Partial igf1

1gzr_critical_residues.tsv

@@ -0,0 +1,69 @@
+# ATOMICA Critical Residue Analysis: 1gzr_all
+# Structure ID: 1gzr
+# Total residues analyzed: 60
+# Mean ATOMICA_SCORE: 0.999531
+# Std Dev: 0.000484
+# Method: ATOMICA_SCORE (cosine similarity with masked residues)
+# Lower scores = More critical for intermolecular interactions
+#
+Rank	Chain_ID	Residue_ID	Residue_Name	ATOMICA_Score	Importance_Delta_Percent	Block_Index
+1	B	20	ASP	0.997627	0.2373	17
+2	B	23	PHE	0.998191	0.1809	20
+3	B	10	LEU	0.998427	0.1573	7
+4	B	53	ASP	0.998653	0.1347	47
+5	B	40	GLN	0.998791	0.1209	34
+6	B	33	SER	0.998974	0.1026	30
+7	B	8	ALA	0.999006	0.0994	5
+8	B	7	GLY	0.999042	0.0958	4
+9	B	19	GLY	0.999089	0.0911	16
+10	B	43	ILE	0.999155	0.0845	37
+11	B	11	VAL	0.999255	0.0745	8
+12	B	30	GLY	0.999292	0.0708	27
+13	B	64	LEU	0.999360	0.0640	58
+14	B	15	GLN	0.999398	0.0602	12
+15	B	32	GLY	0.999432	0.0568	29
+16	B	49	PHE	0.999492	0.0508	43
+17	B	17	VAL	0.999567	0.0433	14
+18	B	58	GLU	0.999569	0.0431	52
+19	B	12	ASP	0.999574	0.0426	9
+20	B	63	PRO	0.999602	0.0398	57
+21	B	44	VAL	0.999609	0.0391	38
+22	B	47	CYS	0.999609	0.0391	41
+23	B	56	ARG	0.999610	0.0390	50
+24	B	42	GLY	0.999615	0.0385	36
+25	B	54	LEU	0.999658	0.0342	48
+26	B	9	GLU	0.999664	0.0336	6
+27	B	31	TYR	0.999674	0.0326	28
+28	B	4	THR	0.999674	0.0326	1
+29	B	45	ASP	0.999676	0.0324	39
+30	B	16	PHE	0.999702	0.0298	13
+31	B	18	CYS	0.999705	0.0295	15
+32	B	24	TYR	0.999721	0.0279	21
+33	B	41	THR	0.999736	0.0264	35
+34	B	48	CYS	0.999736	0.0264	42
+35	B	14	LEU	0.999736	0.0264	11
+36	B	25	PHE	0.999745	0.0255	22
+37	B	62	ALA	0.999745	0.0255	56
+38	B	66	PRO	0.999754	0.0246	60
+39	B	51	SER	0.999758	0.0242	45
+40	B	60	TYR	0.999783	0.0217	54
+41	B	35	SER	0.999789	0.0211	32
+42	B	28	PRO	0.999830	0.0170	25
+43	B	50	ARG	0.999837	0.0163	44
+44	B	55	ARG	0.999844	0.0156	49
+45	B	13	ALA	0.999844	0.0156	10
+46	B	22	GLY	0.999846	0.0154	19
+47	B	27	LYS	0.999847	0.0153	24
+48	B	34	SER	0.999853	0.0147	31
+49	B	61	CYS	0.999855	0.0145	55
+50	B	52	CYS	0.999855	0.0145	46
+51	B	59	MET	0.999880	0.0120	53
+52	B	5	LEU	0.999887	0.0113	2
+53	B	6	CYS	0.999911	0.0089	3
+54	B	26	ASN	0.999928	0.0072	23
+55	B	57	LEU	0.999934	0.0066	51
+56	B	21	ARG	0.999940	0.0060	18
+57	B	29	THR	0.999951	0.0049	26
+58	B	39	PRO	0.999964	0.0036	33
+59	B	65	LYS	0.999978	0.0022	59
+60	B	46	GLU	0.999989	0.0011	40

1gzr_interact_scores.json

@@ -0,0 +1 @@
+{"id": "1gzr_all", "cos_distances": [0.9996740818023682, 0.9998867511749268, 0.9999107122421265, 0.9990419745445251, 0.9990062117576599, 0.9996638298034668, 0.9984265565872192, 0.9992549419403076, 0.9995744228363037, 0.9998443126678467, 0.9997363090515137, 0.9993982315063477, 0.9997018575668335, 0.9995665550231934, 0.9997047781944275, 0.9990887641906738, 0.997627317905426, 0.9999399185180664, 0.9998459815979004, 0.9981908202171326, 0.999721109867096, 0.9997445940971375, 0.9999282360076904, 0.9998467564582825, 0.9998302459716797, 0.9999508857727051, 0.9992923736572266, 0.9996736645698547, 0.9994320869445801, 0.998973548412323, 0.9998533129692078, 0.999788761138916, 0.9999639987945557, 0.9987914562225342, 0.9997355937957764, 0.9996146559715271, 0.9991554021835327, 0.9996086359024048, 0.9996757507324219, 0.9999892115592957, 0.9996094703674316, 0.9997357130050659, 0.9994920492172241, 0.999836802482605, 0.9997580647468567, 0.9998548030853271, 0.9986525774002075, 0.9996579885482788, 0.9998438358306885, 0.9996104836463928, 0.999933660030365, 0.9995685815811157, 0.9998795986175537, 0.9997833371162415, 0.9998546242713928, 0.9997446537017822, 0.9996016621589661, 0.9993603229522705, 0.9999784827232361, 0.9997539520263672, 0.9982069134712219], "block_idx": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61], "time_seconds": 11.6256, "peak_memory_mb": 448.33}

1gzr_metadata.json

@@ -0,0 +1,5 @@
+{
+  "pdb_id": "1gzr",
+  "found": false,
+  "error": "Metadata fetch failed: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1016)>"
+}

1gzr_pymol_commands.pml

@@ -0,0 +1,52 @@
+# ============================================================
+# PyMOL Commands for 1gzr
+# ============================================================
+# Copy and paste these commands into PyMOL
+# ============================================================
+
+# Load structure (adjust path as needed)
+load 1gzr.pdb
+
+# Basic setup
+hide all
+show cartoon
+color grey80, all
+
+# Select and highlight critical residues (Top 10)
+select critical_top10, resi 20+23+10+53+40+33+8+7+19+43 and chain B
+show sticks, critical_top10
+color red, critical_top10
+set stick_radius, 0.3, critical_top10
+
+# Label critical residues
+label critical_top10 and name CA, "%s%s" % (resn,resi)
+set label_size, 14
+set label_color, red
+
+# Create gradient coloring by importance (Top 5 in different reds)
+select critical_rank1, resi 20 and chain B
+color red, critical_rank1
+select critical_rank2, resi 23 and chain B
+color tv_red, critical_rank2
+select critical_rank3, resi 10 and chain B
+color salmon, critical_rank3
+select critical_rank4, resi 53 and chain B
+color lightsalmon, critical_rank4
+select critical_rank5, resi 40 and chain B
+color warmpink, critical_rank5
+
+# Show surface around critical residues
+show surface, byres (critical_top10 around 5)
+set surface_color, white
+set transparency, 0.5
+
+# Center view on critical residues
+zoom critical_top10
+
+# ============================================================
+# Additional useful commands:
+# ============================================================
+# To save session: save 1gzr_critical.pse
+# To save image: png 1gzr_critical.png, dpi=300
+# To highlight most critical (rank 1): select most_critical, critical_rank1
+# ============================================================

1gzr_summary.json

@@ -0,0 +1,20 @@
+{
+  "total_structures": 1,
+  "total_time_seconds": 11.63,
+  "total_time_minutes": 0.19,
+  "time_per_structure": {
+    "mean": 11.6256,
+    "std": 0.0,
+    "min": 11.6256,
+    "max": 11.6256
+  },
+  "output_file": "output/1gzr_interact_scores.json",
+  "input_file": "downloads/pdbs/1gzr.cif",
+  "start_idx": 0,
+  "num_lines": null,
+  "device": "cuda",
+  "gpu_memory_mb": {
+    "mean": 448.33,
+    "max": 448.33
+  }
+}

1gzy_critical_residues.tsv

@@ -0,0 +1,65 @@
+# ATOMICA Critical Residue Analysis: 1gzy_all
+# Structure ID: 1gzy
+# Total residues analyzed: 56
+# Mean ATOMICA_SCORE: 0.999478
+# Std Dev: 0.000512
+# Method: ATOMICA_SCORE (cosine similarity with masked residues)
+# Lower scores = More critical for intermolecular interactions
+#
+Rank	Chain_ID	Residue_ID	Residue_Name	ATOMICA_Score	Importance_Delta_Percent	Block_Index
+1	B	20	ASP	0.997773	0.2227	17
+2	B	23	PHE	0.998050	0.1950	20
+3	B	40	GLN	0.998071	0.1929	30
+4	B	53	ASP	0.998640	0.1360	43
+5	B	8	ALA	0.998712	0.1288	5
+6	B	7	GLY	0.998734	0.1266	4
+7	B	52	CYS	0.998754	0.1246	42
+8	B	43	ILE	0.998772	0.1228	33
+9	B	49	PHE	0.998916	0.1084	39
+10	B	11	VAL	0.999043	0.0957	8
+11	B	4	THR	0.999136	0.0864	1
+12	B	15	GLN	0.999164	0.0836	12
+13	B	19	GLY	0.999243	0.0757	16
+14	B	39	PRO	0.999376	0.0624	29
+15	B	31	TYR	0.999448	0.0552	28
+16	B	58	GLU	0.999482	0.0518	48
+17	B	63	PRO	0.999509	0.0491	53
+18	B	21	ARG	0.999512	0.0488	18
+19	B	56	ARG	0.999552	0.0448	46
+20	B	17	VAL	0.999566	0.0434	14
+21	B	66	PRO	0.999572	0.0428	56
+22	B	54	LEU	0.999577	0.0423	44
+23	B	45	ASP	0.999599	0.0401	35
+24	B	16	PHE	0.999604	0.0396	13
+25	B	42	GLY	0.999613	0.0387	32
+26	B	62	ALA	0.999625	0.0375	52
+27	B	30	GLY	0.999642	0.0358	27
+28	B	14	LEU	0.999656	0.0344	11
+29	B	6	CYS	0.999658	0.0342	3
+30	B	50	ARG	0.999673	0.0327	40
+31	B	64	LEU	0.999675	0.0325	54
+32	B	22	GLY	0.999677	0.0323	19
+33	B	12	ASP	0.999697	0.0303	9
+34	B	18	CYS	0.999734	0.0266	15
+35	B	47	CYS	0.999736	0.0264	37
+36	B	25	PHE	0.999737	0.0263	22
+37	B	48	CYS	0.999754	0.0246	38
+38	B	59	MET	0.999757	0.0243	49
+39	B	44	VAL	0.999778	0.0222	34
+40	B	61	CYS	0.999791	0.0209	51
+41	B	28	PRO	0.999839	0.0161	25
+42	B	65	LYS	0.999845	0.0155	55
+43	B	9	GLU	0.999847	0.0153	6
+44	B	5	LEU	0.999852	0.0148	2
+45	B	13	ALA	0.999864	0.0136	10
+46	B	60	TYR	0.999871	0.0129	50
+47	B	51	SER	0.999880	0.0120	41
+48	B	41	THR	0.999897	0.0103	31
+49	B	26	ASN	0.999905	0.0095	23
+50	B	24	TYR	0.999939	0.0061	21
+51	B	57	LEU	0.999943	0.0057	47
+52	B	10	LEU	0.999950	0.0050	7
+53	B	29	THR	0.999952	0.0048	26
+54	B	27	LYS	0.999957	0.0043	24
+55	B	55	ARG	0.999966	0.0034	45
+56	B	46	GLU	0.999967	0.0033	36

