3	comment

# ------ read input files ------

read seq tb.seq
read upl submission.upl   # read upper distance bounds
read aco tb.aco   # read dihedral angle restraints


# ------ structure calculation ------

calc_all 100 steps=40000   # calculate conformers


# ------ structure calculation ------

overview demo.ovw structures=40 pdb # write overview file and 40 best conformers
name:= tb
rmsdrange:=1..18
cyanalib
read seq tb.seq 



# Copyright (c) 2002-05 Peter Guntert. All rights reserved.
## 7MACROS: caliba - CYANA macro
##
## Parameters: dmin=dmin                 (default: 2.4)
##             dmax=dmax                 (default: 5.5)
##             vmin=Vmin                 (default: 0.0)
##             bb=A                      (default: calculated automatically)
##             sc=B                      (default: A/dmin2)
##             methyl=C                  (default: B/3)
##             weight=w                  (default: 1.0)
##             avedis=d                  (default: 3.4)
##             plot=file                 (required)
##
## Calibrates a peak list, i.e. derives upper limit distance constraints from
## all assigned peaks and adds them to the list of current distance
## constraints. The values dmin and dmax give the minimal and the maximal
## value in A for a distance constraints before possible pseudo atom
## corrections are added. Optionally, only peaks with volume larger than Vmin
## or from a peak list with given filename (without extension) may be
## considered. Peaks are classified into three calibration classes:
## class        peaks/constraints       function
## backbone     all  HN/Ha - HN/Ha, and  HN/Ha - Hb between residues (i, j) with
## |i - j| < 5  V = A/d6
## sidechain    not "backbone" and not "methyl" V = B/d4
## methyl       all involving methyl groups     V = C/d4
##
## The parameters A, B and C are either given by the user or calculated
## automatically as follows:
## The function calsca is used to calculate A by assuming an average distance
## of d A for all constraints from the class "backbone". By default, the
## scalar B is set to B = A/dmin2 in order to intersect the backbone
## calibration curve at dmin, and C is set to B/3 (see also Mumenthaler et
## al., 1997).
## Optionally, the resulting distance constraints may be given the relative
## weight w. Also optionally, a logarithmic plot of volumes versus
## corresponding minimal distances in the selected structures can be
## created.

var echo plt f

syntax dmin=@r=2.4 dmax=@r=5.5 vmin=@r=100.0 bb=@r=-1.0 sc=@r=-1.0 \
       methyl=@r=-1.0 weight=@r=1.0 avedis=@r=3.4 plot=@f.ps=

echo:=off
plt='$plot'.ne.' '

print
print "    Calibration class: backbone"
print
peaks select "H HN HA* HB* QA QB - METHYL, H HN HA* QA - METHYL levels=0..4" info=none
peaks select "+ H HN HA* QA      - METHYL, H HN HA* QA - METHYL levels=5.." info=none
peaks select "/ *,*"
f:=1/d**6
if (bb.le.0.0) bb=calscale('$f',avedis,vmin)
print "    Calibration function: $bb(1PE10.2) * $f"
calibrate bb*$f $dmin $dmax weight=$weight \
          plot=$if(plt,'caliba_bb.grf',' ') log dmin qfactor

print
print "    Calibration class: side-chain"
print
peaks select "! - METHYL, *"
peaks select "/ *, *"
f:=1/d**4
if (sc.le.0.0) sc=bb/(dmin)**2
print "    Calibration function: $sc(1PE10.2) * $f"
calibrate sc*$f $dmin $dmax weight=$weight \
          plot=$if(plt,'caliba_sc.grf',' ') log dmin qfactor

print
print "    Calibration class: methyl"
print
peaks select "METHYL ,*" info=none
peaks select "/ *, *"
f:=1/d**4
if (methyl.le.0.0) methyl=sc/3.0
print "    Calibration function: $methyl(1PE10.2) * $f"
calibrate methyl*$f $dmin $dmax weight=$weight \
          plot=$if(plt,'caliba_me.grf',' ') log dmin qfactor
print

if (plt) then
  print "x0=-160 y0=150 x1=210 y1=350"     >$plot(1:indexr('$plot','.'))grf
  print "marksize=4"                       >>
  print file=caliba_bb.grf                 >>
  print " "                                >>
  print "x0=-160 y0=-100 x1=210 y1=100"    >>
  print file=caliba_sc.grf                 >>
  print " "                                >>
  print "x0=-160 y0=-350 x1=210 y1=-150"   >>
  print file=caliba_me.grf                 >>
  print " "                                >>
  print "X0=0 X1=100 Y0=0 Y1=100 "         >>
  print "x0=-250 x1=250 y0=-350 y1=350 "   >>
  print "clip off "                        >>
  print "rotate=on "                       >>
  print "textsize=14 "                     >>
  print "weight=bold "                     >>
  print "text 6 78 \"Backbone class\" "    >>
  print "text 6 42 \"Side-chain class\" "  >>
  print "text 6 5 \"Methyl group class\" " >>
  print "rotate=off "                      >>.
  graf $plot replace
  remove caliba_bb.grf caliba_sc.grf caliba_me.grf
end if

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