Dendritica (Vetter et al 2001)

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Accession:7907
Dendritica is a collection of programs for relating dendritic geometry and signal propagation. The programs are based on those used for the simulations described in: Vetter, P., Roth, A. & Hausser, M. (2001) For reprint requests and additional information please contact Dr. M. Hausser, email address: m.hausser@ucl.ac.uk
Reference:
1 . Vetter P, Roth A, Häusser M (2001) Propagation of action potentials in dendrites depends on dendritic morphology. J Neurophysiol 85:926-37 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Dendrite;
Brain Region(s)/Organism:
Cell Type(s): Hippocampus CA1 pyramidal GLU cell; Hippocampus CA3 pyramidal GLU cell; Neocortex U1 L2/6 pyramidal intratelencephalic GLU cell; Cerebellum Purkinje GABA cell;
Channel(s): I Na,t; I L high threshold; I p,q; I K; I M; I K,Ca;
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Action Potential Initiation; Bursting; Active Dendrites; Influence of Dendritic Geometry; Detailed Neuronal Models; Axonal Action Potentials; Action Potentials;
Implementer(s): Hausser, M [M.Hausser at ucl.ac.uk];
Search NeuronDB for information about:  Hippocampus CA1 pyramidal GLU cell; Hippocampus CA3 pyramidal GLU cell; Cerebellum Purkinje GABA cell; Neocortex U1 L2/6 pyramidal intratelencephalic GLU cell; I Na,t; I L high threshold; I p,q; I K; I M; I K,Ca;
Files displayed below are from the implementation
/* Relating dendritic geometry and signal propagation   */
/* Philipp Vetter, Arnd Roth and Michael Hausser        */
/* parse.hoc Version 1.0                     11.10.1999 */

xopen("$(NEURONHOME)/lib/hoc/noload.hoc")		/* gets standard GUI */
load_proc("nrnmainmenu")			
stoprun 	= 0                     /* vitally important for fit_praxis */
n_axon_seg  	= 5		/* # nodes in synthetic axon */
equiv 	= 0
printfunc   	= 1
VClampScale 	= 1
nsections 	= 10000		// risetime recording vectors
n 		= 5  
diffvonset=0
hdecay 		= 0

J 	= 46  // number of functional parameters
nfunc 	= 37
ngeom 	= 26
nelec 	= 11
mix = 0


create iseg, hill, myelin[n_axon_seg], node[n_axon_seg], inactive


/****** objects  *******************************************/

begintemplate MyString
public str, n, explanation
strdef str, explanation
double n[1]
endtemplate MyString


begintemplate MyCell
 public n, loc, tag, somatic, distal, spinescale, type
 strdef n, loc, tag, somatic, distal 
 double spinescale[1], type[1]
endtemplate MyCell


/****** global **********************/
objref ppl // point Process locator
objref          pltshape, grph
objref		strob, fileob, vectorlist, sref	/* for I/O operations; buffer */
strob 		= new StringFunctions()
fileob 		= new File()

strdef dcell, dcellname, dcelladdress, dcore, dsuffix
strdef str5
strdef date
date             = "2/12/99"
strdef act7, act8, act9, act10
strdef act0, act1, act2, act3,act4,act5,act6, actname, cellnameact, activecell
strdef ActiveModel, cellname, cell
strdef 	xlab, ylab, dataplotlab, hlpstr, Ylab, suffix
strdef 	helpinfo, helpstr
strdef	str1, origins, cellvar, origindist, str2, sec
strdef 	activecell, cellname, cell, celladdress, celladdressfull /* cellnames */
strdef	cellnameact, core
strdef 	ActiveModel /* name of active m  */
strdef Yvalstr, Xval1str, Xval2str, Xval3str

strdef halfdecay_maxlocation, halfdecay_minlocation 
strdef ap200_minlocation,     ap200_maxlocation
strdef apsoma_minlocation,    apsoma_maxlocation
strdef locs

objref parameters
objref rinloc[3]
objref CellList

CellList = new List("MyCell")
vectorlist = new List("Vector")
parameters = new List("MyString")
grph       = new List("Graph")
pltshape   = new List("PlotShape")