1gzy_interact_scores.json

@@ -0,0 +1 @@
+{"id": "1gzy_all", "cos_distances": [0.9991357326507568, 0.9998522996902466, 0.9996581673622131, 0.9987341165542603, 0.9987120628356934, 0.9998468160629272, 0.9999498128890991, 0.9990431070327759, 0.9996969699859619, 0.9998635053634644, 0.9996559619903564, 0.9991638660430908, 0.9996044635772705, 0.9995655417442322, 0.9997344017028809, 0.9992425441741943, 0.9977730512619019, 0.9995118975639343, 0.9996771812438965, 0.9980500340461731, 0.99993896484375, 0.999737024307251, 0.9999048113822937, 0.9999572038650513, 0.9998394846916199, 0.9999515414237976, 0.9996418356895447, 0.9994475245475769, 0.9993763566017151, 0.9980706572532654, 0.9998969435691833, 0.9996127486228943, 0.9987722039222717, 0.9997783899307251, 0.9995993375778198, 0.9999669790267944, 0.9997356534004211, 0.9997537136077881, 0.9989163875579834, 0.9996727108955383, 0.9998802542686462, 0.9987539052963257, 0.9986399412155151, 0.9995771646499634, 0.9999663829803467, 0.9995518922805786, 0.999943196773529, 0.9994819164276123, 0.999756932258606, 0.9998708963394165, 0.9997910857200623, 0.9996250867843628, 0.9995089173316956, 0.999674916267395, 0.9998450875282288, 0.9995718598365784, 0.9987692832946777], "block_idx": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57], "time_seconds": 11.2436, "peak_memory_mb": 428.65}

1gzy_metadata.json

@@ -0,0 +1,5 @@
+{
+  "pdb_id": "1gzy",
+  "found": false,
+  "error": "Metadata fetch failed: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1016)>"
+}

1gzy_pymol_commands.pml

@@ -0,0 +1,52 @@
+# ============================================================
+# PyMOL Commands for 1gzy
+# ============================================================
+# Copy and paste these commands into PyMOL
+# ============================================================
+
+# Load structure (adjust path as needed)
+load 1gzy.pdb
+
+# Basic setup
+hide all
+show cartoon
+color grey80, all
+
+# Select and highlight critical residues (Top 10)
+select critical_top10, resi 20+23+40+53+8+7+52+43+49+11 and chain B
+show sticks, critical_top10
+color red, critical_top10
+set stick_radius, 0.3, critical_top10
+
+# Label critical residues
+label critical_top10 and name CA, "%s%s" % (resn,resi)
+set label_size, 14
+set label_color, red
+
+# Create gradient coloring by importance (Top 5 in different reds)
+select critical_rank1, resi 20 and chain B
+color red, critical_rank1
+select critical_rank2, resi 23 and chain B
+color tv_red, critical_rank2
+select critical_rank3, resi 40 and chain B
+color salmon, critical_rank3
+select critical_rank4, resi 53 and chain B
+color lightsalmon, critical_rank4
+select critical_rank5, resi 8 and chain B
+color warmpink, critical_rank5
+
+# Show surface around critical residues
+show surface, byres (critical_top10 around 5)
+set surface_color, white
+set transparency, 0.5
+
+# Center view on critical residues
+zoom critical_top10
+
+# ============================================================
+# Additional useful commands:
+# ============================================================
+# To save session: save 1gzy_critical.pse
+# To save image: png 1gzy_critical.png, dpi=300
+# To highlight most critical (rank 1): select most_critical, critical_rank1
+# ============================================================

1gzy_summary.json

@@ -0,0 +1,20 @@
+{
+  "total_structures": 1,
+  "total_time_seconds": 11.25,
+  "total_time_minutes": 0.19,
+  "time_per_structure": {
+    "mean": 11.2436,
+    "std": 0.0,
+    "min": 11.2436,
+    "max": 11.2436
+  },
+  "output_file": "output/1gzy_interact_scores.json",
+  "input_file": "downloads/pdbs/1gzy.cif",
+  "start_idx": 0,
+  "num_lines": null,
+  "device": "cuda",
+  "gpu_memory_mb": {
+    "mean": 428.65,
+    "max": 428.65
+  }
+}

1gzz_critical_residues.tsv

@@ -0,0 +1,68 @@
+# ATOMICA Critical Residue Analysis: 1gzz_all
+# Structure ID: 1gzz
+# Total residues analyzed: 59
+# Mean ATOMICA_SCORE: 0.999551
+# Std Dev: 0.000441
+# Method: ATOMICA_SCORE (cosine similarity with masked residues)
+# Lower scores = More critical for intermolecular interactions
+#
+Rank	Chain_ID	Residue_ID	Residue_Name	ATOMICA_Score	Importance_Delta_Percent	Block_Index
+1	B	3	GLU	0.998343	0.1657	2
+2	B	7	GLY	0.998350	0.1650	6
+3	B	23	PHE	0.998364	0.1636	22
+4	B	20	ASP	0.998399	0.1601	19
+5	B	53	ASP	0.998469	0.1531	46
+6	B	43	ILE	0.998912	0.1088	36
+7	B	2	PRO	0.999052	0.0948	1
+8	B	8	ALA	0.999077	0.0923	7
+9	B	31	TYR	0.999268	0.0732	30
+10	B	45	ASP	0.999272	0.0728	38
+11	B	66	PRO	0.999383	0.0617	59
+12	B	39	PRO	0.999396	0.0604	32
+13	B	49	PHE	0.999424	0.0576	42
+14	B	11	VAL	0.999425	0.0575	10
+15	B	24	TYR	0.999432	0.0568	23
+16	B	64	LEU	0.999433	0.0567	57
+17	B	25	PHE	0.999454	0.0546	24
+18	B	58	GLU	0.999458	0.0542	51
+19	B	15	GLN	0.999483	0.0517	14
+20	B	19	GLY	0.999542	0.0458	18
+21	B	22	GLY	0.999545	0.0455	21
+22	B	42	GLY	0.999594	0.0406	35
+23	B	63	PRO	0.999621	0.0379	56
+24	B	48	CYS	0.999635	0.0365	41
+25	B	47	CYS	0.999648	0.0352	40
+26	B	18	CYS	0.999668	0.0332	17
+27	B	62	ALA	0.999674	0.0326	55
+28	B	44	VAL	0.999722	0.0278	37
+29	B	12	ASP	0.999722	0.0278	11
+30	B	52	CYS	0.999724	0.0276	45
+31	B	14	LEU	0.999726	0.0274	13
+32	B	40	GLN	0.999730	0.0270	33
+33	B	5	LEU	0.999743	0.0257	4
+34	B	21	ARG	0.999744	0.0256	20
+35	B	9	GLU	0.999747	0.0253	8
+36	B	16	PHE	0.999753	0.0247	15
+37	B	38	ALA	0.999763	0.0237	31
+38	B	50	ARG	0.999770	0.0230	43
+39	B	41	THR	0.999779	0.0221	34
+40	B	56	ARG	0.999795	0.0205	49
+41	B	17	VAL	0.999830	0.0170	16
+42	B	30	GLY	0.999839	0.0161	29
+43	B	51	SER	0.999866	0.0134	44
+44	B	61	CYS	0.999867	0.0133	54
+45	B	28	PRO	0.999868	0.0132	27
+46	B	59	MET	0.999891	0.0109	52
+47	B	29	THR	0.999892	0.0108	28
+48	B	26	ASN	0.999897	0.0103	25
+49	B	13	ALA	0.999908	0.0092	12
+50	B	4	THR	0.999910	0.0090	3
+51	B	55	ARG	0.999923	0.0077	48
+52	B	60	TYR	0.999927	0.0073	53
+53	B	27	LYS	0.999931	0.0069	26
+54	B	57	LEU	0.999933	0.0067	50
+55	B	54	LEU	0.999939	0.0061	47
+56	B	46	GLU	0.999958	0.0042	39
+57	B	6	CYS	0.999959	0.0041	5
+58	B	10	LEU	0.999960	0.0040	9
+59	B	65	LYS	0.999988	0.0012	58

1gzz_interact_scores.json

@@ -0,0 +1 @@
+{"id": "1gzz_all", "cos_distances": [0.9990519881248474, 0.9983429908752441, 0.9999103546142578, 0.9997429847717285, 0.9999588131904602, 0.9983497262001038, 0.9990774393081665, 0.9997468590736389, 0.9999595880508423, 0.9994247555732727, 0.9997221231460571, 0.9999080300331116, 0.9997262954711914, 0.9994825124740601, 0.9997528195381165, 0.9998300075531006, 0.9996678829193115, 0.9995419383049011, 0.9983993768692017, 0.9997441172599792, 0.9995450377464294, 0.9983640909194946, 0.9994316101074219, 0.9994535446166992, 0.9998971819877625, 0.9999309182167053, 0.9998683333396912, 0.9998921155929565, 0.9998387098312378, 0.999267578125, 0.9997626543045044, 0.9993959665298462, 0.9997304677963257, 0.9997792840003967, 0.9995937943458557, 0.99891197681427, 0.9997216463088989, 0.9992724061012268, 0.9999580383300781, 0.9996479749679565, 0.9996345043182373, 0.9994242191314697, 0.9997701048851013, 0.9998660683631897, 0.9997237324714661, 0.9984690546989441, 0.9999386072158813, 0.9999228715896606, 0.9997946619987488, 0.9999325275421143, 0.9994576573371887, 0.9998910427093506, 0.999926745891571, 0.9998674392700195, 0.9996744394302368, 0.9996205568313599, 0.9994332790374756, 0.9999878406524658, 0.9993826150894165, 0.998742401599884], "block_idx": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60], "time_seconds": 11.749, "peak_memory_mb": 443.18}

1gzz_metadata.json

@@ -0,0 +1,5 @@
+{
+  "pdb_id": "1gzz",
+  "found": false,
+  "error": "Metadata fetch failed: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1016)>"
+}

1gzz_pymol_commands.pml

@@ -0,0 +1,52 @@
+# ============================================================
+# PyMOL Commands for 1gzz
+# ============================================================
+# Copy and paste these commands into PyMOL
+# ============================================================
+
+# Load structure (adjust path as needed)
+load 1gzz.pdb
+
+# Basic setup
+hide all
+show cartoon
+color grey80, all
+
+# Select and highlight critical residues (Top 10)
+select critical_top10, resi 3+7+23+20+53+43+2+8+31+45 and chain B
+show sticks, critical_top10
+color red, critical_top10
+set stick_radius, 0.3, critical_top10
+
+# Label critical residues
+label critical_top10 and name CA, "%s%s" % (resn,resi)
+set label_size, 14
+set label_color, red
+
+# Create gradient coloring by importance (Top 5 in different reds)
+select critical_rank1, resi 3 and chain B
+color red, critical_rank1
+select critical_rank2, resi 7 and chain B
+color tv_red, critical_rank2
+select critical_rank3, resi 23 and chain B
+color salmon, critical_rank3
+select critical_rank4, resi 20 and chain B
+color lightsalmon, critical_rank4
+select critical_rank5, resi 53 and chain B
+color warmpink, critical_rank5
+
+# Show surface around critical residues
+show surface, byres (critical_top10 around 5)
+set surface_color, white
+set transparency, 0.5
+
+# Center view on critical residues
+zoom critical_top10
+
+# ============================================================
+# Additional useful commands:
+# ============================================================
+# To save session: save 1gzz_critical.pse
+# To save image: png 1gzz_critical.png, dpi=300
+# To highlight most critical (rank 1): select most_critical, critical_rank1
+# ============================================================

