Issue #781: periplasm corner case

data/tmdet-example-annotations/1a0s.json

@@ -12467,6 +12467,7 @@
         }
     ],
     "additional_entry_annotations": {
+        "tm_type": "Tm_Beta",
         "membrane": {
             "normal": {
                 "x": 2.0e-8,

data/tmdet-example-annotations/1afo.json

@@ -868,6 +868,7 @@
         }
     ],
     "additional_entry_annotations": {
+        "tm_type": "Tm_Alpha",
         "membrane": {
             "normal": {
                 "x": 0,

data/tmdet-example-annotations/1jb0.json

@@ -22588,6 +22588,7 @@
         }
     ],
     "additional_entry_annotations": {
+        "tm_type": "Tm_Alpha",
         "membrane": {
             "normal": {
                 "x": 0,

data/tmdet-example-annotations/1q90.json

@@ -19252,6 +19252,7 @@
         }
     ],
     "additional_entry_annotations": {
+        "tm_type": "Tm_Alpha",
         "membrane": {
             "normal": {
                 "x": -1.0e-8,

data/tmdet-example-annotations/1xl4.json

@@ -11406,6 +11406,7 @@
         }
     ],
     "additional_entry_annotations": {
+        "tm_type": "Tm_Alpha",
         "membrane": {
             "normal": {
                 "x": -0.37794915,

data/tmdet-example-annotations/1xl6.json

@@ -11726,6 +11726,7 @@
         }
     ],
     "additional_entry_annotations": {
+        "tm_type": "Tm_Alpha",
         "membrane": {
             "normal": {
                 "x": -3.0e-8,

data/tmdet-example-annotations/2atk.json

@@ -4206,6 +4206,7 @@
         }
     ],
     "additional_entry_annotations": {
+        "tm_type": "Tm_Alpha",
         "membrane": {
             "normal": {
                 "x": 0,

data/tmdet-example-annotations/4x8a.json

@@ -3826,6 +3826,7 @@
         }
     ],
     "additional_entry_annotations": {
+        "tm_type": "Tm_Alpha",
         "membrane": {
             "normal": {
                 "x": 0.04159873,

data/tmdet-example-annotations/5un1.json

@@ -16696,6 +16696,7 @@
         }
     ],
     "additional_entry_annotations": {
+        "tm_type": "Tm_Alpha",
         "membrane": {
             "normal": {
                 "x": 0.09473176,

data/tmdet-example-annotations/5xls.json

@@ -4139,6 +4139,7 @@
         }
     ],
     "additional_entry_annotations": {
+        "tm_type": "Tm_Alpha",
         "membrane": {
             "normal": {
                 "x": 0.91788888,

data/tmdet-example-annotations/6cse.json

@@ -4369,6 +4369,7 @@
         }
     ],
     "additional_entry_annotations": {
+        "tm_type": "Tm_Alpha",
         "membrane": {
             "normal": {
                 "x": 0,

data/tmdet-example-annotations/6csf.json

@@ -4369,6 +4369,7 @@
         }
     ],
     "additional_entry_annotations": {
+        "tm_type": "Tm_Alpha",
         "membrane": {
             "normal": {
                 "x": 0,

data/tmdet-example-annotations/6ly5.json

@@ -66814,6 +66814,7 @@
         }
     ],
     "additional_entry_annotations": {
+        "tm_type": "Ca_Tm",
         "membrane": {
             "normal": {
                 "x": 0,

data/tmdet-example-annotations/6wtx.json

@@ -8968,6 +8968,7 @@
         }
     ],
     "additional_entry_annotations": {
+        "tm_type": "Tm_Alpha",
         "membrane": {
             "normal": {
                 "x": 1.6e-7,

data/tmdet-example-annotations/6xvf.json

@@ -31173,6 +31173,7 @@
         }
     ],
     "additional_entry_annotations": {
+        "tm_type": "Tm_Alpha",
         "membrane": {
             "normal": {
                 "x": 1.00165713,

