I believe I'm having a very similar problem. I'm trying to borrow the geometry of Bill Lyton's model
When I bring up a shape plot, it appears as if there is no soma, however, if I rotate the model, I can see the soma is there. i.e. it appears to be 2d.
I checked that the soma appears to have the right specifications with n3d() and diam3d() and they all seem correct, and soma.diam and psection() give back reasonable numbers. Looking at how electrical signals propagate, the soma doesn't behave electrically like it is 2D (i.e. it has a finite, and reasonable resistance). Any thoughts on what is going on here?
Code: Select all
/* $Id: rlgntc5-10-95.hoc,v 1.2 2003/10/08 15:10:52 billl Exp $ */
ndend = 195
create soma, dend[ndend]
access soma
connect dend[0](0), soma(0.5)
connect dend[1](0), dend[0](1)
connect dend[2](0), dend[0](1)
connect dend[3](0), soma(0.5)
connect dend[4](0), dend[3](1)
connect dend[5](0), dend[3](1)
connect dend[6](0), dend[5](1)
connect dend[7](0), dend[5](1)
connect dend[8](0), soma(0.5)
connect dend[9](0), dend[8](1)
connect dend[10](0), dend[9](1)
connect dend[11](0), dend[10](1)
connect dend[12](0), dend[11](1)
connect dend[13](0), dend[11](1)
connect dend[14](0), dend[10](1)
connect dend[15](0), dend[9](1)
connect dend[16](0), dend[8](1)
connect dend[17](0), dend[16](1)
connect dend[18](0), dend[17](1)
connect dend[19](0), dend[17](1)
connect dend[20](0), dend[16](1)
connect dend[21](0), dend[20](1)
connect dend[22](0), dend[20](1)
connect dend[23](0), dend[8](1)
connect dend[24](0), dend[23](1)
connect dend[25](0), dend[24](1)
connect dend[26](0), dend[24](1)
connect dend[27](0), dend[26](1)
connect dend[28](0), dend[27](1)
connect dend[29](0), dend[27](1)
connect dend[30](0), dend[26](1)
connect dend[31](0), dend[23](1)
connect dend[32](0), soma(0.5)
connect dend[33](0), dend[32](1)
connect dend[34](0), dend[33](1)
connect dend[35](0), dend[34](1)
connect dend[36](0), dend[34](1)
connect dend[37](0), dend[33](1)
connect dend[38](0), dend[37](1)
connect dend[39](0), dend[37](1)
connect dend[40](0), dend[39](1)
connect dend[41](0), dend[40](1)
connect dend[42](0), dend[40](1)
connect dend[43](0), dend[39](1)
connect dend[44](0), dend[43](1)
connect dend[45](0), dend[43](1)
connect dend[46](0), dend[32](1)
connect dend[47](0), dend[46](1)
connect dend[48](0), dend[47](1)
connect dend[49](0), dend[48](1)
connect dend[50](0), dend[48](1)
connect dend[51](0), dend[47](1)
connect dend[52](0), dend[46](1)
connect dend[53](0), dend[46](1)
connect dend[54](0), dend[53](1)
connect dend[55](0), dend[53](1)
connect dend[56](0), dend[55](1)
connect dend[57](0), dend[55](1)
connect dend[58](0), dend[57](1)
connect dend[59](0), dend[57](1)
connect dend[60](0), dend[59](1)
connect dend[61](0), dend[59](1)
connect dend[62](0), soma(0.5)
connect dend[63](0), dend[62](1)
connect dend[64](0), dend[63](1)
connect dend[65](0), dend[64](1)
connect dend[66](0), dend[65](1)
connect dend[67](0), dend[66](1)
connect dend[68](0), dend[66](1)
connect dend[69](0), dend[65](1)
connect dend[70](0), dend[64](1)
connect dend[71](0), dend[70](1)
connect dend[72](0), dend[71](1)
connect dend[73](0), dend[71](1)
connect dend[74](0), dend[70](1)
connect dend[75](0), dend[63](1)
connect dend[76](0), dend[75](1)
connect dend[77](0), dend[76](1)
connect dend[78](0), dend[77](1)
connect dend[79](0), dend[77](1)
connect dend[80](0), dend[76](1)
connect dend[81](0), dend[75](1)
connect dend[82](0), dend[81](1)
connect dend[83](0), dend[82](1)
connect dend[84](0), dend[82](1)
connect dend[85](0), dend[84](1)