1gzz_summary.json

@@ -0,0 +1,20 @@
+{
+  "total_structures": 1,
+  "total_time_seconds": 11.75,
+  "total_time_minutes": 0.2,
+  "time_per_structure": {
+    "mean": 11.749,
+    "std": 0.0,
+    "min": 11.749,
+    "max": 11.749
+  },
+  "output_file": "output/1gzz_interact_scores.json",
+  "input_file": "downloads/pdbs/1gzz.cif",
+  "start_idx": 0,
+  "num_lines": null,
+  "device": "cuda",
+  "gpu_memory_mb": {
+    "mean": 443.18,
+    "max": 443.18
+  }
+}

1h02_critical_residues.tsv

@@ -0,0 +1,72 @@
+# ATOMICA Critical Residue Analysis: 1h02_all
+# Structure ID: 1h02
+# Total residues analyzed: 63
+# Mean ATOMICA_SCORE: 0.999701
+# Std Dev: 0.000296
+# Method: ATOMICA_SCORE (cosine similarity with masked residues)
+# Lower scores = More critical for intermolecular interactions
+#
+Rank	Chain_ID	Residue_ID	Residue_Name	ATOMICA_Score	Importance_Delta_Percent	Block_Index
+1	B	10	LEU	0.998652	0.1348	7
+2	B	23	PHE	0.998713	0.1287	20
+3	B	20	ASP	0.998798	0.1202	17
+4	B	53	ASP	0.999032	0.0968	48
+5	B	8	ALA	0.999199	0.0801	5
+6	B	31	TYR	0.999285	0.0715	28
+7	B	33	SER	0.999307	0.0693	30
+8	B	12	ASP	0.999495	0.0505	9
+9	B	11	VAL	0.999519	0.0481	8
+10	B	43	ILE	0.999548	0.0452	38
+11	B	58	GLU	0.999572	0.0428	53
+12	B	45	ASP	0.999577	0.0423	40
+13	B	15	GLN	0.999591	0.0409	12
+14	B	24	TYR	0.999629	0.0371	21
+15	B	18	CYS	0.999637	0.0363	15
+16	B	7	GLY	0.999652	0.0348	4
+17	B	19	GLY	0.999676	0.0324	16
+18	B	65	LYS	0.999678	0.0322	60
+19	B	38	ALA	0.999681	0.0319	33
+20	B	14	LEU	0.999695	0.0305	11
+21	B	56	ARG	0.999744	0.0256	51
+22	B	42	GLY	0.999752	0.0248	37
+23	B	4	THR	0.999759	0.0241	1
+24	B	6	CYS	0.999775	0.0225	3
+25	B	41	THR	0.999780	0.0220	36
+26	B	48	CYS	0.999781	0.0219	43
+27	B	63	PRO	0.999781	0.0219	58
+28	B	62	ALA	0.999792	0.0208	57
+29	B	16	PHE	0.999794	0.0206	13
+30	B	51	SER	0.999795	0.0205	46
+31	B	47	CYS	0.999802	0.0198	42
+32	B	67	ALA	0.999808	0.0192	62
+33	B	44	VAL	0.999816	0.0184	39
+34	B	9	GLU	0.999816	0.0184	6
+35	B	46	GLU	0.999817	0.0183	41
+36	B	17	VAL	0.999822	0.0178	14
+37	B	32	GLY	0.999824	0.0176	29
+38	B	25	PHE	0.999826	0.0174	22
+39	B	54	LEU	0.999834	0.0166	49
+40	B	49	PHE	0.999835	0.0165	44
+41	B	60	TYR	0.999837	0.0163	55
+42	B	22	GLY	0.999838	0.0162	19
+43	B	57	LEU	0.999855	0.0145	52
+44	B	34	SER	0.999859	0.0141	31
+45	B	5	LEU	0.999860	0.0140	2
+46	B	21	ARG	0.999871	0.0129	18
+47	B	35	SER	0.999876	0.0124	32
+48	B	50	ARG	0.999877	0.0123	45
+49	B	66	PRO	0.999888	0.0112	61
+50	B	64	LEU	0.999896	0.0104	59
+51	B	59	MET	0.999898	0.0102	54
+52	B	26	ASN	0.999900	0.0100	23
+53	B	28	PRO	0.999911	0.0089	25
+54	B	40	GLN	0.999917	0.0083	35
+55	B	68	LYS	0.999920	0.0080	63
+56	B	30	GLY	0.999933	0.0067	27
+57	B	13	ALA	0.999942	0.0058	10
+58	B	29	THR	0.999946	0.0054	26
+59	B	55	ARG	0.999947	0.0053	50
+60	B	61	CYS	0.999951	0.0049	56
+61	B	52	CYS	0.999958	0.0042	47
+62	B	39	PRO	0.999974	0.0026	34
+63	B	27	LYS	0.999988	0.0012	24

1h02_interact_scores.json

@@ -0,0 +1 @@
+{"id": "1h02_all", "cos_distances": [0.9997590780258179, 0.9998599290847778, 0.9997750520706177, 0.9996517896652222, 0.9991991519927979, 0.9998161196708679, 0.9986518621444702, 0.9995194673538208, 0.9994946718215942, 0.9999415278434753, 0.9996949434280396, 0.9995907545089722, 0.9997938275337219, 0.9998221397399902, 0.9996367692947388, 0.9996756911277771, 0.9987984895706177, 0.9998705387115479, 0.99983811378479, 0.998712956905365, 0.9996286630630493, 0.9998259544372559, 0.9999004602432251, 0.9999876022338867, 0.9999111294746399, 0.9999461770057678, 0.9999328255653381, 0.9992853403091431, 0.9998242855072021, 0.9993069171905518, 0.999859094619751, 0.9998762607574463, 0.9996805191040039, 0.9999738931655884, 0.9999170303344727, 0.9997804164886475, 0.9997521042823792, 0.9995484948158264, 0.9998159408569336, 0.9995774030685425, 0.9998168349266052, 0.9998023509979248, 0.9997807741165161, 0.9998350143432617, 0.9998772740364075, 0.9997947812080383, 0.9999583959579468, 0.9990324974060059, 0.9998336434364319, 0.9999465942382812, 0.999744176864624, 0.999854564666748, 0.9995720982551575, 0.9998982548713684, 0.999836802482605, 0.9999510049819946, 0.999792218208313, 0.9997812509536743, 0.999896228313446, 0.9996775388717651, 0.9998880624771118, 0.999807596206665, 0.9999198913574219, 0.9991495013237], "block_idx": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64], "time_seconds": 11.8211, "peak_memory_mb": 453.49}

1h02_metadata.json

@@ -0,0 +1,5 @@
+{
+  "pdb_id": "1h02",
+  "found": false,
+  "error": "Metadata fetch failed: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1016)>"
+}

1h02_pymol_commands.pml

@@ -0,0 +1,52 @@
+# ============================================================
+# PyMOL Commands for 1h02
+# ============================================================
+# Copy and paste these commands into PyMOL
+# ============================================================
+
+# Load structure (adjust path as needed)
+load 1h02.pdb
+
+# Basic setup
+hide all
+show cartoon
+color grey80, all
+
+# Select and highlight critical residues (Top 10)
+select critical_top10, resi 10+23+20+53+8+31+33+12+11+43 and chain B
+show sticks, critical_top10
+color red, critical_top10
+set stick_radius, 0.3, critical_top10
+
+# Label critical residues
+label critical_top10 and name CA, "%s%s" % (resn,resi)
+set label_size, 14
+set label_color, red
+
+# Create gradient coloring by importance (Top 5 in different reds)
+select critical_rank1, resi 10 and chain B
+color red, critical_rank1
+select critical_rank2, resi 23 and chain B
+color tv_red, critical_rank2
+select critical_rank3, resi 20 and chain B
+color salmon, critical_rank3
+select critical_rank4, resi 53 and chain B
+color lightsalmon, critical_rank4
+select critical_rank5, resi 8 and chain B
+color warmpink, critical_rank5
+
+# Show surface around critical residues
+show surface, byres (critical_top10 around 5)
+set surface_color, white
+set transparency, 0.5
+
+# Center view on critical residues
+zoom critical_top10
+
+# ============================================================
+# Additional useful commands:
+# ============================================================
+# To save session: save 1h02_critical.pse
+# To save image: png 1h02_critical.png, dpi=300
+# To highlight most critical (rank 1): select most_critical, critical_rank1
+# ============================================================

1h02_summary.json

@@ -0,0 +1,20 @@
+{
+  "total_structures": 1,
+  "total_time_seconds": 11.82,
+  "total_time_minutes": 0.2,
+  "time_per_structure": {
+    "mean": 11.8211,
+    "std": 0.0,
+    "min": 11.8211,
+    "max": 11.8211
+  },
+  "output_file": "output/1h02_interact_scores.json",
+  "input_file": "downloads/pdbs/1h02.cif",
+  "start_idx": 0,
+  "num_lines": null,
+  "device": "cuda",
+  "gpu_memory_mb": {
+    "mean": 453.49,
+    "max": 453.49
+  }
+}

1pmx_critical_residues.tsv

@@ -0,0 +1,94 @@
+# ATOMICA Critical Residue Analysis: 1pmx_all
+# Structure ID: 1pmx
+# Total residues analyzed: 85
+# Mean ATOMICA_SCORE: 0.999794
+# Std Dev: 0.000235
+# Method: ATOMICA_SCORE (cosine similarity with masked residues)
+# Lower scores = More critical for intermolecular interactions
+#
+Rank	Chain_ID	Residue_ID	Residue_Name	ATOMICA_Score	Importance_Delta_Percent	Block_Index
+1	A	33	SER	0.998971	0.1029	32
+2	A	20	ASP	0.998972	0.1028	19
+3	A	23	PHE	0.999062	0.0938	22
+4	A	67	ALA	0.999155	0.0845	66
+5	A	8	ALA	0.999186	0.0814	7
+6	A	31	TYR	0.999221	0.0779	30
+7	A	2	PRO	0.999393	0.0607	1
+8	B	110	LEU	0.999411	0.0589	79
+9	A	43	ILE	0.999434	0.0566	42
+10	A	7	GLY	0.999471	0.0529	6
+11	B	114	MET	0.999477	0.0523	83
+12	A	64	LEU	0.999621	0.0379	63
+13	A	53	ASP	0.999627	0.0373	52
+14	B	111	ARG	0.999643	0.0357	80
+15	A	25	PHE	0.999668	0.0332	24
+16	A	32	GLY	0.999692	0.0308	31
+17	A	9	GLU	0.999707	0.0293	8
+18	A	15	GLN	0.999746	0.0254	14
+19	A	48	CYS	0.999750	0.0250	47
+20	B	101	ARG	0.999770	0.0230	70
+21	B	104	PHE	0.999779	0.0221	73
+22	A	58	GLU	0.999780	0.0220	57
+23	A	49	PHE	0.999784	0.0216	48
+24	B	108	ALA	0.999798	0.0202	77
+25	A	55	ARG	0.999804	0.0196	54
+26	B	116	GLY	0.999804	0.0196	85
+27	A	5	LEU	0.999806	0.0194	4
+28	A	44	VAL	0.999808	0.0192	43
+29	A	11	VAL	0.999831	0.0169	10
+30	A	40	GLN	0.999833	0.0167	39
+31	B	102	ASN	0.999842	0.0158	71
+32	A	19	GLY	0.999845	0.0155	18
+33	A	12	ASP	0.999856	0.0144	11
+34	A	41	THR	0.999858	0.0142	40
+35	A	56	ARG	0.999864	0.0136	55
+36	A	66	PRO	0.999864	0.0136	65
+37	B	103	CYS	0.999866	0.0134	72
+38	A	69	SER	0.999872	0.0128	68
+39	A	16	PHE	0.999877	0.0123	15
+40	B	115	TYR	0.999881	0.0119	84
+41	A	3	GLU	0.999883	0.0117	2
+42	A	24	TYR	0.999887	0.0113	23
+43	A	45	ASP	0.999890	0.0110	44
+44	A	21	ARG	0.999891	0.0109	20
+45	A	6	CYS	0.999894	0.0106	5
+46	A	14	LEU	0.999895	0.0105	13
+47	A	63	PRO	0.999900	0.0100	62
+48	A	34	SER	0.999900	0.0100	33
+49	A	47	CYS	0.999901	0.0099	46
+50	A	18	CYS	0.999905	0.0095	17
+51	A	65	LYS	0.999906	0.0094	64
+52	B	113	CYS	0.999907	0.0093	82
+53	B	106	SER	0.999909	0.0091	75
+54	B	109	ALA	0.999910	0.0090	78
+55	A	59	MET	0.999913	0.0087	58
+56	A	28	PRO	0.999917	0.0083	27
+57	A	42	GLY	0.999917	0.0083	41
+58	A	29	THR	0.999918	0.0082	28
+59	A	68	LYS	0.999919	0.0081	67
+60	A	60	TYR	0.999920	0.0080	59
+61	A	57	LEU	0.999923	0.0077	56
+62	A	4	THR	0.999926	0.0074	3
+63	A	35	SER	0.999928	0.0072	34
+64	A	27	LYS	0.999937	0.0063	26
+65	B	107	VAL	0.999938	0.0062	76
+66	B	112	ARG	0.999939	0.0061	81
+67	A	62	ALA	0.999939	0.0061	61
+68	A	36	ARG	0.999940	0.0060	35
+69	A	52	CYS	0.999940	0.0060	51
+70	A	22	GLY	0.999942	0.0058	21
+71	A	37	ARG	0.999947	0.0053	36
+72	A	70	ALA	0.999951	0.0049	69
+73	A	61	CYS	0.999953	0.0047	60
+74	A	17	VAL	0.999956	0.0044	16
+75	A	38	ALA	0.999961	0.0039	37
+76	A	10	LEU	0.999962	0.0038	9
+77	A	54	LEU	0.999969	0.0031	53
+78	A	51	SER	0.999971	0.0029	50
+79	B	105	GLU	0.999972	0.0028	74
+80	A	46	GLU	0.999983	0.0017	45
+81	A	50	ARG	0.999986	0.0014	49
+82	A	13	ALA	0.999986	0.0014	12
+83	A	30	GLY	0.999988	0.0012	29
+84	A	26	ASN	0.999993	0.0007	25
+85	A	39	PRO	0.999996	0.0004	38

