fix positioning of tall labware to avoid crashing

protoBuilds/051557/dilution.ot2.apiv2.py.json

@@ -1,5 +1,5 @@
 {
-    "content": "from opentrons.types import Mount\n\nmetadata = {\n    'protocolName': 'Lipid Quantification',\n    'author': 'Nick <[email protected]>',\n    'apiLevel': '2.13'\n}\n\n\ndef run(ctx):\n\n    [num_sample_columns, mount_m20, mount_m300] = get_values(  # noqa: F821\n        'num_sample_columns', 'mount_m20', 'mount_m300')\n\n    # labware\n    plate = ctx.load_labware('abgene_96_wellplate_2200ul', '4')\n    tubeblock = ctx.load_labware(\n        'opentrons_24_aluminumblock_nest_1.5ml_snapcap', '5')\n    reservoir = ctx.load_labware(\n        'eppendorf_7_reservoir_30000ul', '8',\n        'triton (channel 1) and triglyceride (channel 1)')\n    tipracks20 = [ctx.load_labware('opentrons_96_tiprack_20ul', '2')]\n    tipracks300 = [ctx.load_labware('opentrons_96_tiprack_300ul', '3')]\n    tiprack20_s = ctx.load_labware('opentrons_96_tiprack_20ul', '10')\n\n    # pipettes\n    m20 = ctx.load_instrument('p20_multi_gen2', mount_m20,\n                              tip_racks=tipracks20)\n    m300 = ctx.load_instrument('p300_multi_gen2', mount_m300,\n                               tip_racks=tipracks300)\n\n    # reagents\n    triton = reservoir.rows()[0][0]\n    triglyceride = reservoir.rows()[0][1]\n    offset_triglyceride = -41\n    standards = tubeblock.wells()[:5]\n    standards_dests_sets = [\n        row[:3] for row in plate.rows()[1:6]]\n    triton_dests = plate.rows()[0][:3+num_sample_columns]\n    triglyceride_dests = triton_dests\n\n    def slow_withdraw(pip, well, delay_seconds=2.0):\n        pip.default_speed /= 16\n        if delay_seconds > 0:\n            ctx.delay(seconds=delay_seconds)\n        pip.move_to(well.top())\n        pip.default_speed *= 16\n\n    tips_single = tiprack20_s.wells()\n    default_current = 0.6\n    mount = Mount.LEFT if m20.mount == 'left' else Mount.RIGHT\n\n    # offset tip pickup\n    def pick_up_single():\n        ctx._hw_manager.hardware._attached_instruments[\n            mount].update_config_item(\n                'pick_up_current', default_current/8)\n        tip = tips_single.pop()\n        m20.pick_up_tip(tip)\n        ctx._hw_manager.hardware._attached_instruments[\n            mount].update_config_item(\n                'pick_up_current', default_current)\n\n    # transfer standards\n    vol_standard = 3\n    if standards[0].depth > tips_single[0].depth - 5:  # account for overlap\n        h_asp = tips_single[0].depth - 5\n    else:\n        h_asp = standards[0].depth - 5\n    if plate.wells()[0].depth > tips_single[0].depth - 5:\n        h_disp = tips_single[0].depth - 5\n    else:\n        h_disp = plate.wells()[0].depth - 5\n\n    for s, dest_set in zip(standards, standards_dests_sets):\n        for d in dest_set:\n            pick_up_single()\n            m20.aspirate(vol_standard, s.top(-1*h_asp))\n            slow_withdraw(m20, s)\n            m20.dispense(vol_standard, d.top(-1*h_disp))\n            m20.drop_tip()\n\n    ctx.pause('Remove silicone mats from pre-plated sample wells.')\n\n    # transfer triton\n    vol_triton = 10.0\n    for d in triton_dests:\n        m20.pick_up_tip()\n        m20.aspirate(vol_triton, triton.bottom(5))\n        slow_withdraw(m20, triton)\n        m20.dispense(vol_triton, d.top(-1*h_disp))\n        slow_withdraw(m20, d)\n        m20.drop_tip()\n\n    ctx.pause('Cover plate, shake 2 minutes @ 900 r.p.m., incubate 1 hour \\\n@ 37C, and 20 minutes @ room temperature.')\n\n    # transfer triglyceride\n    vol_triglyceride = 300.0\n    for d in triglyceride_dests:\n        m300.pick_up_tip()\n        m300.aspirate(\n            vol_triglyceride, triglyceride.bottom(5-offset_triglyceride))\n        slow_withdraw(m300, triglyceride)\n        m300.dispense(vol_triglyceride, d.bottom(5))\n        slow_withdraw(m300, d)\n        m300.drop_tip()\n",