connect dend[86](0), dend[84](1)
connect dend[87](0), dend[86](1)
connect dend[88](0), dend[86](1)
connect dend[89](0), dend[88](1)
connect dend[90](0), dend[88](1)
connect dend[91](0), dend[90](1)
connect dend[92](0), dend[90](1)
connect dend[93](0), dend[90](1)
connect dend[94](0), dend[81](1)
connect dend[95](0), dend[62](1)
connect dend[96](0), soma(0.5)
connect dend[97](0), dend[96](1)
connect dend[98](0), dend[97](1)
connect dend[99](0), dend[98](1)
connect dend[100](0), dend[99](1)
connect dend[101](0), dend[99](1)
connect dend[102](0), dend[98](1)
connect dend[103](0), dend[102](1)
connect dend[104](0), dend[102](1)
connect dend[105](0), dend[97](1)
connect dend[106](0), dend[105](1)
connect dend[107](0), dend[105](1)
connect dend[108](0), dend[96](1)
connect dend[109](0), dend[108](1)
connect dend[110](0), dend[109](1)
connect dend[111](0), dend[109](1)
connect dend[112](0), dend[111](1)
connect dend[113](0), dend[112](1)
connect dend[114](0), dend[112](1)
connect dend[115](0), dend[114](1)
connect dend[116](0), dend[114](1)
connect dend[117](0), dend[111](1)
connect dend[118](0), dend[111](1)
connect dend[119](0), dend[108](1)
connect dend[120](0), dend[119](1)
connect dend[121](0), dend[119](1)
connect dend[122](0), dend[121](1)
connect dend[123](0), dend[121](1)
connect dend[124](0), dend[119](1)
connect dend[125](0), soma(0.5)
connect dend[126](0), dend[125](1)
connect dend[127](0), dend[125](1)
connect dend[128](0), dend[127](1)
connect dend[129](0), dend[128](1)
connect dend[130](0), dend[129](1)
connect dend[131](0), dend[130](1)
connect dend[132](0), dend[131](1)
connect dend[133](0), dend[131](1)
connect dend[134](0), dend[133](1)
connect dend[135](0), dend[133](1)
connect dend[136](0), dend[130](1)
connect dend[137](0), dend[136](1)
connect dend[138](0), dend[136](1)
connect dend[139](0), dend[138](1)
connect dend[140](0), dend[139](1)
connect dend[141](0), dend[139](1)
connect dend[142](0), dend[139](1)
connect dend[143](0), dend[138](1)
connect dend[144](0), dend[129](1)
connect dend[145](0), dend[144](1)
connect dend[146](0), dend[145](1)
connect dend[147](0), dend[145](1)
connect dend[148](0), dend[144](1)
connect dend[149](0), dend[128](1)
connect dend[150](0), dend[149](1)
connect dend[151](0), dend[150](1)
connect dend[152](0), dend[150](1)
connect dend[153](0), dend[152](1)
connect dend[154](0), dend[152](1)
connect dend[155](0), dend[149](1)
connect dend[156](0), dend[149](1)
connect dend[157](0), dend[156](1)
connect dend[158](0), dend[156](1)
connect dend[159](0), dend[158](1)
connect dend[160](0), dend[158](1)
connect dend[161](0), dend[127](1)
connect dend[162](0), soma(0.5)
connect dend[163](0), dend[162](1)
connect dend[164](0), dend[163](1)
connect dend[165](0), dend[163](1)
connect dend[166](0), dend[165](1)
connect dend[167](0), dend[166](1)
connect dend[168](0), dend[167](1)
connect dend[169](0), dend[168](1)
connect dend[170](0), dend[169](1)
connect dend[171](0), dend[170](1)
connect dend[172](0), dend[170](1)
connect dend[173](0), dend[169](1)
connect dend[174](0), dend[168](1)
connect dend[175](0), dend[167](1)
connect dend[176](0), dend[166](1)
connect dend[177](0), dend[176](1)
connect dend[178](0), dend[176](1)
connect dend[179](0), dend[165](1)
connect dend[180](0), dend[179](1)
connect dend[181](0), dend[179](1)
connect dend[182](0), dend[179](1)
connect dend[183](0), dend[182](1)
connect dend[184](0), dend[182](1)
connect dend[185](0), dend[182](1)
connect dend[186](0), dend[162](1)
connect dend[187](0), dend[186](1)
connect dend[188](0), dend[187](1)
connect dend[189](0), dend[188](1)