1pmx_interact_scores.json

@@ -0,0 +1 @@
+{"id": "1pmx_all", "cos_distances": [0.9993932247161865, 0.999882698059082, 0.9999262094497681, 0.9998061060905457, 0.999894380569458, 0.9994714260101318, 0.9991861581802368, 0.9997074604034424, 0.9999622702598572, 0.9998310208320618, 0.9998555183410645, 0.9999861121177673, 0.999894917011261, 0.9997460842132568, 0.9998766183853149, 0.9999558925628662, 0.9999046325683594, 0.9998449087142944, 0.9989724159240723, 0.999890923500061, 0.9999417066574097, 0.9990619421005249, 0.9998874068260193, 0.9996681809425354, 0.9999929666519165, 0.9999372959136963, 0.9999169111251831, 0.9999178647994995, 0.9999876022338867, 0.9992205500602722, 0.9996917247772217, 0.9989709854125977, 0.9999004602432251, 0.9999277591705322, 0.9999399185180664, 0.9999472498893738, 0.9999606609344482, 0.9999958276748657, 0.9998332262039185, 0.999858021736145, 0.9999173283576965, 0.9994339346885681, 0.999807596206665, 0.999889612197876, 0.9999829530715942, 0.999900758266449, 0.999750018119812, 0.999783992767334, 0.9999859929084778, 0.9999713897705078, 0.9999402761459351, 0.9996273517608643, 0.9999685287475586, 0.999803900718689, 0.9998642206192017, 0.9999232888221741, 0.9997795820236206, 0.9999130368232727, 0.9999203681945801, 0.9999528527259827, 0.9999390244483948, 0.9999004006385803, 0.9996211528778076, 0.999906063079834, 0.9998643398284912, 0.9991553425788879, 0.9999185800552368, 0.9998721480369568, 0.9999514818191528, 0.99977046251297, 0.9998423457145691, 0.9998655319213867, 0.9997788071632385, 0.9999719262123108, 0.9999092221260071, 0.999937891960144, 0.9997978210449219, 0.9999096393585205, 0.9994111061096191, 0.9996432662010193, 0.9999388456344604, 0.9999073147773743, 0.9994773268699646, 0.9998812675476074, 0.9998040199279785, 0.9996482729911804], "block_idx": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86], "time_seconds": 14.1872, "peak_memory_mb": 617.83}

1pmx_metadata.json

@@ -0,0 +1,5 @@
+{
+  "pdb_id": "1pmx",
+  "found": false,
+  "error": "Metadata fetch failed: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1016)>"
+}

1pmx_pymol_commands.pml

@@ -0,0 +1,52 @@
+# ============================================================
+# PyMOL Commands for 1pmx
+# ============================================================
+# Copy and paste these commands into PyMOL
+# ============================================================
+
+# Load structure (adjust path as needed)
+load 1pmx.pdb
+
+# Basic setup
+hide all
+show cartoon
+color grey80, all
+
+# Select and highlight critical residues (Top 10)
+select critical_top10, resi 33+20+23+67+8+31+2+110+43+7 and chain A
+show sticks, critical_top10
+color red, critical_top10
+set stick_radius, 0.3, critical_top10
+
+# Label critical residues
+label critical_top10 and name CA, "%s%s" % (resn,resi)
+set label_size, 14
+set label_color, red
+
+# Create gradient coloring by importance (Top 5 in different reds)
+select critical_rank1, resi 33 and chain A
+color red, critical_rank1
+select critical_rank2, resi 20 and chain A
+color tv_red, critical_rank2
+select critical_rank3, resi 23 and chain A
+color salmon, critical_rank3
+select critical_rank4, resi 67 and chain A
+color lightsalmon, critical_rank4
+select critical_rank5, resi 8 and chain A
+color warmpink, critical_rank5
+
+# Show surface around critical residues
+show surface, byres (critical_top10 around 5)
+set surface_color, white
+set transparency, 0.5
+
+# Center view on critical residues
+zoom critical_top10
+
+# ============================================================
+# Additional useful commands:
+# ============================================================
+# To save session: save 1pmx_critical.pse
+# To save image: png 1pmx_critical.png, dpi=300
+# To highlight most critical (rank 1): select most_critical, critical_rank1
+# ============================================================

1pmx_summary.json

@@ -0,0 +1,20 @@
+{
+  "total_structures": 1,
+  "total_time_seconds": 14.19,
+  "total_time_minutes": 0.24,
+  "time_per_structure": {
+    "mean": 14.1872,
+    "std": 0.0,
+    "min": 14.1872,
+    "max": 14.1872
+  },
+  "output_file": "output/1pmx_interact_scores.json",
+  "input_file": "downloads/pdbs/1pmx.cif",
+  "start_idx": 0,
+  "num_lines": null,
+  "device": "cuda",
+  "gpu_memory_mb": {
+    "mean": 617.83,
+    "max": 617.83
+  }
+}

1wqj_critical_residues.tsv

@@ -0,0 +1,150 @@
+# ATOMICA Critical Residue Analysis: 1wqj_all
+# Structure ID: 1wqj
+# Total residues analyzed: 141
+# Mean ATOMICA_SCORE: 0.999918
+# Std Dev: 0.000076
+# Method: ATOMICA_SCORE (cosine similarity with masked residues)
+# Lower scores = More critical for intermolecular interactions
+#
+Rank	Chain_ID	Residue_ID	Residue_Name	ATOMICA_Score	Importance_Delta_Percent	Block_Index
+1	B	46	CYS	0.999620	0.0380	43
+2	B	42	LEU	0.999678	0.0322	39
+3	I	23	PHE	0.999681	0.0319	101
+4	B	34	CYS	0.999704	0.0296	31
+5	I	43	ILE	0.999748	0.0252	121
+6	B	78	VAL	0.999759	0.0241	75
+7	B	69	LEU	0.999766	0.0234	66
+8	B	35	CYS	0.999766	0.0234	32
+9	B	55	SER	0.999772	0.0228	52
+10	I	8	ALA	0.999778	0.0222	86
+11	I	30	GLY	0.999782	0.0218	108
+12	I	20	ASP	0.999782	0.0218	98
+13	B	36	ALA	0.999784	0.0216	33
+14	B	23	CYS	0.999796	0.0204	20
+15	B	32	CYS	0.999808	0.0192	29
+16	I	33	SER	0.999819	0.0181	111
+17	B	40	LEU	0.999823	0.0177	37
+18	B	47	GLY	0.999825	0.0175	44
+19	I	31	TYR	0.999838	0.0162	109
+20	B	63	ARG	0.999840	0.0160	60
+21	B	9	CYS	0.999847	0.0153	6
+22	B	44	MET	0.999848	0.0152	41
+23	I	54	LEU	0.999858	0.0142	132
+24	I	53	ASP	0.999859	0.0141	131
+25	B	39	ALA	0.999861	0.0139	36
+26	B	76	GLN	0.999862	0.0138	73
+27	B	48	VAL	0.999862	0.0138	45
+28	B	12	GLU	0.999872	0.0128	9
+29	B	79	CYS	0.999872	0.0128	76
+30	B	27	VAL	0.999883	0.0117	24
+31	B	57	LEU	0.999884	0.0116	54
+32	I	6	CYS	0.999887	0.0113	84
+33	B	64	GLY	0.999888	0.0112	61
+34	B	11	GLU	0.999889	0.0111	8
+35	B	62	PRO	0.999889	0.0111	59
+36	B	38	CYS	0.999890	0.0110	35
+37	B	72	LEU	0.999891	0.0109	69
+38	B	71	THR	0.999895	0.0105	68
+39	I	48	CYS	0.999896	0.0104	126
+40	B	37	THR	0.999897	0.0103	34
+41	I	45	ASP	0.999898	0.0102	123
+42	B	70	HIS	0.999899	0.0101	67
+43	B	58	ARG	0.999899	0.0101	55
+44	I	42	GLY	0.999903	0.0097	120
+45	B	24	GLU	0.999908	0.0092	21
+46	B	80	MET	0.999911	0.0089	77
+47	B	68	PRO	0.999916	0.0084	65
+48	I	2	PRO	0.999917	0.0083	80
+49	B	65	VAL	0.999918	0.0082	62
+50	B	75	GLY	0.999920	0.0080	72
+51	B	6	CYS	0.999921	0.0079	3
+52	B	17	CYS	0.999922	0.0078	14
+53	I	38	ALA	0.999922	0.0078	116
+54	I	16	PHE	0.999922	0.0078	94
+55	I	63	PRO	0.999923	0.0077	141
+56	B	30	PRO	0.999924	0.0076	27
+57	I	5	LEU	0.999925	0.0075	83
+58	I	62	ALA	0.999926	0.0074	140
+59	B	5	HIS	0.999926	0.0074	2
+60	B	7	PRO	0.999927	0.0073	4
+61	B	10	SER	0.999928	0.0072	7
+62	B	52	ARG	0.999929	0.0071	49
+63	B	18	ARG	0.999929	0.0071	15
+64	B	33	GLY	0.999929	0.0071	30
+65	B	4	ILE	0.999930	0.0070	1
+66	I	51	SER	0.999932	0.0068	129
+67	B	73	MET	0.999935	0.0065	70
+68	B	43	GLY	0.999939	0.0061	40
+69	B	16	ARG	0.999939	0.0061	13
+70	I	59	MET	0.999941	0.0059	137
+71	I	52	CYS	0.999941	0.0059	130
+72	B	28	ARG	0.999942	0.0058	25
+73	I	17	VAL	0.999943	0.0057	95
+74	B	20	PRO	0.999945	0.0055	17
+75	B	51	PRO	0.999946	0.0054	48
+76	I	47	CYS	0.999946	0.0054	125
+77	I	12	ASP	0.999948	0.0052	90
+78	I	26	ASN	0.999949	0.0051	104
+79	I	34	SER	0.999950	0.0050	112
+80	I	50	ARG	0.999952	0.0048	128
+81	I	18	CYS	0.999953	0.0047	96
+82	I	27	LYS	0.999953	0.0047	105
+83	B	82	LEU	0.999953	0.0047	79
+84	I	3	GLU	0.999953	0.0047	81
+85	I	57	LEU	0.999956	0.0044	135
+86	I	19	GLY	0.999958	0.0042	97
+87	B	50	THR	0.999958	0.0042	47
+88	I	13	ALA	0.999959	0.0041	91
+89	I	21	ARG	0.999961	0.0039	99
+90	B	26	LEU	0.999961	0.0039	23
+91	I	7	GLY	0.999962	0.0038	85
+92	B	21	VAL	0.999965	0.0035	18
+93	I	10	LEU	0.999966	0.0034	88
+94	B	29	GLU	0.999967	0.0033	26
+95	B	31	GLY	0.999968	0.0032	28
+96	I	44	VAL	0.999970	0.0030	122
+97	B	41	GLY	0.999970	0.0030	38
+98	I	25	PHE	0.999971	0.0029	103
+99	B	67	LYS	0.999972	0.0028	64
+100	I	37	ARG	0.999973	0.0027	115
+101	I	58	GLU	0.999975	0.0025	136
+102	I	56	ARG	0.999976	0.0024	134
+103	I	32	GLY	0.999977	0.0023	110
+104	B	19	PRO	0.999977	0.0023	16
+105	I	55	ARG	0.999977	0.0023	133
+106	I	24	TYR	0.999978	0.0022	102
+107	B	45	PRO	0.999979	0.0021	42
+108	I	36	ARG	0.999980	0.0020	114
+109	I	61	CYS	0.999980	0.0020	139
+110	I	11	VAL	0.999981	0.0019	89
+111	B	8	PRO	0.999981	0.0019	5
+112	B	59	CYS	0.999981	0.0019	56
+113	I	28	PRO	0.999981	0.0019	106
+114	I	60	TYR	0.999981	0.0019	138
+115	B	54	GLY	0.999982	0.0018	51
+116	I	9	GLU	0.999982	0.0018	87
+117	B	14	LEU	0.999982	0.0018	11
+118	I	35	SER	0.999982	0.0018	113
+119	B	15	ALA	0.999984	0.0016	12
+120	I	49	PHE	0.999984	0.0016	127
+121	I	4	THR	0.999984	0.0016	82
+122	B	25	GLU	0.999984	0.0016	22
+123	I	39	PRO	0.999985	0.0015	117
+124	B	61	PRO	0.999985	0.0015	58
+125	I	40	GLN	0.999986	0.0014	118
+126	B	53	CYS	0.999987	0.0013	50
+127	I	29	THR	0.999987	0.0013	107
+128	I	41	THR	0.999987	0.0013	119
+129	I	46	GLU	0.999987	0.0013	124
+130	B	22	GLY	0.999987	0.0013	19
+131	B	60	TYR	0.999988	0.0012	57
+132	B	49	TYR	0.999988	0.0012	46
+133	B	56	GLY	0.999988	0.0012	53
+134	I	22	GLY	0.999988	0.0012	100
+135	B	77	GLY	0.999988	0.0012	74
+136	I	15	GLN	0.999988	0.0012	93
+137	I	14	LEU	0.999989	0.0011	92
+138	B	66	GLU	0.999989	0.0011	63
+139	B	74	HIS	0.999989	0.0011	71
+140	B	81	GLU	0.999996	0.0004	78
+141	B	13	LYS	0.999998	0.0002	10