objref multi
objref dlog
objref vbox1
objref  splot, waveform, wave
objref 	cellc, sens[3], geomorder
objref  st, impR,imp, vclamp, Vclamp, Iclamp,  synapse, Synapse /*point processes*/
objref	dendrites, dendritesI, dendritesII, dendritesIII	/*sectionlists*/
objref	trunk, all, branchpoints, terminations, distlist
objref 	Soma, Distal, Parent 	/* sectionrefs */
objref	tdist, adist, bdist, xdist, dist, nbdist, nadist, gdist	/*distance vecs*/
objref  vpk, amp, vmax, plat, olat, half, ref, ref2, ref3, ref4, dvdr, vrest /*distlist vcs*/
objref  Zmismatch, Rmismatch, aZmismatch, aRmismatch			
objref  Zback, Rback, aZback, aRback					
objref  Zfwd, Rfwd, aZfwd, aRfwd				
objref  Z, R2, aZ, aR							
objref	dAr, Ar, mdiam, cdiam, rdiam, sections	/*gdist vectors*/
objref 	branchpointdiam, relareadiam, ralldiam, updst, somadist/*brchpt*/
objref	somadist_noend, updst_noend, branchpointdiam_noend
objref	ralldiam_noend, relareadiam_noend, ralldiam_noend
objref 	tap_dist, tap_ddist, tap_ddiam
objref 	terminationdist		/*termination vecs*/
objref 	vsoma,vdend,vnode,voltrec,synapserec,vtrace  /*recording vecs*/
objref  cf /* for Roth Purkinje cell DendriteII SectionList */


/************** local *******************************************************/

d = 6
objref 	Tdist[2], Adist[2], Bdist[2], Xdist[2],Gdist[2] /*el*/
objref	Nbdist[2], Nadist[2]
objref 	DAr[2], AR[2]			/* dArea(gdist),Area(gdist)*/ 
objref 	amp,vmax,plat,olat,half,vpk,dvdr,vrest /*sim*/ 
objref	ZMismatch[d],RMismatch[d],AZmismatch[d],ARmismatch[d] /*distlist vecs*/
objref	ZBack[d], AZback[d],RBack[d], ARback[d], ZFwd[d]
objref	AZfwd[d], RFwd[d], ARfwd[d], Zs[d], AZ[d], Rs[d], ARs[d]
objref	branchpoints, all, trunk, terminations /* SectionLists */
objref	origin, originsec


/************* geometry *****************************************************/

objref 	children, branchselection					
objref 	Mdiam[2], Rdiam[2], Cdiam[2], Sections[2] /* equiv_diam */
objref 	Branchpointdiam[2],Relareadiam[2],Ralldiam[2] /*branchpt vecs*/
objref	Updst[2], Somadist[2]
objref	Somadist_noend[2], Updst_noend[2]
objref	Branchpointdiam_noend[2], Ralldiam_noend[2]
objref	Relareadiam_noend[2]

objref	Terminationdist[2]			/* termination vecs  */
objref	diameterlist, branchpointd, relaread, ralld	/* get_rall()   */
objref 	dchild, dparent, dY, ch				/* ralldiameter()   */
objref 	updstances
objref 	Rpas, Rpas_percent, Zpas, Zpas_percent	// Impedance for list
objref 	Ract, Ract_percent, Zact, Zact_percent


/********* impedance *********************************************************/

objref 	seglist, gk, gna
objref 	datavec						/* cosine fitting  */
objref  pa_connection, ch_connection, childref, childvar, parentref
objref 	gpas,cmem					/* intrasection_on/off*/
objref 	peaktimes,selection, segnum
objref 	vrec[nsections],trec[nsections], Zfrequency	/* for AP rising phase */

/********* statistics ********************************************************/

double 	param[10]					/* statistics.hoc */
objref 	data[3][50][3] // [functional/geometric/elgeom][#][fxn]
objref 	Data[3][50][3] // [functional/geometric/elgeom][#][fxn]
objref 	corr[40], goodcorr[7]
objref 	recvec[2000]
objref  ref3,ref4,ref5

/************* other  ****************************/

objref 	link,link2 	/* for electrotonic distance */
objref 	time
objref 	tobj
objref 	vrec[11000]
objref 	vlt, rin, tau
objref	info[200]	/* output */
objref 	AP200v
objref 	branchpt_noend, all_noend