+    "content": "from opentrons.types import Mount\n\nmetadata = {\n    'protocolName': 'Lipid Quantification',\n    'author': 'Nick <[email protected]>',\n    'apiLevel': '2.13'\n}\n\n\ndef run(ctx):\n\n    [num_sample_columns, mount_m20, mount_m300] = get_values(  # noqa: F821\n        'num_sample_columns', 'mount_m20', 'mount_m300')\n\n    # labware\n    plate = ctx.load_labware('abgene_96_wellplate_2200ul', '4')\n    tubeblock = ctx.load_labware(\n        'opentrons_24_aluminumblock_nest_1.5ml_snapcap', '5')\n    reservoir = ctx.load_labware(\n        'eppendorf_7_reservoir_30000ul', '11',\n        'triton (channel 1) and triglyceride (channel 1)')\n    tipracks20 = [ctx.load_labware('opentrons_96_tiprack_20ul', '8')]\n    tipracks300 = [ctx.load_labware('opentrons_96_tiprack_300ul', '3')]\n    tiprack20_s = ctx.load_labware('opentrons_96_tiprack_20ul', '10')\n\n    # pipettes\n    m20 = ctx.load_instrument('p20_multi_gen2', mount_m20,\n                              tip_racks=tipracks20)\n    m300 = ctx.load_instrument('p300_multi_gen2', mount_m300,\n                               tip_racks=tipracks300)\n\n    # reagents\n    triton = reservoir.rows()[0][0]\n    triglyceride = reservoir.rows()[0][1]\n    offset_triglyceride = -41\n    standards = tubeblock.wells()[:5]\n    standards_dests_sets = [\n        row[:3] for row in plate.rows()[1:6]]\n    triton_dests = plate.rows()[0][:3+num_sample_columns]\n    triglyceride_dests = triton_dests\n\n    def slow_withdraw(pip, well, delay_seconds=2.0):\n        pip.default_speed /= 16\n        if delay_seconds > 0:\n            ctx.delay(seconds=delay_seconds)\n        pip.move_to(well.top(5))\n        pip.default_speed *= 16\n\n    tips_single = tiprack20_s.wells()\n    default_current = 0.6\n    mount = Mount.LEFT if m20.mount == 'left' else Mount.RIGHT\n\n    # offset tip pickup\n    def pick_up_single():\n        ctx._hw_manager.hardware._attached_instruments[\n            mount].update_config_item(\n                'pick_up_current', default_current/8)\n        tip = tips_single.pop()\n        m20.pick_up_tip(tip)\n        ctx._hw_manager.hardware._attached_instruments[\n            mount].update_config_item(\n                'pick_up_current', default_current)\n\n    # transfer standards\n    vol_standard = 3\n    if standards[0].depth > tips_single[0].depth - 5:  # account for overlap\n        h_asp = tips_single[0].depth - 5\n    else:\n        h_asp = standards[0].depth - 5\n    if plate.wells()[0].depth > tips_single[0].depth - 5:\n        h_disp = tips_single[0].depth - 5\n    else:\n        h_disp = plate.wells()[0].depth - 5\n\n    for s, dest_set in zip(standards, standards_dests_sets):\n        for d in dest_set:\n            pick_up_single()\n            m20.aspirate(vol_standard, s.top(-1*h_asp))\n            slow_withdraw(m20, s)\n            m20.dispense(vol_standard, d.top(-1*h_disp))\n            m20.drop_tip()\n\n    ctx.pause('Remove silicone mats from pre-plated sample wells.')\n\n    # transfer triton\n    vol_triton = 10.0\n    for d in triton_dests:\n        m20.pick_up_tip()\n        m20.move_to(triton.top(5))\n        m20.aspirate(vol_triton, triton.bottom(5))\n        slow_withdraw(m20, triton)\n        m20.dispense(vol_triton, d.top(-1*h_disp))\n        slow_withdraw(m20, d)\n        m20.drop_tip()\n\n    ctx.pause('Cover plate, shake 2 minutes @ 900 r.p.m., incubate 1 hour \\\n@ 37C, and 20 minutes @ room temperature.')\n\n    # transfer triglyceride\n    vol_triglyceride = 300.0\n    for d in triglyceride_dests:\n        m300.pick_up_tip()\n        m300.move_to(triglyceride.top(5))\n        m300.aspirate(\n            vol_triglyceride, triglyceride.bottom(5-offset_triglyceride))\n        slow_withdraw(m300, triglyceride)\n        m300.dispense(vol_triglyceride, d.bottom(5))\n        slow_withdraw(m300, d)\n        m300.drop_tip()\n",
     "custom_labware_defs": [
         {
             "brand": {
@@ -1570,12 +1570,6 @@
         }
     ],
     "labware": [
-        {
-            "name": "Opentrons 96 Tip Rack 20 \u00b5L on 2",
-            "share": false,
-            "slot": "2",
-            "type": "opentrons_96_tiprack_20ul"
-        },
         {
             "name": "Opentrons 96 Tip Rack 300 \u00b5L on 3",
             "share": false,
@@ -1595,17 +1589,23 @@
             "type": "opentrons_24_aluminumblock_nest_1.5ml_snapcap"
         },
         {
-            "name": "triton (channel 1) and triglyceride (channel 1) on 8",
+            "name": "Opentrons 96 Tip Rack 20 \u00b5L on 8",
             "share": false,
             "slot": "8",
-            "type": "eppendorf_7_reservoir_30000ul"
+            "type": "opentrons_96_tiprack_20ul"
         },
         {
             "name": "Opentrons 96 Tip Rack 20 \u00b5L on 10",
             "share": false,
             "slot": "10",
             "type": "opentrons_96_tiprack_20ul"
         },
+        {
+            "name": "triton (channel 1) and triglyceride (channel 1) on 11",
+            "share": false,
+            "slot": "11",
+            "type": "eppendorf_7_reservoir_30000ul"
+        },
         {
             "name": "Opentrons Fixed Trash on 12",
             "share": false,