1wqj_interact_scores.json

@@ -0,0 +1 @@
+{"id": "1wqj_all", "cos_distances": [0.9999297857284546, 0.9999263286590576, 0.9999206066131592, 0.9999268651008606, 0.999981164932251, 0.9998472332954407, 0.9999279379844666, 0.9998887777328491, 0.9998717308044434, 0.999997615814209, 0.9999822974205017, 0.9999837279319763, 0.9999393224716187, 0.9999215602874756, 0.9999290108680725, 0.9999774694442749, 0.9999446868896484, 0.999965250492096, 0.9999873638153076, 0.9997963905334473, 0.9999079704284668, 0.9999842047691345, 0.9999614357948303, 0.9998832941055298, 0.9999418258666992, 0.9999669790267944, 0.9999237060546875, 0.9999679327011108, 0.9998079538345337, 0.9999293684959412, 0.9997044205665588, 0.99976646900177, 0.9997840523719788, 0.999896764755249, 0.9998902678489685, 0.9998608231544495, 0.9998233914375305, 0.9999699592590332, 0.9996780157089233, 0.9999387860298157, 0.999848484992981, 0.9999785423278809, 0.9996199607849121, 0.9998250603675842, 0.9998624324798584, 0.9999877214431763, 0.9999582767486572, 0.9999456405639648, 0.999928891658783, 0.9999865293502808, 0.999981701374054, 0.9997716546058655, 0.9999879002571106, 0.9998842477798462, 0.9998986721038818, 0.9999812841415405, 0.9999876022338867, 0.9999854564666748, 0.9998890161514282, 0.9998396039009094, 0.9998884201049805, 0.99991774559021, 0.9999887943267822, 0.9999722242355347, 0.999915599822998, 0.9997663497924805, 0.9998986124992371, 0.9998947381973267, 0.9998911023139954, 0.9999349117279053, 0.9999889731407166, 0.9999204874038696, 0.9998615980148315, 0.9999879598617554, 0.9997594952583313, 0.9998718500137329, 0.9999105930328369, 0.9999963045120239, 0.9999533891677856, 0.9999169111251831, 0.9999534487724304, 0.9999840259552002, 0.9999253153800964, 0.9998870491981506, 0.9999620914459229, 0.9997779130935669, 0.9999822378158569, 0.9999655485153198, 0.9999807476997375, 0.999948263168335, 0.9999587535858154, 0.9999885559082031, 0.9999884963035583, 0.9999220967292786, 0.9999433755874634, 0.9999526739120483, 0.9999576807022095, 0.999782383441925, 0.999961256980896, 0.9999879002571106, 0.9996806383132935, 0.9999781250953674, 0.9999709725379944, 0.9999494552612305, 0.9999526739120483, 0.9999812841415405, 0.9999865293502808, 0.9997819662094116, 0.9998383522033691, 0.9999769926071167, 0.9998185038566589, 0.99994957447052, 0.999982476234436, 0.9999797344207764, 0.9999731779098511, 0.9999219179153442, 0.9999849796295166, 0.9999862313270569, 0.9999867677688599, 0.9999032020568848, 0.9997478723526001, 0.9999698400497437, 0.9998980760574341, 0.999987006187439, 0.9999464750289917, 0.9998958110809326, 0.9999837279319763, 0.9999521970748901, 0.9999322891235352, 0.9999412298202515, 0.9998593330383301, 0.9998577237129211, 0.9999774694442749, 0.9999763369560242, 0.9999564290046692, 0.9999749660491943, 0.9999405145645142, 0.9999812841415405, 0.9999799728393555, 0.9999258518218994, 0.9999225735664368, 0.999724268913269], "block_idx": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142], "time_seconds": 21.8475, "peak_memory_mb": 938.89}

1wqj_metadata.json

@@ -0,0 +1,5 @@
+{
+  "pdb_id": "1wqj",
+  "found": false,
+  "error": "Metadata fetch failed: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1016)>"
+}

1wqj_pymol_commands.pml

@@ -0,0 +1,52 @@
+# ============================================================
+# PyMOL Commands for 1wqj
+# ============================================================
+# Copy and paste these commands into PyMOL
+# ============================================================
+
+# Load structure (adjust path as needed)
+load 1wqj.pdb
+
+# Basic setup
+hide all
+show cartoon
+color grey80, all
+
+# Select and highlight critical residues (Top 10)
+select critical_top10, resi 46+42+23+34+43+78+69+35+55+8 and chain B
+show sticks, critical_top10
+color red, critical_top10
+set stick_radius, 0.3, critical_top10
+
+# Label critical residues
+label critical_top10 and name CA, "%s%s" % (resn,resi)
+set label_size, 14
+set label_color, red
+
+# Create gradient coloring by importance (Top 5 in different reds)
+select critical_rank1, resi 46 and chain B
+color red, critical_rank1
+select critical_rank2, resi 42 and chain B
+color tv_red, critical_rank2
+select critical_rank3, resi 23 and chain I
+color salmon, critical_rank3
+select critical_rank4, resi 34 and chain B
+color lightsalmon, critical_rank4
+select critical_rank5, resi 43 and chain I
+color warmpink, critical_rank5
+
+# Show surface around critical residues
+show surface, byres (critical_top10 around 5)
+set surface_color, white
+set transparency, 0.5
+
+# Center view on critical residues
+zoom critical_top10
+
+# ============================================================
+# Additional useful commands:
+# ============================================================
+# To save session: save 1wqj_critical.pse
+# To save image: png 1wqj_critical.png, dpi=300
+# To highlight most critical (rank 1): select most_critical, critical_rank1
+# ============================================================

1wqj_summary.json

@@ -0,0 +1,20 @@
+{
+  "total_structures": 1,
+  "total_time_seconds": 21.85,
+  "total_time_minutes": 0.36,
+  "time_per_structure": {
+    "mean": 21.8475,
+    "std": 0.0,
+    "min": 21.8475,
+    "max": 21.8475
+  },
+  "output_file": "output/1wqj_interact_scores.json",
+  "input_file": "downloads/pdbs/1wqj.cif",
+  "start_idx": 0,
+  "num_lines": null,
+  "device": "cuda",
+  "gpu_memory_mb": {
+    "mean": 938.89,
+    "max": 938.89
+  }
+}