/************* graphics **************************/

strdef 	Nathreshold
objref 	save_window_, rvp_,scene_vector_[4]	/* old window_settings */
objref 	number					/* mx(),mn()	*/
objref 	histy,histx				/* hist()	*/
objref 	onex, oney				/* various plot */
objref 	gaussy, gaussx				/* gauss()	*/
objref 	barx, bary				/* bar()    */
objref 	Ix, v1, v2				/* sort() */
objref 	x1,y1, figure[50]			/* fig()  */
objref 	colour, add				/* fig */
strdef 	figsymbol
objref 	ix, iy, ixn, iyn, ir
objref 	veca, vecb, vecc // rawdata
objref 	vecx, vecy
objref 	infox, infoy, infoxn, infoyn, infor
objref 	filterx, filtery
objref 	rollingx, rollingy

objref  rand

vecy	= new Vector()
vecx	= new Vector()
veca	= new Vector()
vecb	= new Vector()
vecc	= new Vector()
infox	= new Vector()
infoy	= new Vector()
infoxn	= new Vector()
infoyn	= new Vector()
infor	= new Vector()

double val[10]
ref2 = new Vector()
v2 = new Vector()








/***************************************************************/


proc get() { local i,n 

	/* get cell $s1 */
	/* use ActiveModel $s2 */
	/* load data if numarg=3 */

  	forall delete_section()		// clear all sections & vectors
	for i = 0, vectorlist.count()-1 {vectorlist.object(i).resize(0)}

	n = numarg()
	if (n<1)	 cell        = "p18.hoc"  else cell        = $s1
	if (n<2)	 ActiveModel = act0 else ActiveModel = $s2
	if (n>2) 	 Read        = 0    else Read        = 1

	get_settings(cell,ActiveModel)	
	xopen(cell)			  	// read hoc file
        if (!equiv) forall if (L/nseg > 7) nseg = int(L/7) + 1
	make_sectionrefs()
	create inactive
	inactive { L=0.001 nseg = 1 diam = 0.001 }
	connect_axon()
	if (equiv) remove_axon()


        Soma.sec st     = new IClamp(originx)
        Soma.sec vclamp = new SEClamp(originx)
	Soma.sec synapse  = new syn2(originx)

	set_vclamp(origins,originx)

	make_vectors()	
	make_sectionlists()
  	insert_channels()	
	set_spinedensity(cell)
	reset()
	set_origin()
	if (Read) { geometry_read(cell)  active_read(cell,ActiveModel)  } 
	get_gdist(1)
	get_gdist(0)
   }


/*************************************************************************/


proc get_somadist() { local d, i, n

		n = numarg()
		if (n>0) str2 = $s1        else str2 = "p18.hoc"
		if (n>1) ActiveModel = $s2 else ActiveModel = act0
		if (n>2) d = $4            else d = 200

		get(str2,ActiveModel,1)
		name_somadist(d)
		active_read(cell,ActiveModel)
		geometry_read(cell)
		for i = 0,1 { get_gdist(1-i) }
		}


/*************************************************************************/


proc connect_axon() { 	local a,i,n  

	/* Create axon  (similar to Mainen et al (Neuron, 1995) */
		
	if (numarg()== 0) n = 0 else n = $1

	create iseg
	create node[n_axon_seg] 
	create hill
	create myelin[n_axon_seg]


	a = 0
	Soma.sec   	for(x) 		  a += area(x) 
			      	  equiv_diam = sqrt(a/(4*PI))
	  		if (swc)  equiv_diam = equivdiam /*DukeSouth*/


	for i=0,n_axon_seg-1 {		
	iseg          { L=15  nseg=5  diam=equiv_diam/10 } /*Sloper&Powell 1982,Fig.71*/
  	myelin[i]     { L=100 nseg=5  diam=iseg.diam  }
    	node[i]       { L=1.0 nseg=1  diam=iseg.diam*.75 }} 
	hill          { L=10  nseg=5  diam(0:1)=4*iseg.diam:iseg.diam }

				Soma.sec      	connect hill(0), 0.5
				hill          	connect iseg(0), 1
				iseg       	connect myelin[0](0), 1
				myelin[0]  	connect node[0](0), 1
	for i=0,n_axon_seg-2  { node[i]	connect myelin[i+1](0),1
		  		myelin[i+1] 	connect node[i+1](0),1 }
	Axon = 1

             }


proc add_axon() { 
		connect_axon()
		origin.sec  distance(0,originx)
		insert_channels()
		reset()p
		Axon = 1
		define_shape()
		}