data/tmdet-example-annotations/7xna.json

@@ -0,0 +1,2979 @@
+{
+    "data_resource": "PDBTM",
+    "resource_version": " 956",
+    "software_version": "3.2.134",
+    "resource_entry_url": "http://pdbtm.unitmp.org/entry/7xna",
+    "model_coordinates_url": "http://pdbtm.unitmp.org/api/v1/entry/7xna.trpdb",
+    "release_date": "04/08/2022",
+    "pdb_id": "7xna",
+    "includes_het_groups": false,
+    "chains": [
+        {
+            "chain_label": "A",
+            "additional_chain_annotations": {
+                "type": "alpha",
+                "num_tm": "7"
+            },
+            "residues": [
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 2,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "66",
+                    "aa_type": "THR"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 2,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "67",
+                    "aa_type": "SER"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 2,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "68",
+                    "aa_type": "ASN"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 2,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "69",
+                    "aa_type": "ALA"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "70",
+                    "aa_type": "VAL"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "71",
+                    "aa_type": "LEU"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "72",
+                    "aa_type": "THR"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "73",
+                    "aa_type": "PHE"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "74",
+                    "aa_type": "ILE"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "75",
+                    "aa_type": "TYR"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "76",
+                    "aa_type": "PHE"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "77",
+                    "aa_type": "VAL"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "78",
+                    "aa_type": "VAL"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "79",
+                    "aa_type": "CYS"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "80",
+                    "aa_type": "ILE"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "81",
+                    "aa_type": "ILE"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "82",
+                    "aa_type": "GLY"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "83",
+                    "aa_type": "LEU"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "84",
+                    "aa_type": "CYS"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "85",
+                    "aa_type": "GLY"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "86",
+                    "aa_type": "ASN"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "87",
+                    "aa_type": "THR"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "88",
+                    "aa_type": "LEU"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "89",
+                    "aa_type": "VAL"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "90",
+                    "aa_type": "ILE"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "91",
+                    "aa_type": "TYR"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "92",
+                    "aa_type": "VAL"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "93",
+                    "aa_type": "ILE"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "94",
+                    "aa_type": "LEU"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "95",
+                    "aa_type": "ARG"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "96",
+                    "aa_type": "TYR"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "97",
+                    "aa_type": "ALA"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "98",
+                    "aa_type": "LYS"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "99",
+                    "aa_type": "MET"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "100",
+                    "aa_type": "LYS"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "101",
+                    "aa_type": "THR"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "102",
+                    "aa_type": "ILE"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "103",
+                    "aa_type": "THR"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "104",
+                    "aa_type": "ASN"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "105",
+                    "aa_type": "ILE"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "106",
+                    "aa_type": "TYR"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "107",
+                    "aa_type": "ILE"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "108",
+                    "aa_type": "LEU"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "109",
+                    "aa_type": "ASN"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "110",
+                    "aa_type": "LEU"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "111",
+                    "aa_type": "ALA"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "112",
+                    "aa_type": "ILE"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "113",
+                    "aa_type": "ALA"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "114",
+                    "aa_type": "ASN"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "115",
+                    "aa_type": "GLU"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "116",
+                    "aa_type": "LEU"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "117",
+                    "aa_type": "PHE"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "118",
+                    "aa_type": "MET"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "119",
+                    "aa_type": "LEU"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "120",
+                    "aa_type": "GLY"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "121",
+                    "aa_type": "LEU"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "122",
+                    "aa_type": "PRO"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "123",
+                    "aa_type": "PHE"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "124",
+                    "aa_type": "LEU"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "125",
+                    "aa_type": "ALA"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "126",
+                    "aa_type": "MET"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 2,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "127",
+                    "aa_type": "GLN"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 2,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "128",
+                    "aa_type": "VAL"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 2,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "129",
+                    "aa_type": "ALA"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 2,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "130",