2dsp_critical_residues.tsv

@@ -0,0 +1,156 @@
+# ATOMICA Critical Residue Analysis: 2dsp_all
+# Structure ID: 2dsp
+# Total residues analyzed: 147
+# Mean ATOMICA_SCORE: 0.999922
+# Std Dev: 0.000070
+# Method: ATOMICA_SCORE (cosine similarity with masked residues)
+# Lower scores = More critical for intermolecular interactions
+#
+Rank	Chain_ID	Residue_ID	Residue_Name	ATOMICA_Score	Importance_Delta_Percent	Block_Index
+1	I	29	THR	0.999673	0.0327	118
+2	B	46	CYS	0.999702	0.0298	45
+3	B	42	LEU	0.999704	0.0296	41
+4	B	55	SER	0.999736	0.0264	54
+5	I	23	PHE	0.999752	0.0248	112
+6	B	47	GLY	0.999765	0.0235	46
+7	B	35	CYS	0.999767	0.0233	34
+8	B	69	LEU	0.999768	0.0232	67
+9	B	78	VAL	0.999787	0.0213	76
+10	I	10	LEU	0.999803	0.0197	99
+11	I	8	ALA	0.999804	0.0196	97
+12	I	64	LEU	0.999805	0.0195	143
+13	B	34	CYS	0.999806	0.0194	33
+14	B	9	CYS	0.999807	0.0193	8
+15	B	44	MET	0.999808	0.0192	43
+16	B	23	CYS	0.999813	0.0187	22
+17	I	19	GLY	0.999817	0.0183	108
+18	B	76	GLN	0.999827	0.0173	74
+19	B	38	CYS	0.999830	0.0170	37
+20	I	52	CYS	0.999834	0.0166	131
+21	I	43	ILE	0.999835	0.0165	122
+22	B	32	CYS	0.999835	0.0165	31
+23	B	40	LEU	0.999840	0.0160	39
+24	I	61	CYS	0.999848	0.0152	140
+25	B	41	GLY	0.999851	0.0149	40
+26	B	26	LEU	0.999852	0.0148	25
+27	I	20	ASP	0.999857	0.0143	109
+28	B	39	ALA	0.999862	0.0138	38
+29	B	36	ALA	0.999869	0.0131	35
+30	B	65	VAL	0.999874	0.0126	63
+31	I	67	ALA	0.999877	0.0123	146
+32	B	33	GLY	0.999877	0.0123	32
+33	I	25	PHE	0.999878	0.0122	114
+34	B	75	GLY	0.999879	0.0121	73
+35	B	57	LEU	0.999882	0.0118	56
+36	B	28	ARG	0.999884	0.0116	27
+37	B	79	CYS	0.999885	0.0115	77
+38	I	42	GLY	0.999885	0.0115	121
+39	B	11	GLU	0.999886	0.0114	10
+40	I	7	GLY	0.999895	0.0105	96
+41	I	55	ARG	0.999898	0.0102	134
+42	B	7	PRO	0.999903	0.0097	6
+43	B	14	LEU	0.999907	0.0093	13
+44	B	13	LYS	0.999908	0.0092	12
+45	B	4	ILE	0.999910	0.0090	3
+46	B	48	VAL	0.999910	0.0090	47
+47	I	54	LEU	0.999911	0.0089	133
+48	I	48	CYS	0.999911	0.0089	127
+49	I	53	ASP	0.999912	0.0088	132
+50	B	72	LEU	0.999914	0.0086	70
+51	B	73	MET	0.999914	0.0086	71
+52	B	71	THR	0.999914	0.0086	69
+53	B	37	THR	0.999921	0.0079	36
+54	B	15	ALA	0.999922	0.0078	14
+55	B	24	GLU	0.999922	0.0078	23
+56	B	45	PRO	0.999922	0.0078	44
+57	B	58	ARG	0.999929	0.0071	57
+58	B	3	ALA	0.999929	0.0071	2
+59	I	45	ASP	0.999931	0.0069	124
+60	I	6	CYS	0.999933	0.0067	95
+61	I	15	GLN	0.999937	0.0063	104
+62	I	5	LEU	0.999937	0.0063	94
+63	B	43	GLY	0.999938	0.0062	42
+64	B	10	SER	0.999939	0.0061	9
+65	I	17	VAL	0.999943	0.0057	106
+66	I	40	GLN	0.999944	0.0056	119
+67	I	26	ASN	0.999946	0.0054	115
+68	I	50	ARG	0.999946	0.0054	129
+69	B	70	HIS	0.999947	0.0053	68
+70	B	51	PRO	0.999947	0.0053	50
+71	B	18	ARG	0.999947	0.0053	17
+72	I	12	ASP	0.999949	0.0051	101
+73	I	18	CYS	0.999949	0.0051	107
+74	I	62	ALA	0.999951	0.0049	141
+75	B	31	GLY	0.999951	0.0049	30
+76	B	12	GLU	0.999952	0.0048	11
+77	B	68	PRO	0.999953	0.0047	66
+78	B	59	CYS	0.999953	0.0047	58
+79	B	90	GLU	0.999955	0.0045	88
+80	I	44	VAL	0.999956	0.0044	123
+81	B	27	VAL	0.999957	0.0043	26
+82	B	17	CYS	0.999958	0.0042	16
+83	B	81	GLU	0.999958	0.0042	79
+84	B	30	PRO	0.999958	0.0042	29
+85	B	64	GLY	0.999958	0.0042	62
+86	B	8	PRO	0.999960	0.0040	7
+87	I	11	VAL	0.999960	0.0040	100
+88	I	59	MET	0.999960	0.0040	138
+89	B	87	ALA	0.999961	0.0039	85
+90	B	2	GLU	0.999961	0.0039	1
+91	B	52	ARG	0.999962	0.0038	51
+92	B	92	LEU	0.999962	0.0038	90
+93	B	91	SER	0.999964	0.0036	89
+94	B	25	GLU	0.999964	0.0036	24
+95	B	16	ARG	0.999965	0.0035	15
+96	I	58	GLU	0.999965	0.0035	137
+97	I	51	SER	0.999966	0.0034	130
+98	I	13	ALA	0.999967	0.0033	102
+99	I	9	GLU	0.999968	0.0032	98
+100	B	6	CYS	0.999968	0.0032	5
+101	B	22	GLY	0.999970	0.0030	21
+102	I	21	ARG	0.999970	0.0030	110
+103	B	88	ILE	0.999970	0.0030	86
+104	B	89	GLN	0.999972	0.0028	87
+105	B	50	THR	0.999972	0.0028	49
+106	B	5	HIS	0.999974	0.0026	4
+107	B	84	GLU	0.999974	0.0026	82
+108	I	3	GLU	0.999974	0.0026	92
+109	B	67	LYS	0.999974	0.0026	65
+110	B	62	PRO	0.999974	0.0026	61
+111	I	56	ARG	0.999974	0.0026	135
+112	I	60	TYR	0.999975	0.0025	139
+113	B	20	PRO	0.999975	0.0025	19
+114	B	85	ILE	0.999975	0.0025	83
+115	I	68	LYS	0.999976	0.0024	147
+116	B	60	TYR	0.999976	0.0024	59
+117	B	66	GLU	0.999977	0.0023	64
+118	B	82	LEU	0.999977	0.0023	80
+119	I	24	TYR	0.999978	0.0022	113
+120	I	49	PHE	0.999978	0.0022	128
+121	I	4	THR	0.999979	0.0021	93
+122	B	80	MET	0.999979	0.0021	78
+123	B	54	GLY	0.999980	0.0020	53
+124	I	63	PRO	0.999981	0.0019	142
+125	B	86	GLU	0.999981	0.0019	84
+126	B	61	PRO	0.999982	0.0018	60
+127	B	21	VAL	0.999982	0.0018	20
+128	B	56	GLY	0.999982	0.0018	55
+129	I	16	PHE	0.999983	0.0017	105
+130	I	57	LEU	0.999984	0.0016	136
+131	I	14	LEU	0.999985	0.0015	103
+132	I	66	PRO	0.999985	0.0015	145
+133	I	22	GLY	0.999986	0.0014	111
+134	B	74	HIS	0.999987	0.0013	72
+135	B	53	CYS	0.999988	0.0012	52
+136	B	77	GLY	0.999989	0.0011	75
+137	B	49	TYR	0.999989	0.0011	48
+138	B	19	PRO	0.999991	0.0009	18
+139	I	47	CYS	0.999991	0.0009	126
+140	I	65	LYS	0.999991	0.0009	144
+141	I	46	GLU	0.999991	0.0009	125
+142	I	27	LYS	0.999992	0.0008	116
+143	I	28	PRO	0.999994	0.0006	117
+144	I	41	THR	0.999994	0.0006	120
+145	B	83	ALA	0.999996	0.0004	81
+146	I	2	PRO	0.999996	0.0004	91
+147	B	29	GLU	0.999997	0.0003	28

2dsp_interact_scores.json

@@ -0,0 +1 @@
+{"id": "2dsp_all", "cos_distances": [0.999961256980896, 0.9999287128448486, 0.9999096393585205, 0.9999736547470093, 0.9999681711196899, 0.9999030828475952, 0.9999602437019348, 0.9998071193695068, 0.9999390840530396, 0.999886155128479, 0.9999517798423767, 0.9999080300331116, 0.9999068379402161, 0.9999216794967651, 0.999964714050293, 0.9999579191207886, 0.999947190284729, 0.9999909400939941, 0.9999750852584839, 0.9999821186065674, 0.9999696016311646, 0.99981290102005, 0.9999217391014099, 0.9999638795852661, 0.9998519420623779, 0.9999573230743408, 0.9998836517333984, 0.9999972581863403, 0.9999582171440125, 0.9999512434005737, 0.9998348951339722, 0.9998773336410522, 0.9998060464859009, 0.9997667670249939, 0.9998694062232971, 0.9999213814735413, 0.999829888343811, 0.9998615980148315, 0.9998399019241333, 0.9998511075973511, 0.9997041821479797, 0.999937891960144, 0.9998075366020203, 0.9999222755432129, 0.9997024536132812, 0.9997649192810059, 0.9999101161956787, 0.9999887943267822, 0.9999722242355347, 0.9999470710754395, 0.9999617338180542, 0.9999880194664001, 0.9999796152114868, 0.9997360110282898, 0.999982476234436, 0.999882161617279, 0.9999285936355591, 0.9999532699584961, 0.9999762773513794, 0.9999820590019226, 0.9999743103981018, 0.9999584555625916, 0.9998742341995239, 0.9999769330024719, 0.9999740719795227, 0.9999529719352722, 0.9997683763504028, 0.9999469518661499, 0.9999141693115234, 0.9999139904975891, 0.9999140501022339, 0.9999873638153076, 0.9998786449432373, 0.9998270869255066, 0.9999886155128479, 0.999786913394928, 0.9998847246170044, 0.9999792575836182, 0.9999579191207886, 0.9999771118164062, 0.9999957084655762, 0.9999736547470093, 0.9999752640724182, 0.9999812841415405, 0.9999608993530273, 0.9999698996543884, 0.9999719858169556, 0.9999549388885498, 0.9999635219573975, 0.9999619126319885, 0.9999961853027344, 0.9999740123748779, 0.9999788999557495, 0.9999374151229858, 0.9999331831932068, 0.9998947978019714, 0.9998036623001099, 0.9999680519104004, 0.9998030662536621, 0.9999604225158691, 0.9999485015869141, 0.9999669194221497, 0.9999847412109375, 0.9999372959136963, 0.9999825954437256, 0.999943196773529, 0.9999493956565857, 0.9998172521591187, 0.999857485294342, 0.9999696016311646, 0.9999864101409912, 0.9997518062591553, 0.999977707862854, 0.9998782873153687, 0.9999457597732544, 0.9999918937683105, 0.9999935626983643, 0.9996733069419861, 0.9999439716339111, 0.9999942779541016, 0.9998854398727417, 0.9998347759246826, 0.9999562501907349, 0.9999310374259949, 0.9999914169311523, 0.9999911189079285, 0.9999111294746399, 0.9999781250953674, 0.9999461770057678, 0.9999655485153198, 0.9998344779014587, 0.9999120235443115, 0.9999110698699951, 0.999897837638855, 0.9999743700027466, 0.9999843239784241, 0.9999650716781616, 0.9999604225158691, 0.9999745488166809, 0.9998480081558228, 0.9999508857727051, 0.9999807476997375, 0.9998051524162292, 0.999991238117218, 0.9999847412109375, 0.9998772144317627, 0.9999759197235107, 0.9998613595962524], "block_idx": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148], "time_seconds": 22.6489, "peak_memory_mb": 971.68}

2dsp_metadata.json

@@ -0,0 +1,5 @@
+{
+  "pdb_id": "2dsp",
+  "found": false,
+  "error": "Metadata fetch failed: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1016)>"
+}

