@> 516 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> 1029 atoms and 1 coordinate set(s) were parsed in 0.04s.
Visualizations and results¶
Original Structure Visualization¶
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@> 516 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> 1029 atoms and 1 coordinate set(s) were parsed in 0.03s.
3j97M_TEMP Blue:1xtgB Red:3j97M
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AlphaFold predictions¶
Best AF prediction to fold 1¶
No max_af_pdb1
Best AF prediction to fold 2¶
@> 465 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> 1029 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> 465 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> 1029 atoms and 1 coordinate set(s) were parsed in 0.04s.
3j97M_TEMP
Blue:ShallowMsa_030_unrelaxed_rank_002_alphafold2_ptm_model_3_seed_000 Red:3j97M
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EsmFold Prediction¶
Out[10]:
| fold_pair | fold | TMscore_fold1 | TMscore_fold2 | cluster_num | TM_mean_cluster_pdb1 | TM_mean_cluster_pdb2 | sample_count | is_fold_1 | is_fold_2 | cluster_fold_1 | cluster_fold_2 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | 1dzlA_5keqF | ShallowMsa_000_1.pdb | 0.21478 | 0.22071 | 000 | 0.281451 | 0.2755 | 10 | 1 | 0 | 1 | 0 |
| 1 | 1dzlA_5keqF | ShallowMsa_000_0.pdb | 0.23730 | 0.24378 | 000 | 0.281451 | 0.2755 | 10 | 1 | 0 | 1 | 0 |
| 2 | 1dzlA_5keqF | ShallowMsa_000_2.pdb | 0.38172 | 0.36978 | 000 | 0.281451 | 0.2755 | 10 | 1 | 0 | 1 | 0 |
| 3 | 1dzlA_5keqF | ShallowMsa_000_3.pdb | 0.38407 | 0.38314 | 000 | 0.281451 | 0.2755 | 10 | 1 | 0 | 1 | 0 |
| 4 | 1dzlA_5keqF | ShallowMsa_000_7.pdb | 0.18823 | 0.17477 | 000 | 0.281451 | 0.2755 | 10 | 1 | 0 | 1 | 0 |
Best EsmFold prediction to fold 1¶
single positional indexer is out-of-bounds name 'pdb_file1_' is not defined
Best EsmFold prediction to fold 2¶
@> 1029 atoms and 1 coordinate set(s) were parsed in 0.04s.
@> 465 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> 1029 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> 465 atoms and 1 coordinate set(s) were parsed in 0.02s.
reference and target coordinate arrays must have same number of atoms 0.43601 ShallowMsa_023_3_TEMP
Blue:3j97M Red:ShallowMsa_023_3
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Out[13]:
| fold_pair | fold | TMscore_fold1 | TMscore_fold2 | cluster_num | TM_mean_cluster_pdb1 | TM_mean_cluster_pdb2 | sample_count | is_fold_1 | is_fold_2 | cluster_fold_1 | cluster_fold_2 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 4220 | 1xtgB_3j97M | ShallowMsa_023_3.pdb | 0.35030 | 0.43601 | 023 | 0.336885 | 0.384610 | 10 | 0 | 1 | 0 | 1 |