/*************************************************************************/

proc remove_axon() {

		forsec "iseg" delete_section()  // take out axon 9.2.99
		forsec "hill" delete_section()
		forsec "myelin" delete_section()
		//forsec "node" delete_section() not the node - used for calcs

		origin.sec distance(0,originx)
		Axon = 0	
		define_shape()
		}


/*************************************************************************/


proc insert_channels() { local d, D /* insert channels and set reversal potentials */

		origin.sec distance(0,originx)	

		forall {				
			insert pas  /* generic conductance with reverse potential */
 			insert pk   /* backpropagaton tools */
			insert na  
			insert kv
 			}

	D=0
	forsec all	if (maxdist()>D) D=maxdist()
	D = 5/D
	
	if (!kap_rel) D = 1/100
	
	forsec all {

		d=mn(500,distance(0.5))
		

		if(Kap_current && d<=100) {  	// diam>0.5 condition omitted
			insert kap 
			for(x) factor_kap(x) = 1+distance(x)*D
								} else uninsert kap

		if(Kad_current && d>100) {  // diam>0.5 condition omitted
			insert kad 
			if (!kap_rel) for(x) factor_kad(x) = 1+mn(500,distance(x))*D
			if (kap_rel)  for(x) factor_kad(x) = 1+distance(x)*D

								}  else uninsert kad
		if(Iq_current) 	insert qq  else uninsert qq
		if(Ca_current) 	insert cad else uninsert cad
		if(Ca_current) 	insert ca  else uninsert ca
		if(KCa_current) insert kca else uninsert kca
		if(Km_current) 	insert km  else uninsert km
		     }

		forsec "myelin" uninsert kv /* no delayed rectifiers in myelin */

		/* set reversal potentials */
		forall 				e_pas     = -70
		forall if(ismembrane("k_ion"))  ek  	  = Ek
		forall if(ismembrane("na_ion")) ena	  = Ena 
		forall if(ismembrane("na_ion"))	vshift_na = -5  
		forall if(ismembrane("ca_ion")) { eca     = 140   
  			     			  ion_style("ca_ion",0,1,0,0,0)
  			     			  vshift_ca = 0		          }
  		   }

/*************************************************************************/

proc make_sectionlists() { 	local i /* make sectionlists */

		dendrites    = new SectionList() /* dendrites        */
		dendritesI   = new SectionList() /* partI dendrites  */
		dendritesII  = new SectionList() /* for Purkinje spines */
		dendritesIII = new SectionList() /* Rapp Purkinje */
		branchpt_noend 	= new SectionList()
		all_noend	= new SectionList()
		all		= new SectionList()
			
		forall 		  all.append()
		forsec "inactive" all.remove()
		forsec "myelin"   all.remove()	/* remove axon from list */
		forsec "node"     all.remove()
		forsec "hill"     all.remove()
		forsec "iseg"     all.remove()			     	
		forsec all     dendrites.append()
		forsec "soma"  	dendrites.remove()
		forsec dendrites dendritesI.append()

		/* trunk, all, branchpoints & terminations */

		origin.sec distance(0,originx)

		Distal.sec  trunk.append() 	/* trunk */
		Distal.sec  Parent = new SectionRef()
		Distal.sec sref = new SectionRef()
		root = 0

		while (!root)  { Parent.sec get_parent()
				 Parent.sec trunk.append() this_section() }

		forsec all { 
				if (!isterminal()) all_noend.append() 

			      	branchpoint()
			      	if (branchnumber>=1) {branchpoints.append()
						if (!isterminal()) branchpt_noend.append()}
			      	if (branchnumber==-1) terminations.append() 		
			   }

		}

/*************************************************************************/

func isterminal() {	/* returns 1 if the downstream sections are [parts of] a terminal branch */ 


			if (equiv) return 1
			get_children()
			forsec children { subtree_traverse("this_section() sref = new SectionRef()")
					  sref.sec branchpoint()

			  if (branchnumber==0)  while (branchnumber == 0) {
				sref.sec subtree_traverse("this_section() sref = new SectionRef()")
				sref.sec branchpoint()  	    }
					  if (branchnumber==1) return 0
 					}
			return 1
		} 