connect dend[190](0), dend[188](1)
connect dend[191](0), dend[187](1)
connect dend[192](0), dend[186](1)
connect dend[193](0), dend[192](1)
connect dend[194](0), dend[192](1)
soma {
pt3dadd(27, -6.5, 0.000, 0.001)
pt3dadd(27, -6.5, 6.750, 14.197)
pt3dadd(27, -6.5, 14.250, 17.042)
pt3dadd(27, -6.5, 19.500, 17.924)
pt3dadd(27, -6.5, 21.750, 17.813)
pt3dadd(27, -6.5, 29.250, 12.720)
pt3dadd(27, -6.5, 36.000, 0.001)
}
dend[0] {
pt3dadd(32.386, -0.068, 30.458, 1.110)
pt3dadd(34.216, 1.284, 30.458, 1.110)
pt3dadd(33.932, 2.750, 30.458, 1.110)
pt3dadd(32.989, 4.602, 30.458, 1.110)
pt3dadd(32.523, 5.420, 30.458, 0.930)
pt3dadd(33.080, 6.920, 30.458, 0.930)
pt3dadd(34.523, 7.625, 30.458, 0.930)
pt3dadd(36.170, 8.341, 30.458, 0.740)
pt3dadd(36.761, 9.215, 30.458, 0.560)
pt3dadd(36.102, 9.602, 30.458, 0.560)
pt3dadd(35.216, 10.614, 30.458, 0.740)
pt3dadd(34.114, 11.398, 30.458, 0.740)
pt3dadd(33.250, 11.989, 30.458, 0.560)
pt3dadd(32.784, 12.807, 30.458, 0.370)
pt3dadd(32.716, 14.068, 30.458, 0.370)
pt3dadd(31.807, 15.500, 30.458, 0.560)
pt3dadd(31.330, 16.523, 30.458, 0.740)
pt3dadd(30.443, 17.318, 30.458, 0.740)
pt3dadd(29.545, 18.533, 30.458, 0.740)
pt3dadd(29.250, 20.000, 30.458, 0.560)
pt3dadd(29.000, 20.830, 30.458, 0.740)
pt3dadd(29.352, 22.114, 30.458, 0.740)
pt3dadd(29.318, 22.955, 30.458, 0.740)
pt3dadd(29.886, 24.034, 30.458, 1.300)
pt3dadd(29.648, 24.659, 30.458, 1.480)
pt3dadd(29.602, 25.500, 30.458, 1.480)
}
dend[1] {
pt3dadd(29.602, 25.500, 30.458, 1.480)
pt3dadd(28.932, 26.307, 30.458, 1.300)
pt3dadd(28.273, 26.898, 30.458, 0.930)
pt3dadd(27.784, 28.148, 30.458, 0.740)
pt3dadd(28.170, 28.795, 30.458, 0.560)
pt3dadd(28.739, 30.091, 30.458, 0.560)
pt3dadd(28.489, 30.920, 30.458, 0.560)
pt3dadd(26.920, 32.739, 30.458, 0.560)
pt3dadd(26.000, 34.159, 32.188, 0.740)
pt3dadd(25.955, 35.216, 32.188, 0.740)
pt3dadd(26.500, 36.716, 32.188, 0.740)
pt3dadd(26.205, 38.386, 32.188, 0.740)
pt3dadd(25.625, 41.523, 32.188, 0.740)
pt3dadd(24.705, 43.159, 32.188, 0.560)
pt3dadd(24.432, 44.409, 32.188, 0.740)
pt3dadd(24.341, 46.091, 32.188, 0.930)
pt3dadd(24.477, 47.568, 32.188, 0.740)
pt3dadd(24.830, 48.852, 32.188, 0.740)
pt3dadd(24.102, 50.716, 32.188, 0.740)
pt3dadd(23.375, 52.568, 32.188, 0.560)
pt3dadd(23.125, 53.398, 32.188, 0.740)
pt3dadd(24.318, 54.727, 32.188, 0.740)
pt3dadd(25.534, 55.636, 32.188, 0.560)
pt3dadd(26.102, 56.920, 32.188, 0.740)
pt3dadd(26.239, 58.409, 32.188, 0.560)
pt3dadd(24.898, 60.023, 32.188, 0.560)
pt3dadd(25.227, 61.727, 32.188, 0.560)
pt3dadd(25.807, 62.807, 32.188, 0.930)
pt3dadd(27.182, 64.773, 32.188, 0.930)
pt3dadd(27.534, 66.057, 34.708, 0.560)
pt3dadd(26.841, 67.284, 34.708, 0.560)
pt3dadd(26.750, 68.966, 34.708, 0.560)
pt3dadd(26.670, 70.648, 34.708, 0.740)
pt3dadd(27.443, 71.955, 34.708, 0.740)
pt3dadd(28.489, 72.216, 34.708, 0.560)
pt3dadd(29.523, 72.477, 34.708, 0.560)
pt3dadd(31.216, 72.352, 34.708, 0.560)
pt3dadd(32.909, 72.227, 34.708, 0.560)
pt3dadd(35.795, 73.432, 34.708, 0.560)
pt3dadd(37.250, 73.739, 32.917, 0.740)
pt3dadd(38.511, 73.739, 32.917, 0.740)
pt3dadd(40.193, 74.159, 32.917, 0.740)
pt3dadd(41.670, 74.784, 32.917, 0.740)
pt3dadd(42.511, 76.045, 32.917, 0.740)
pt3dadd(43.773, 77.102, 32.917, 0.560)
pt3dadd(44.398, 77.727, 42.917, 0.370)
pt3dadd(44.614, 78.159, 42.917, 0.370)
pt3dadd(43.977, 79.420, 42.917, 0.370)
pt3dadd(44.193, 79.625, 42.917, 1.110)
pt3dadd(42.932, 79.625, 42.917, 1.110)
pt3dadd(43.352, 80.466, 42.333, 1.110)
pt3dadd(42.932, 82.148, 42.333, 1.110)
}
dend[2] {
pt3dadd(29.602, 25.500, 30.458, 1.480)
// too much code just like this...