+                    "aa_type": "LEU"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 2,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "131",
+                    "aa_type": "GLU"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 2,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "132",
+                    "aa_type": "HIS"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 2,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "133",
+                    "aa_type": "TRP"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 2,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "134",
+                    "aa_type": "PRO"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 2,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "135",
+                    "aa_type": "PHE"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 2,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "136",
+                    "aa_type": "GLY"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 2,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "137",
+                    "aa_type": "LYS"
+                },
+                {
+                    "site_data": [
+                        {
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+                    "pdb_res_label": "503",
+                    "aa_type": "VAL"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "504",
+                    "aa_type": "LEU"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "505",
+                    "aa_type": "THR"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "506",
+                    "aa_type": "TYR"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "507",
+                    "aa_type": "ALA"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "508",
+                    "aa_type": "ASN"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "509",
+                    "aa_type": "SER"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "510",
+                    "aa_type": "CYS"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "511",
+                    "aa_type": "ALA"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "512",
+                    "aa_type": "ASN"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "513",
+                    "aa_type": "PRO"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "514",
+                    "aa_type": "ILE"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "515",
+                    "aa_type": "LEU"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "516",
+                    "aa_type": "TYR"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "517",
+                    "aa_type": "ALA"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "518",
+                    "aa_type": "PHE"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 3,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "519",
+                    "aa_type": "LEU"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "520",
+                    "aa_type": "ASP"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "521",
+                    "aa_type": "ASP"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "522",
+                    "aa_type": "ASN"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "523",
+                    "aa_type": "PHE"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "524",
+                    "aa_type": "LYS"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "525",
+                    "aa_type": "LYS"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "526",
+                    "aa_type": "SER"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "527",
+                    "aa_type": "PHE"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "528",
+                    "aa_type": "GLN"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "529",
+                    "aa_type": "ASN"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "530",
+                    "aa_type": "VAL"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "531",
+                    "aa_type": "LEU"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "532",
+                    "aa_type": "CYS"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "533",
+                    "aa_type": "LEU"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "534",
+                    "aa_type": "VAL"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "535",
+                    "aa_type": "LYS"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "536",
+                    "aa_type": "VAL"
+                },
+                {
+                    "site_data": [
+                        {
+                            "site_id_ref": 1,
+                            "confidence_classification": "curated"
+                        }
+                    ],
+                    "pdb_res_label": "537",
+                    "aa_type": "SER"
+                }
+            ]
+        }
+    ],
+    "sites": [
+        {
+            "site_id": 1,
+            "label": "Side1"
+        },
+        {
+            "site_id": 2,
+            "label": "Side2"
+        },
+        {
+            "site_id": 3,
+            "label": "Transmembrane Alpha Helix"
+        },
+        {
+            "site_id": 4,
+            "label": "Transmembrane Beta strand"
+        },
+        {
+            "site_id": 5,
+            "label": "Transmembrane Re-entrant Loop"
+        },
+        {
+            "site_id": 6,
+            "label": "Interfacial Helix"
+        },
+        {
+            "site_id": 7,
+            "label": "Unknown localization"
+        },
+        {
+            "site_id": 8,
+            "label": "Membrane Inside"
+        }
+    ],
+    "evidence_code_ontology": [
+        {
+            "eco_term": "computational combinatorial evidence used in automatic assertion",
+            "eco_code": "ECO_0000246"
+        }
+    ],
+    "additional_entry_annotations": {
+        "tm_type": "Tm_Alpha",
+        "membrane": {
+            "normal": {
+                "x": 0,
+                "y": 0,
+                "z": 16.75
+            },
+            "radius": 28,
+            "transformation_matrix": {
+                "rowx": {
+                    "x": 1,
+                    "y": 0,
+                    "z": 0,
+                    "t": 4.59613371
+                },
+                "rowy": {
+                    "x": 0,
+                    "y": 1,
+                    "z": 0,
+                    "t": 30.78532982
+                },
+                "rowz": {
+                    "x": 0,
+                    "y": 0,
+                    "z": 1,
+                    "t": -40.18399811
+                }
+            }
+        },
+        "biomatrix": {
+            "chain_deletes": [
+                "B"
+            ]
+        },
+        "ent_cif_mapping_results": {
+            "ent_cif_chain_map": {
+                "A": [
+                    "A"
+                ],
+                "B": [
+                    "B"
+                ]
+            },
+            "cif_chain_derivatives": [],
+            "pdbtm_derivatives_and_cif_chain_map": []
+        }
+    }
+}