| 4003 | 1xtgB_3j97M | ShallowMsa_001_6.pdb | 0.35030 | 0.43601 | 001 | 0.336757 | 0.389363 | 10 | 0 | 1 | 0 | 1 |
| 4545 | 1xtgB_3j97M | ShallowMsa_055_7.pdb | 0.35030 | 0.43601 | 055 | 0.351460 | 0.425005 | 10 | 0 | 1 | 0 | 1 |
| 4074 | 1xtgB_3j97M | ShallowMsa_008_4.pdb | 0.35030 | 0.43601 | 008 | 0.340221 | 0.401615 | 10 | 0 | 1 | 0 | 1 |
| 4083 | 1xtgB_3j97M | ShallowMsa_009_5.pdb | 0.35030 | 0.43601 | 009 | 0.338572 | 0.401912 | 10 | 0 | 1 | 0 | 1 |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 4388 | 1xtgB_3j97M | ShallowMsa_040_5.pdb | 0.34902 | 0.34033 | 040 | 0.339580 | 0.374688 | 10 | 0 | 1 | 0 | 1 |
| 4390 | 1xtgB_3j97M | ShallowMsa_040_0.pdb | 0.33911 | 0.33958 | 040 | 0.339580 | 0.374688 | 10 | 0 | 1 | 0 | 1 |
| 4054 | 1xtgB_3j97M | ShallowMsa_006_8.pdb | 0.36277 | 0.33874 | 006 | 0.361336 | 0.397556 | 10 | 0 | 1 | 0 | 1 |
| 4394 | 1xtgB_3j97M | ShallowMsa_040_9.pdb | 0.33880 | 0.33174 | 040 | 0.339580 | 0.374688 | 10 | 0 | 1 | 0 | 1 |
| 4218 | 1xtgB_3j97M | ShallowMsa_023_6.pdb | 0.33338 | 0.32821 | 023 | 0.336885 | 0.384610 | 10 | 0 | 1 | 0 | 1 |
590 rows × 12 columns
Contact maps Msa Transformers¶
Out[15]:
array(['1qb3A_3qy2A', '3l5nB_2a73B', '5l35G_5l35D', '4ydqB_4twaA',
'2mwfA_2nntA', '1qlnA_1h38D', '1xezA_3o44A', '1zk9A_3jv6A',
'1xjuB_1xjtA', '3meeA_4b3oB', '3r9jC_2kxoA', '5f5rB_5f3kA',
'1nqjB_1nqdA', '4yhdG_7ahlE', '1mnmD_1mnmC', '2bzyB_2lqwA',
'3lowA_3m1bF', '1iytA_2naoF', '2kb8A_6vw2A', '5et5A_3ifaA',
'1nocA_1qomB', '4o01D_4o0pA', '3v0tA_3uyiA', '4q79F_4uv2D',
'2uy7D_5fluE', '5c1vB_5c1vA', '2k42A_1ceeB', '2lelA_2k0qA',
'1miqB_1qs8B', '3t5oA_4a5wB', '6c6sD_2ougC', '3lqcA_1xntA',
'3mkoA_5ineA', '5jytA_2qkeE', '4dxrA_4dxtA', '2kkwA_2n0aD',
'5c3iF_3kuyA', '5tpnA_1g2cF', '3j7vG_3j7wB', '1svfC_4wsgC',
'5jztG_5jzhA', '5bmyA_5b3zA', '2z9oB_1repC', '2n54B_2hdmA',
'3g0hA_3ewsB', '1rk4B_1k0nA', '1kctA_3t1pA', '2c1vB_2c1uC',
'2lv1A_6lniA', '4pyjA_4pyiA', '2qqjA_4qdsA', '1xtgB_3j97M',
'4n9wA_4nc9C', '2lepA_4hddA', '5lj3M_3tp2A', '5i2sA_5i2mA',
'5ly6B_5aoeB', '4tsyD_3zwgN', '3m7pA_3ejhA', '1eboE_5fhcJ',
'2jmrA_4j3oF', '2namA_1uxmK', '4qhhA_4qhfA', '1dzlA_5keqF',
'4rmbB_4rmbA', '2pbkB_3njqA', '4xwsD_4y0mJ', '2h44A_1rkpA',
'5wrgC_1wyyB', '1jfkA_2nxqB', '3kdsG_2ce7C', '3hdfA_3hdeA',
'3ztjE_5hmgA', '1x0gD_1x0gA', '3l9qB_4rr2D', '1nrjB_2gedB',
'4rwqB_4rwnA', '2p3vD_2p3vA', '4h2aA_3j9cA', '5hk5H_4jphB',
'4zrbH_4zrbC', '2vfxL_3gmhL', '4gqcB_4gqcC'], dtype=object)