/*************************************************************************/

proc make_distvectors() {	local k,i,j 
			/* create distance vectors */
			/* for trunk, all, branchpoints, terminations */
			/* called by get() */

	for k = 0,1 { /* loop physical & electrotonic */
	L_switch(1-k)

	origin.sec distance(0,originx)
	tdist.resize(0)
	adist.resize(0)
	bdist.resize(0)
	xdist.resize(0)
	nbdist.resize(0)
	nadist.resize(0)

	forsec trunk        for j = 1,nseg {tdist.append(fdistance((j-.5)/nseg)) }
	forsec all          for j = 1,nseg {adist.append(fdistance((j-.5)/nseg)) }
	forsec branchpoints for j = 1,nseg {bdist.append(fdistance((j-.5)/nseg)) }
	forsec terminations for j = 1,nseg {xdist.append(fdistance((j-.5)/nseg)) }
	forsec branchpt_noend for j=1,nseg {nbdist.append(fdistance((j-.5)/nseg))}
	forsec all_noend    for j = 1,nseg {nadist.append(fdistance((j-.5)/nseg))}

			}
		}				 



proc switch()	{ 	local i,k,n,d /* switches cell, Length & dist */
			i = $1
			k = $2
			n = $3			
			d = n-1


		if (n == 1) distlist = trunk
		if (n == 2) distlist = all
		if (n == 3) distlist = branchpoints
		if (n == 4) distlist = terminations
		if (n == 5) distlist = branchpt_noend
		if (n == 6) distlist = all_noend

		tdist 		= Tdist[k] 
		adist 		= Adist[k] 
		bdist 		= Bdist[k] 
		xdist		= Xdist[k]
		nbdist		= Nbdist[k]
		nadist		= Nadist[k]

		if (n == 1) dist = tdist
		if (n == 2) dist = adist
		if (n == 3) dist = bdist
		if (n == 4) dist = xdist
		if (n == 5) dist = nbdist
		if (n == 6) dist = nadist
	
		Zmismatch	= ZMismatch[d]
		aZmismatch	= AZmismatch[d]
		Rmismatch	= RMismatch[d]
		aRmismatch	= ARmismatch[d]
		Zback		= ZBack[d]
		aZback		= AZback[d]
		Rback		= RBack[d]
		aRback		= ARback[d]
		Zfwd		= ZFwd[d]
		aZfwd		= AZfwd[d]
		Rfwd		= RFwd[d]
		aRfwd		= ARfwd[d]
		Z		= Zs[d]
		aZ		= AZ[d]
		R2		= Rs[d]
		aR		= ARs[d]

		gdist		= Gdist[k]	/* gdist based */
		dAr		= DAr[k]	/* dArea(r) */
		Ar		= AR[k]	        /* Area(r) */
		sections	= Sections[k]   /* mean diameter(r) */
		mdiam		= Mdiam[k]	/* # sections (r) */
		cdiam		= Cdiam[k]	/* equiv_cross-sectional diam(r) */
		rdiam		= Rdiam[k]	/* equiv_ralldiameter(r) */
		somadist	= Somadist[k]   /* somadist based */
		updst		= Updst[k]	
		branchpointdiam = Branchpointdiam[k]	
		ralldiam	= Ralldiam[k]		
		relareadiam	= Relareadiam[k]	
		ralldiam	= Ralldiam[k]		
		terminationdist = Terminationdist[k]	
		somadist_noend	= Somadist_noend[k]  /* somadist based */
		updst_noend		= Updst_noend[k]	
		branchpointdiam_noend	= Branchpointdiam_noend[k]	
		ralldiam_noend		= Ralldiam_noend[k]		
		relareadiam_noend	= Relareadiam_noend[k]	
		ralldiam_noend		= Ralldiam_noend[k]		
		}

/*************************************************************************/

proc dist_switch()	{	 /* set dist to use for calculations */
				 /* $1 == 1 tdist trunk */
				 /* $1 == 2 adist all   */
				 /* $1 == 3 bdist branchpoints */
				 /* $1 == 4 xdist terminations */
				 /* $1 == 4 nbdist branchpt_noend */
				 /* $1 == 4 nadist all_noend */

				if (numarg() == 1) currentdist = $1 
				switch(currentcell,electrotonicL,currentdist)
			}

/*************************************************************************/

proc L_switch() 	{/* switch length measurement $1==1 physical, $1==0 electrotonic */

				if (numarg() != 0) electrotonicL = $1
				switch(currentcell,electrotonicL,currentdist)
				origin.sec distance(0,originx)
  		   	}