data/tmdet-example-annotations/7yuy.json

@@ -15089,6 +15089,7 @@
         }
     ],
     "additional_entry_annotations": {
+        "tm_type": "Tm_Alpha",
         "membrane": {
             "normal": {
                 "x": 0,

src/apps/tm-viewer/index.html

@@ -122,7 +122,8 @@
                 '6csf',
                 '5un1',
                 '6wtx',
-                '7yuy'
+                '7yuy',
+                '5ng5'
             ];
             idList.forEach((pdbId) => addControl(pdbId, () => load(pdbId)));
             addControl('Reset', () => {

src/extensions/tmdet/labeling.ts

@@ -42,7 +42,8 @@ export const TmDetLabelProvider: LociLabelProvider = {
 
             let chainList =  TmDetChainListCache.get(pdbId);
             if (!chainList) {
-                chainList = createResidueListsPerChain(descriptor.chains, descriptor.side1);
+                const tmType = descriptor.additional_entry_annotations.tm_type;
+                chainList = createResidueListsPerChain(descriptor.chains, descriptor.side1, tmType);
                 TmDetChainListCache.set(pdbId, chainList);
             }
 

src/extensions/tmdet/tmdet-color-theme.ts

@@ -41,7 +41,8 @@ export function TmDetColorTheme(
         descriptorChains = pdbtmDescriptor.chains;
     }
 
-    const chainList = createResidueListsPerChain(descriptorChains, pdbtmDescriptor.side1);
+    const tmType = pdbtmDescriptor.additional_entry_annotations.tm_type;
+    const chainList = createResidueListsPerChain(descriptorChains, pdbtmDescriptor.side1, tmType);
     if (pdbId) {
         TmDetChainListCache.set(pdbId, chainList);
     }
@@ -127,8 +128,10 @@ export function getChainAndResidueIds(location: Location) {
     };
 }
 
-export function createResidueListsPerChain(chains: PDBTMChain[], side1: string|null) {
+export function createResidueListsPerChain(chains: PDBTMChain[], side1: string|null, tmType: string) {
+
     const chainList: ChainList = [];
+    const hasBeta = chains.some(chain => chain.additional_chain_annotations.type == "beta");
 
     chains.forEach((chain: PDBTMChain) => {
         const chainType = chain.additional_chain_annotations.type;
@@ -137,7 +140,17 @@ export function createResidueListsPerChain(chains: PDBTMChain[], side1: string|n
         chain.residues.forEach((residue) => {
             let siteId = residue.site_data![0].site_id_ref - 1;
             let siteColorId = siteId;
-            if (chainType == "beta") {
+            if (tmType == "Tm_Alpha" && hasBeta && side1 == "Periplasm") {
+                if (siteId == SiteIndexes.Side1) {
+                    siteColorId = SiteIndexes.Periplasm;
+                } else if (siteId == SiteIndexes.Side2) {
+                    if (chainType == "non_tm" || chainType == "alpha") {
+                        siteColorId = SiteIndexes.Side1;
+                    } else if (chainType == "beta") {
+                        siteColorId = SiteIndexes.Side2;
+                    }
+                }
+            } else if (chainType == "beta") {
                 if (side1 == "Periplasm" && siteColorId == SiteIndexes.Side1
                     || side1 == "Outside" && siteColorId == SiteIndexes.Side2) {
                     siteColorId = SiteIndexes.Periplasm;

src/extensions/tmdet/types.ts

@@ -39,6 +39,7 @@ export type PDBTMDescriptor = {
     chains: PDBTMChain[],
     site: { site_id: number, label: string }[],
     additional_entry_annotations: {
+        tm_type: string,
         membrane: {
             normal: PDBTMVec3,
             transformation_matrix: PDBTMTransformationMatrix,