2dsp_pymol_commands.pml

@@ -0,0 +1,52 @@
+# ============================================================
+# PyMOL Commands for 2dsp
+# ============================================================
+# Copy and paste these commands into PyMOL
+# ============================================================
+
+# Load structure (adjust path as needed)
+load 2dsp.pdb
+
+# Basic setup
+hide all
+show cartoon
+color grey80, all
+
+# Select and highlight critical residues (Top 10)
+select critical_top10, resi 29+46+42+55+23+47+35+69+78+10 and chain I
+show sticks, critical_top10
+color red, critical_top10
+set stick_radius, 0.3, critical_top10
+
+# Label critical residues
+label critical_top10 and name CA, "%s%s" % (resn,resi)
+set label_size, 14
+set label_color, red
+
+# Create gradient coloring by importance (Top 5 in different reds)
+select critical_rank1, resi 29 and chain I
+color red, critical_rank1
+select critical_rank2, resi 46 and chain B
+color tv_red, critical_rank2
+select critical_rank3, resi 42 and chain B
+color salmon, critical_rank3
+select critical_rank4, resi 55 and chain B
+color lightsalmon, critical_rank4
+select critical_rank5, resi 23 and chain I
+color warmpink, critical_rank5
+
+# Show surface around critical residues
+show surface, byres (critical_top10 around 5)
+set surface_color, white
+set transparency, 0.5
+
+# Center view on critical residues
+zoom critical_top10
+
+# ============================================================
+# Additional useful commands:
+# ============================================================
+# To save session: save 2dsp_critical.pse
+# To save image: png 2dsp_critical.png, dpi=300
+# To highlight most critical (rank 1): select most_critical, critical_rank1
+# ============================================================

2dsp_summary.json

@@ -0,0 +1,20 @@
+{
+  "total_structures": 1,
+  "total_time_seconds": 22.65,
+  "total_time_minutes": 0.38,
+  "time_per_structure": {
+    "mean": 22.6489,
+    "std": 0.0,
+    "min": 22.6489,
+    "max": 22.6489
+  },
+  "output_file": "output/2dsp_interact_scores.json",
+  "input_file": "downloads/pdbs/2dsp.cif",
+  "start_idx": 0,
+  "num_lines": null,
+  "device": "cuda",
+  "gpu_memory_mb": {
+    "mean": 971.68,
+    "max": 971.68
+  }
+}

2dsq_critical_residues.tsv

@@ -0,0 +1,417 @@
+# ATOMICA Critical Residue Analysis: 2dsq_all
+# Structure ID: 2dsq
+# Total residues analyzed: 408
+# Mean ATOMICA_SCORE: 0.999987
+# Std Dev: 0.000013
+# Method: ATOMICA_SCORE (cosine similarity with masked residues)
+# Lower scores = More critical for intermolecular interactions
+#
+Rank	Chain_ID	Residue_ID	Residue_Name	ATOMICA_Score	Importance_Delta_Percent	Block_Index
+1	A	46	CYS	0.999910	0.0090	180
+2	A	21	VAL	0.999913	0.0087	155
+3	I	64	LEU	0.999927	0.0073	135
+4	G	151	CYS	0.999931	0.0069	280
+5	B	21	VAL	0.999938	0.0062	18
+6	H	216	GLY	0.999947	0.0053	398
+7	G	219	GLU	0.999950	0.0050	338
+8	A	42	LEU	0.999952	0.0048	176
+9	I	23	PHE	0.999952	0.0048	108
+10	H	209	TRP	0.999952	0.0048	391
+11	C	29	THR	0.999954	0.0046	254
+12	B	78	VAL	0.999955	0.0045	75
+13	B	55	SER	0.999956	0.0044	52
+14	C	7	GLY	0.999956	0.0044	232
+15	A	55	SER	0.999958	0.0042	189
+16	B	42	LEU	0.999958	0.0042	39
+17	H	223	ASP	0.999958	0.0042	405
+18	A	32	CYS	0.999959	0.0041	166
+19	B	46	CYS	0.999960	0.0040	43
+20	I	7	GLY	0.999960	0.0040	92
+21	B	23	CYS	0.999960	0.0040	20
+22	G	202	LEU	0.999960	0.0040	321
+23	C	8	ALA	0.999960	0.0040	233
+24	B	34	CYS	0.999961	0.0039	31
+25	A	44	MET	0.999961	0.0039	178
+26	A	78	VAL	0.999961	0.0039	212
+27	C	23	PHE	0.999962	0.0038	248
+28	B	32	CYS	0.999963	0.0037	29
+29	G	216	GLY	0.999964	0.0036	335
+30	H	151	CYS	0.999964	0.0036	354
+31	B	44	MET	0.999964	0.0036	41
+32	I	8	ALA	0.999965	0.0035	93
+33	G	217	SER	0.999965	0.0035	336
+34	A	11	GLU	0.999965	0.0035	145
+35	A	23	CYS	0.999968	0.0032	157
+36	C	41	THR	0.999969	0.0031	255
+37	C	43	ILE	0.999969	0.0031	257
+38	C	20	ASP	0.999969	0.0031	245
+39	I	20	ASP	0.999969	0.0031	105
+40	G	186	PHE	0.999969	0.0031	307
+41	A	57	LEU	0.999970	0.0030	191
+42	H	148	LYS	0.999970	0.0030	351
+43	G	160	GLU	0.999970	0.0030	289
+44	H	202	LEU	0.999970	0.0030	384
+45	C	3	GLU	0.999970	0.0030	228
+46	A	79	CYS	0.999971	0.0029	213
+47	H	222	GLY	0.999971	0.0029	404
+48	B	9	CYS	0.999972	0.0028	6
+49	A	48	VAL	0.999972	0.0028	182
+50	B	48	VAL	0.999972	0.0028	45
+51	A	34	CYS	0.999972	0.0028	168
+52	G	223	ASP	0.999972	0.0028	342
+53	A	18	ARG	0.999973	0.0027	152
+54	B	79	CYS	0.999973	0.0027	76
+55	H	186	PHE	0.999973	0.0027	376
+56	B	57	LEU	0.999973	0.0027	54
+57	G	180	ASN	0.999973	0.0027	301
+58	B	65	VAL	0.999974	0.0026	62
+59	G	175	LYS	0.999974	0.0026	296
+60	A	76	GLN	0.999975	0.0025	210
+61	B	6	CYS	0.999975	0.0025	3
+62	G	165	ALA	0.999975	0.0025	294
+63	G	209	TRP	0.999975	0.0025	328
+64	A	20	PRO	0.999976	0.0024	154
+65	A	52	ARG	0.999976	0.0024	186
+66	B	28	ARG	0.999976	0.0024	25
+67	I	43	ILE	0.999976	0.0024	114
+68	H	217	SER	0.999976	0.0024	399
+69	G	227	GLN	0.999976	0.0024	346
+70	G	200	ALA	0.999977	0.0023	319
+71	C	48	CYS	0.999978	0.0022	262
+72	I	48	CYS	0.999978	0.0022	119
+73	B	47	GLY	0.999978	0.0022	44
+74	B	16	ARG	0.999979	0.0021	13
+75	B	72	LEU	0.999979	0.0021	69
+76	A	41	GLY	0.999979	0.0021	175
+77	B	76	GLN	0.999979	0.0021	73
+78	A	12	GLU	0.999979	0.0021	146
+79	A	28	ARG	0.999980	0.0020	162
+80	G	159	VAL	0.999980	0.0020	288
+81	H	180	ASN	0.999980	0.0020	370
+82	B	20	PRO	0.999980	0.0020	17
+83	B	45	PRO	0.999980	0.0020	42
+84	G	231	ASN	0.999980	0.0020	350
+85	H	212	LYS	0.999981	0.0019	394
+86	A	65	VAL	0.999981	0.0019	199
+87	C	54	LEU	0.999981	0.0019	268
+88	H	181	CYS	0.999981	0.0019	371
+89	B	67	LYS	0.999981	0.0019	64
+90	A	72	LEU	0.999981	0.0019	206
+91	A	3	ALA	0.999981	0.0019	137
+92	A	37	THR	0.999981	0.0019	171
+93	C	26	ASN	0.999981	0.0019	251
+94	G	212	LYS	0.999981	0.0019	331
+95	A	47	GLY	0.999982	0.0018	181
+96	H	225	ASN	0.999982	0.0018	407
+97	B	31	GLY	0.999982	0.0018	28
+98	H	189	SER	0.999982	0.0018	379
+99	C	42	GLY	0.999983	0.0017	256
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2dsq_interact_scores.json

@@ -0,0 +1 @@
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0.9999763369560242, 0.9999926090240479, 0.9999843835830688, 0.9999940395355225, 0.9999987483024597, 0.9999711513519287, 0.9999583959579468, 0.9999986290931702, 0.9999817609786987, 0.9999990463256836, 0.9999821186065674], "block_idx": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 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2dsq_metadata.json

@@ -0,0 +1,5 @@
+{
+  "pdb_id": "2dsq",
+  "found": false,
+  "error": "Metadata fetch failed: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1016)>"
+}

2dsq_pymol_commands.pml

@@ -0,0 +1,52 @@
+# ============================================================
+# PyMOL Commands for 2dsq
+# ============================================================
+# Copy and paste these commands into PyMOL
+# ============================================================
+
+# Load structure (adjust path as needed)
+load 2dsq.pdb
+
+# Basic setup
+hide all
+show cartoon
+color grey80, all
+
+# Select and highlight critical residues (Top 10)
+select critical_top10, resi 46+21+64+151+21+216+219+42+23+209 and chain A
+show sticks, critical_top10
+color red, critical_top10
+set stick_radius, 0.3, critical_top10
+
+# Label critical residues
+label critical_top10 and name CA, "%s%s" % (resn,resi)
+set label_size, 14
+set label_color, red
+
+# Create gradient coloring by importance (Top 5 in different reds)
+select critical_rank1, resi 46 and chain A
+color red, critical_rank1
+select critical_rank2, resi 21 and chain A
+color tv_red, critical_rank2
+select critical_rank3, resi 64 and chain I
+color salmon, critical_rank3
+select critical_rank4, resi 151 and chain G
+color lightsalmon, critical_rank4
+select critical_rank5, resi 21 and chain B
+color warmpink, critical_rank5
+
+# Show surface around critical residues
+show surface, byres (critical_top10 around 5)
+set surface_color, white
+set transparency, 0.5
+
+# Center view on critical residues
+zoom critical_top10
+
+# ============================================================
+# Additional useful commands:
+# ============================================================
+# To save session: save 2dsq_critical.pse
+# To save image: png 2dsq_critical.png, dpi=300
+# To highlight most critical (rank 1): select most_critical, critical_rank1
+# ============================================================

2dsq_summary.json

@@ -0,0 +1,20 @@
+{
+  "total_structures": 1,
+  "total_time_seconds": 105.74,
+  "total_time_minutes": 1.76,
+  "time_per_structure": {
+    "mean": 105.7401,
+    "std": 0.0,
+    "min": 105.7401,
+    "max": 105.7401
+  },
+  "output_file": "output/2dsq_interact_scores.json",
+  "input_file": "downloads/pdbs/2dsq.cif",
+  "start_idx": 0,
+  "num_lines": null,
+  "device": "cuda",
+  "gpu_memory_mb": {
+    "mean": 2731.16,
+    "max": 2731.16
+  }
+}