/*************************************************************************/

proc make_vectors() { local i,k,d /* create all Vectors needed during simulation */



			for d = 0,5 {
			ZMismatch[d]	= new Vector()
			AZmismatch[d]	= new Vector()
			RMismatch[d]	= new Vector()
			ARmismatch[d]	= new Vector()
			ZBack[d]	= new Vector()
			AZback[d]	= new Vector()
			RBack[d]	= new Vector()
			ARback[d]	= new Vector()
			ZFwd[d]		= new Vector()
			AZfwd[d]	= new Vector()
			RFwd[d]		= new Vector()
			ARfwd[d]	= new Vector()
			Zs[d]		= new Vector()
			AZ[d]		= new Vector()
			Rs[d]		= new Vector()
			ARs[d]		= new Vector()
						}

	for k=0,1 { 
			Tdist[k] 		= new Vector()
			Adist[k] 		= new Vector()
			Bdist[k] 		= new Vector()
			Xdist[k] 		= new Vector()
			Nbdist[k] 		= new Vector()
			Nadist[k] 		= new Vector()
			DAr[k]			= new Vector()	/* dArea(r) */
			AR[k]			= new Vector()	/* Area(r) */
			Sections[k]		= new Vector()	/* mean diameter(r) */
			Mdiam[k]		= new Vector()	/* # sections (r) */
			Cdiam[k]		= new Vector()	/* equiv_cross-sectional diam(r) */
			Rdiam[k]		= new Vector()	/* equiv_ralldiameter(r) */
			Gdist[k]		= new Vector()	/* distance vector */
			Somadist[k]		= new Vector()	/* branchpoint-related */
			Updst[k]		= new Vector()
			Branchpointdiam[k]	= new Vector()
			Ralldiam[k]		= new Vector()
			Relareadiam[k]		= new Vector()
			Ralldiam[k]		= new Vector()
			Somadist_noend[k]	= new Vector()	/* branchpoint-related */
			Updst_noend[k]		= new Vector()
			Branchpointdiam_noend[k]	= new Vector()
			Ralldiam_noend[k]	= new Vector()
			Relareadiam_noend[k]	= new Vector()
			Ralldiam_noend[k]	= new Vector()
			Terminationdist[k]	= new Vector()  }    

			single_vectors()
				}

/*************************************************************************/

proc single_vectors()	{

		trunk		= new SectionList()
		all		= new SectionList()
		branchpoints	= new SectionList()
		terminations	= new SectionList()
		vpk 		= new Vector()
		amp 		= new Vector()
		vmax		= new Vector()
		plat		= new Vector()
		olat		= new Vector()
		half		= new Vector()
		dvdr		= new Vector()
		vrest		= new Vector()
		vsoma   	= new Vector()
		vdend   	= new Vector()
		vnode		= new Vector()
		voltrec 	= new Vector()
		synapserec 	= new Vector()

		Zfrequency	= new Vector()
		number 		= new Vector()		/* graphics */
		gaussx 		= new Vector()
		histx 		= new Vector()
		peaktimes 	= new Vector()
		segnum	 	= new Vector()
		selection 	= new Vector()
		diameterlist	= new Vector()		/* geometry */
		dchild		= new Vector()
		dparent		= new Vector()
		dY		= new Vector()
		ch		= new Vector()
		branchpointd	= new Vector()
		relaread	= new Vector()
		ralld		= new Vector()

		time 		= new Vector()	
		tobj    	= new Vector() 		/* used for all sorts of things */
		vlt   		= new Vector()
		ref		= new Vector()
		rin     	= new Vector(cells)
		tau  		= new Vector(cells)
		colour 		= new Vector(10,1)
		colour.x[0] 	= 2
		colour.x[1] 	= 3
		colour.x[2] 	= 4
		colour.x[3] 	= 9
		colour.x[4] 	= 5
		colour.x[5] 	= 6
		colour.x[6] 	= 7
		colour.x[7] 	= 8
		colour.x[8] 	= 5

		add		= new Vector(50,1)
		add.x[0] 	= 0			/* only first cells adds plot */
		waveform        = new Vector(0)
		wave            = new Vector(1)
	if (numarg()==0)	{ rec_set()  }
			}

/*************************************************************************/



proc set_origin() { 	local n
		/* set origin & calculate el L & distance vectors */
		n = numarg()
		if (n>0) origins = $s1
		if (n>1) originx = $2
		sprint(str1,"%s origin = new SectionRef()",origins)
		execute(str1)
		originsec = new SectionList()
		sprint(str1,"%s originsec.append()",origins)
		execute(str1)
		origin.sec distance(0,originx)
		set_electrotonic()
	        make_distvectors()
		print "origin set"

		  }


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