www.neuron.yale.edu

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First build a toy model with just enough complexity to be used as a test case. A stylized model consisting of an axon, soma, and dendrite will suffice. Attach an AlphaSynapse to one of its sections and assign reasonable parameters to this mechanism.

Next define a procedure called onepoint that expects two arguments and does the following:
  calls a procedure that moves synapse to $2 
    in currently accessed section (can use putsyn.hoc for this--
    see http://www.neuron.yale.edu/neuron/static/courses/2008/course/family/putsyn.ho
    --but will have to change the statement
      dend AlphaSynapse[0].loc($1)
    to
      AlphaSynapse[0].loc($1)
    )
  runs a simulation with tstop sufficiently large
    that soma.v(0) will have reached its peak
  calls a procedure that finds the amplitude of the somatic epsp
  calculates distance from this node to soma(0)
  appends epsp amplitude and $1*distance($2) to ampvec and distvec, respectively

Then write additional code that does the following:
  sets up Vector recording of soma.v(0)
  creates a pair of Vectors called distvec and ampvec
    distvec will hold distance between soma(0) and each node in cell
    ampvec will hold amplitude of somatic epsp
      produced by a synapse at those locations
  makes soma the currently accessed section
  attaches a synapse to 0 end of currently accessed section
  uses distance() to specify soma(0) as origin for path distances
  // take care of all nodes in soma
  for (x) onepoint(1, x)
  // deal with all nodes in basilars
  for each section in basilars
    for (x) if (x>0) onepoint(-1, x)
  // deal with all nodes in apicals
  for each section in apicals
    for (x) if (x>0) onepoint(1, x)
  normalize the amplitudes in ampvec
  plot ampvec vs. distvec

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// topology
create soma, bas, ap
access soma
connect ap(0), soma(1)
connect bas(0), soma(0)

// subsets
objref apicals, basilars
apicals = new SectionList()
basilars = new SectionList()
ap apicals.append()
bas basilars.append()

// geometry
soma {
  diam = 15
  L = 15
  nseg = 1
}
ap {
  diam = 2.5
  L = 3000
  nseg = 69 // appropriate for d_lambda 0.1, given cm and Ra
}
bas {
  diam = 1
  L = 1000
  nseg = 37 // appropriate for d_lambda 0.1, given cm and Ra
}

// biophysics
forall {
  cm = 1 // uf/cm2
  Ra = 100 // ohm cm
  insert pas
  g_pas = 2e-5 // S/cm2
  // resting membrane potential will equal e_pas = -70 mV
}

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load_file("nrngui.hoc")

TSTOP = 50 // long enough for even the slowest somatic epsp to peak
V_INIT = -70 // resting potential of model cell

load_file("cell.hoc")

///// instrumentation

objref syn
soma syn = new AlphaSynapse(0) // make soma(0) the "reference point"
syn.onset = 1 // ms
syn.tau = 1 // ms
syn.gmax = 1e-4 // uS
syn.e = 0 // mV

objref vsoma
vsoma = new Vector() // for recordings of vsoma
soma vsoma.record(&v(0)) // record soma.v(0) waveform

///// simulation control code

tstop = TSTOP
v_init = V_INIT

objref ampvec, distvec
ampvec = new Vector() // for soma psp amplitudes
distvec = new Vector() // for synaptic distances from soma(0)
soma distance() // make soma(0) the origin for distance measurements

// $1 is 1 or -1 (specifies whether distance should be - or +)
//   i.e. is syn on a basilar or an apical dendrite
// $2 is location of node in currently accessed section
proc onepoint() { local vmax
  syn.loc($2) // move syn to currentsection($2)
//  print secname(), " ", $2 // to verify proper operation of program
  distvec.append($1*distance($2))
  run()
  // assumes that cell was initialized to resting steady state!
  vmax = vsoma.max() - vsoma.x[0] // extract psp amplitude from waveform
  ampvec.append(vmax)
}

objref g // for Graph that shows results

proc allpoints() { local vmax
  // throw out old results
  ampvec = new Vector()
  distvec = new Vector()
  // deal with all neurites
  printf("Working")
  soma for(x) {
    onepoint(1,x)
    printf(".") // indicate progress
  }
  forsec basilars for (x) if (x>0) {
    onepoint(-1,x)
    printf(".")
  }
  forsec apicals for (x) if (x>0) {
    onepoint(1,x)
    printf(".")
  }
  printf("done!\n")
  // normalize amplitudes
  vmax = ampvec.max()
  ampvec.div(vmax)
  g = new Graph()
  ampvec.mark(g, distvec, "O", 5) // medium small black filled circle
  g.exec_menu("View = plot") // autoscale axes
}

allpoints()

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    ///// instrumentation
    objref syn
    apic[43] syn = new AlphaSynapse(0) // make soma(0) the "reference point"  CHANGED THIS FROM SOMA TO APIC[43] BUT IT DIDNT DO ANYTHING
    syn.onset = 1 // ms
    syn.tau = 1 // ms
    syn.gmax = 500e-6 // uS
    syn.e = 0 // mV 

    objref vseg
    vseg = new Vector() // for recordings of voltage at a segment

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    tstop = TSTOP
    v_init = V_INIT

    objref ampvec, distvec
    ampvec = new Vector() // for soma psp amplitudes
    distvec = new Vector() // for synaptic distances from soma(0)
    apic[43] distance() // make apic[43](0) the origin for distance measurements