2dsr_critical_residues.tsv

@@ -0,0 +1,227 @@
+# ATOMICA Critical Residue Analysis: 2dsr_all
+# Structure ID: 2dsr
+# Total residues analyzed: 218
+# Mean ATOMICA_SCORE: 0.999953
+# Std Dev: 0.000050
+# Method: ATOMICA_SCORE (cosine similarity with masked residues)
+# Lower scores = More critical for intermolecular interactions
+#
+Rank	Chain_ID	Residue_ID	Residue_Name	ATOMICA_Score	Importance_Delta_Percent	Block_Index
+1	I	7	GLY	0.999701	0.0299	164
+2	I	3	GLU	0.999748	0.0252	160
+3	I	64	LEU	0.999770	0.0230	218
+4	G	218	GLY	0.999777	0.0223	67
+5	G	195	HIS	0.999818	0.0182	44
+6	G	223	LYS	0.999823	0.0177	72
+7	I	23	PHE	0.999829	0.0171	180
+8	G	152	SER	0.999830	0.0170	1
+9	B	78	VAL	0.999841	0.0159	154
+10	I	43	ILE	0.999852	0.0148	197
+11	B	35	CYS	0.999864	0.0136	111
+12	G	188	ASN	0.999867	0.0133	37
+13	B	55	SER	0.999869	0.0131	131
+14	G	210	ARG	0.999870	0.0130	59
+15	B	42	LEU	0.999870	0.0130	118
+16	B	47	GLY	0.999875	0.0125	123
+17	I	20	ASP	0.999878	0.0122	177
+18	B	80	MET	0.999879	0.0121	156
+19	I	8	ALA	0.999880	0.0120	165
+20	G	216	LEU	0.999881	0.0119	65
+21	I	40	GLN	0.999882	0.0118	194
+22	B	76	GLN	0.999884	0.0116	152
+23	I	48	CYS	0.999884	0.0116	202
+24	G	225	GLU	0.999888	0.0112	74
+25	B	72	LEU	0.999888	0.0112	148
+26	G	219	GLY	0.999889	0.0111	68
+27	B	34	CYS	0.999891	0.0109	110
+28	G	220	LEU	0.999893	0.0107	69
+29	B	9	CYS	0.999894	0.0106	85
+30	I	31	TYR	0.999895	0.0105	188
+31	B	20	PRO	0.999897	0.0103	96
+32	G	201	GLN	0.999897	0.0103	50
+33	B	11	GLU	0.999900	0.0100	87
+34	I	29	THR	0.999900	0.0100	186
+35	B	36	ALA	0.999901	0.0099	112
+36	I	33	SER	0.999901	0.0099	190
+37	G	173	GLU	0.999902	0.0098	22
+38	B	79	CYS	0.999903	0.0097	155
+39	B	32	CYS	0.999908	0.0092	108
+40	G	204	LYS	0.999909	0.0091	53
+41	G	214	VAL	0.999911	0.0089	63
+42	G	185	ARG	0.999914	0.0086	34
+43	B	14	LEU	0.999918	0.0082	90
+44	B	6	CYS	0.999919	0.0081	82
+45	B	57	LEU	0.999919	0.0081	133
+46	I	19	GLY	0.999921	0.0079	176
+47	B	44	MET	0.999922	0.0078	120
+48	G	209	ASP	0.999925	0.0075	58
+49	G	182	ASN	0.999925	0.0075	31
+50	B	69	LEU	0.999927	0.0073	145
+51	I	42	GLY	0.999929	0.0071	196
+52	B	25	GLU	0.999929	0.0071	101
+53	B	64	GLY	0.999931	0.0069	140
+54	B	10	SER	0.999931	0.0069	86
+55	G	180	ILE	0.999932	0.0068	29
+56	B	39	ALA	0.999933	0.0067	115
+57	B	23	CYS	0.999934	0.0066	99
+58	I	52	CYS	0.999934	0.0066	206
+59	B	60	TYR	0.999940	0.0060	136
+60	B	24	GLU	0.999940	0.0060	100
+61	I	61	CYS	0.999940	0.0060	215
+62	B	65	VAL	0.999941	0.0059	141
+63	I	53	ASP	0.999941	0.0059	207
+64	I	4	THR	0.999941	0.0059	161
+65	B	27	VAL	0.999941	0.0059	103
+66	G	172	HIS	0.999944	0.0056	21
+67	B	30	PRO	0.999946	0.0054	106
+68	B	48	VAL	0.999950	0.0050	124
+69	G	203	GLY	0.999951	0.0049	52
+70	B	81	GLU	0.999952	0.0048	157
+71	B	75	GLY	0.999952	0.0048	151
+72	G	197	ALA	0.999952	0.0048	46
+73	B	63	ARG	0.999953	0.0047	139
+74	G	229	HIS	0.999954	0.0046	78
+75	I	63	PRO	0.999955	0.0045	217
+76	I	49	PHE	0.999955	0.0045	203
+77	G	159	ARG	0.999956	0.0044	8
+78	I	60	TYR	0.999957	0.0043	214
+79	I	62	ALA	0.999957	0.0043	216
+80	B	46	CYS	0.999957	0.0043	122
+81	I	51	SER	0.999958	0.0042	205
+82	B	71	THR	0.999958	0.0042	147
+83	G	226	LEU	0.999959	0.0041	75
+84	I	18	CYS	0.999960	0.0040	175
+85	B	21	VAL	0.999960	0.0040	97
+86	B	40	LEU	0.999961	0.0039	116
+87	I	54	LEU	0.999962	0.0038	208
+88	G	200	GLY	0.999962	0.0038	49
+89	B	62	PRO	0.999963	0.0037	138
+90	B	38	CYS	0.999963	0.0037	114
+91	B	3	ALA	0.999963	0.0037	79
+92	I	45	ASP	0.999965	0.0035	199
+93	B	33	GLY	0.999966	0.0034	109
+94	B	50	THR	0.999966	0.0034	126
+95	G	191	PRO	0.999966	0.0034	40
+96	B	28	ARG	0.999966	0.0034	104
+97	G	202	ARG	0.999967	0.0033	51
+98	G	156	GLU	0.999968	0.0032	5
+99	B	4	ILE	0.999968	0.0032	80
+100	B	67	LYS	0.999968	0.0032	143
+101	G	196	PRO	0.999968	0.0032	45
+102	G	227	ASP	0.999970	0.0030	76
+103	I	12	ASP	0.999970	0.0030	169
+104	I	30	GLY	0.999970	0.0030	187
+105	B	43	GLY	0.999971	0.0029	119
+106	B	7	PRO	0.999971	0.0029	83
+107	B	54	GLY	0.999971	0.0029	130
+108	I	5	LEU	0.999972	0.0028	162
+109	G	164	LEU	0.999972	0.0028	13
+110	I	59	MET	0.999972	0.0028	213
+111	B	82	LEU	0.999972	0.0028	158
+112	G	170	ARG	0.999973	0.0027	19
+113	B	70	HIS	0.999973	0.0027	146
+114	B	8	PRO	0.999973	0.0027	84
+115	B	51	PRO	0.999974	0.0026	127
+116	I	28	PRO	0.999974	0.0026	185
+117	G	154	GLN	0.999975	0.0025	3
+118	G	187	GLY	0.999975	0.0025	36
+119	B	18	ARG	0.999975	0.0025	94
+120	I	11	VAL	0.999975	0.0025	168
+121	G	207	CYS	0.999977	0.0023	56
+122	G	193	GLN	0.999977	0.0023	42
+123	G	213	GLY	0.999977	0.0023	62
+124	G	168	GLN	0.999978	0.0022	17
+125	G	206	TRP	0.999978	0.0022	55
+126	G	161	LEU	0.999979	0.0021	10
+127	I	6	CYS	0.999979	0.0021	163
+128	B	16	ARG	0.999979	0.0021	92
+129	G	189	PHE	0.999979	0.0021	38
+130	G	205	CYS	0.999979	0.0021	54
+131	G	157	LEU	0.999979	0.0021	6
+132	B	37	THR	0.999979	0.0021	113
+133	I	50	ARG	0.999980	0.0020	204
+134	B	77	GLY	0.999980	0.0020	153
+135	B	5	HIS	0.999980	0.0020	81
+136	G	183	CYS	0.999981	0.0019	32
+137	I	44	VAL	0.999982	0.0018	198
+138	I	26	ASN	0.999982	0.0018	183
+139	I	58	GLU	0.999982	0.0018	212
+140	I	46	GLU	0.999982	0.0018	200
+141	G	228	CYS	0.999982	0.0018	77
+142	I	25	PHE	0.999982	0.0018	182
+143	G	208	VAL	0.999983	0.0017	57
+144	I	56	ARG	0.999984	0.0016	210
+145	I	47	CYS	0.999984	0.0016	201
+146	B	17	CYS	0.999984	0.0016	93
+147	I	13	ALA	0.999984	0.0016	170
+148	G	160	ALA	0.999984	0.0016	9
+149	I	32	GLY	0.999984	0.0016	189
+150	B	66	GLU	0.999984	0.0016	142
+151	G	175	LEU	0.999985	0.0015	24
+152	I	17	VAL	0.999985	0.0015	174
+153	B	13	LYS	0.999985	0.0015	89
+154	I	22	GLY	0.999985	0.0015	179
+155	G	211	LYS	0.999985	0.0015	60
+156	B	41	GLY	0.999985	0.0015	117
+157	G	215	LYS	0.999985	0.0015	64
+158	G	184	ASP	0.999985	0.0015	33
+159	B	52	ARG	0.999986	0.0014	128
+160	G	171	THR	0.999986	0.0014	20
+161	G	179	PRO	0.999986	0.0014	28
+162	G	153	CYS	0.999986	0.0014	2
+163	G	162	GLU	0.999986	0.0014	11
+164	B	15	ALA	0.999987	0.0013	91
+165	B	73	MET	0.999987	0.0013	149
+166	G	174	ASP	0.999987	0.0013	23
+167	G	190	HIS	0.999987	0.0013	39
+168	G	221	GLU	0.999987	0.0013	70
+169	I	39	PRO	0.999987	0.0013	193
+170	B	68	PRO	0.999988	0.0012	144
+171	I	16	PHE	0.999988	0.0012	173
+172	G	165	ALA	0.999988	0.0012	14
+173	G	166	ALA	0.999988	0.0012	15
+174	G	155	SER	0.999988	0.0012	4
+175	I	41	THR	0.999988	0.0012	195
+176	I	55	ARG	0.999989	0.0011	209
+177	B	49	TYR	0.999989	0.0011	125
+178	B	45	PRO	0.999989	0.0011	121
+179	I	38	ALA	0.999989	0.0011	192
+180	G	176	TYR	0.999989	0.0011	25
+181	G	222	PRO	0.999990	0.0010	71
+182	G	167	SER	0.999990	0.0010	16
+183	G	198	LEU	0.999990	0.0010	47
+184	G	192	LYS	0.999990	0.0010	41
+185	B	22	GLY	0.999990	0.0010	98
+186	G	217	PRO	0.999990	0.0010	66
+187	G	194	CYS	0.999991	0.0009	43
+188	B	58	ARG	0.999991	0.0009	134
+189	I	24	TYR	0.999991	0.0009	181
+190	B	31	GLY	0.999991	0.0009	107
+191	G	163	ARG	0.999992	0.0008	12
+192	I	14	LEU	0.999992	0.0008	171
+193	B	26	LEU	0.999992	0.0008	102
+194	I	27	LYS	0.999993	0.0007	184
+195	I	34	SER	0.999993	0.0007	191
+196	I	10	LEU	0.999993	0.0007	167
+197	G	181	PRO	0.999993	0.0007	30
+198	I	2	PRO	0.999993	0.0007	159
+199	G	177	ILE	0.999994	0.0006	26
+200	I	21	ARG	0.999994	0.0006	178
+201	G	224	GLY	0.999994	0.0006	73
+202	G	186	ASN	0.999995	0.0005	35
+203	B	12	GLU	0.999995	0.0005	88
+204	I	9	GLU	0.999995	0.0005	166
+205	B	56	GLY	0.999995	0.0005	132
+206	G	178	ILE	0.999995	0.0005	27
+207	G	158	HIS	0.999996	0.0004	7
+208	G	212	THR	0.999996	0.0004	61
+209	B	19	PRO	0.999996	0.0004	95
+210	I	57	LEU	0.999996	0.0004	211
+211	G	169	SER	0.999996	0.0004	18
+212	I	15	GLN	0.999996	0.0004	172
+213	B	29	GLU	0.999997	0.0003	105
+214	G	199	ASP	0.999997	0.0003	48
+215	B	74	HIS	0.999997	0.0003	150
+216	B	59	CYS	0.999998	0.0002	135
+217	B	53	CYS	0.999998	0.0002	129
+218	B	61	PRO	0.999999	0.0001	137