protocols/051557/dilution.ot2.apiv2.py

@@ -17,9 +17,9 @@ def run(ctx):
     tubeblock = ctx.load_labware(
         'opentrons_24_aluminumblock_nest_1.5ml_snapcap', '5')
     reservoir = ctx.load_labware(
-        'eppendorf_7_reservoir_30000ul', '8',
+        'eppendorf_7_reservoir_30000ul', '11',
         'triton (channel 1) and triglyceride (channel 1)')
-    tipracks20 = [ctx.load_labware('opentrons_96_tiprack_20ul', '2')]
+    tipracks20 = [ctx.load_labware('opentrons_96_tiprack_20ul', '8')]
     tipracks300 = [ctx.load_labware('opentrons_96_tiprack_300ul', '3')]
     tiprack20_s = ctx.load_labware('opentrons_96_tiprack_20ul', '10')
 
@@ -43,7 +43,7 @@ def slow_withdraw(pip, well, delay_seconds=2.0):
         pip.default_speed /= 16
         if delay_seconds > 0:
             ctx.delay(seconds=delay_seconds)
-        pip.move_to(well.top())
+        pip.move_to(well.top(5))
         pip.default_speed *= 16
 
     tips_single = tiprack20_s.wells()
@@ -86,6 +86,7 @@ def pick_up_single():
     vol_triton = 10.0
     for d in triton_dests:
         m20.pick_up_tip()
+        m20.move_to(triton.top(5))
         m20.aspirate(vol_triton, triton.bottom(5))
         slow_withdraw(m20, triton)
         m20.dispense(vol_triton, d.top(-1*h_disp))
@@ -99,6 +100,7 @@ def pick_up_single():
     vol_triglyceride = 300.0
     for d in triglyceride_dests:
         m300.pick_up_tip()
+        m300.move_to(triglyceride.top(5))
         m300.aspirate(
             vol_triglyceride, triglyceride.bottom(5-offset_triglyceride))
         slow_withdraw(m300, triglyceride)