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   proc onepoint() { local vmax  
     // syn.loc($2) // move syn to currentsection($2) //NO LONGER HAVE TO DO THIS
    //  print secname(), " ", $2 // to verify proper operation of program
      distvec.append($1*distance($2))  //I THINK THIS WILL STILL WORK
      run()
      // assumes that cell was initialized to resting steady state!
      vmax = vseg.max() - vseg.x[0] // extract psp amplitude from waveform
      ampvec.append(vmax)
}

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    objref g // for Graph that shows results

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   proc allpoints() { local vmax
      // throw out old results
      ampvec = new Vector() 
      distvec = new Vector()
      // deal with all neurites
      printf("Working")
//looks like below makes things positive or negative
      soma for(x) {
        onepoint(1,x)
        printf(".") // indicate progress
      }
      forsec basilars for (x) if (x>0) {
        onepoint(-1,x)
        printf(".")
      }
forsec apicals for(x) if (x==44 || x==45 || x==46 || x==47){ \\ right here I am trying to say x can equal 44 or 45 or 46 or 47
        onepoint(1,x)
        printf(".")
      }

      forsec apicals for (x) if (x!=44||45||46||47){ \\  trying to say NOT 44 or 45 or 46 or 47
        onepoint(-1,x)
        printf(".")
      }
      printf("done!\n")

      // normalize amplitudes
      vmax = ampvec.max()
      ampvec.div(vmax)
      g = new Graph()
      ampvec.mark(g, distvec, "O", 5) // medium small black filled circle
      g.exec_menu("View = plot") // autoscale axes
    }

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rniv: subscript out of range x
     allpoints()  
                  ^
        onepoint(1, 0)
      allpoints()

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NEURON {
  SUFFIX max
  RANGE v0, vm, vepsp
}

ASSIGNED {
  v (millivolt)
  vm (millivolt)
  v0 (millivolt)
  vepsp (millivolt)
}

INITIAL {
  v0 = v
  vm = v
  vepsp = vm - v0
}

BREAKPOINT { 
  if (v > v0) {
    vm = v
    vepsp = vm - v0
  }
}

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objref g
g = new Graph()
forall for (x) g.mark(distance(), vepsp_max(x), "O", 5)
g.exec_menu("View = plot")

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///// instrumentation

objref syn
ap syn = new AlphaSynapse(.5) // place a synapse at x=.5 on the ap section.
syn.onset = 1 // ms
syn.tau = 1 // ms
syn.gmax = 1e-4 // uS
syn.e = 0 // mV

objref vsoma
vsoma = new Vector() // for recordings of vsoma
soma vsoma.record(&v(0)) // record soma.v(0) waveform

///// simulation control code

tstop = TSTOP
v_init = V_INIT

objref ampvec, distvec
ampvec = new Vector() // for soma psp amplitudes
distvec = new Vector() // for synaptic distances from soma(0)
ap distance(.5) // want to make apical(.5) the origin for distance measurements  This doesn't work but I am not sure why

// $1 is 1 or -1 (specifies whether distance should be - or +)
//i.e. is syn on a basilar or an apical dendrite
// $2 is location of node in currently accessed section
proc onepoint() { local vmax
//syn.loc($2) // move syn to currentsection($2)
// print secname(), " ", $2 // to verify proper operation of program
 distvec.append($1*distance($2))
 run()
 // assumes that cell was initialized to resting steady state!
 vmax = vsoma.max() - vsoma.x[0] // extract psp amplitude from waveform
 ampvec.append(vmax)
}

objref g // for Graph that shows results

proc allpoints() { local vmax
 // throw out old results
 ampvec = new Vector()
 distvec = new Vector()
 // deal with all neurites
 printf("Working")
 soma for(x) {
 onepoint(1,x)
 printf(".") // indicate progress
 }
 forsec basilars for (x) if (x>0) {
 onepoint(-1,x)
 printf(".")
 }
 forsec apicals for (x) if (x>0) {
 onepoint(1,x)
 printf(".")
 }
 printf("done!\n")
 // normalize amplitudes
 vmax = ampvec.max()
 ampvec.div(vmax)
 g = new Graph()
 ampvec.mark(g, distvec, "O", 5) // medium small black filled circle
 g.exec_menu("View = plot") // autoscale axes
}

allpoints()

forall insert max

objref h
h = new Graph()
forall for (x) h.mark(distance(), vepsp_max(x), "O", 5)
h.exec_menu("View = plot")

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    create axon
    access axon
    {nseg = 5  L=1000}
    for (x) print x, distance(0,x)

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for (x) print x, distance(1,x)

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for (x) print x, distance(.5,x)

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load_file("nrngui.hoc")

Tstop = 50 // long enough for even the slowest somatic epsp to peak
V_INIT = -70 // resting potential of model cell

load_file("cell.hoc")

///// instrumentation

objref syn
ap syn = new AlphaSynapse(.5) // place a synapse
syn.get_loc()
syn.onset = 1 // ms
syn.tau = 1 // ms
syn.gmax = 1 // uS
syn.e = 0 // mV

ap distance()	// I wish this is setting the origin midway in the apical section

forall insert max

run()

objref g
g = new Graph()
forall for (x,0) g.mark(distance(x), vepsp_max(x), "O", 5)
g.exec_menu("View = plot")

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objref sh
sh = new PlotShape()
sh.variable("max")
sh.scale(some number, other number)

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//put the max amplitute epsp of every segment and section in a vector
objref ampvec
ampvec = new Vector()
forall for (x,0) ampvec.append(vepsp_max(x))

//set the scale of the plot
upperV=ampvec.max()
lowerV=ampvec.min()

//make plot
objref sh
sh = new PlotShape()
sh.variable("max")
sh.scale(lowerV, upperV)