@> 827 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> 808 atoms and 1 coordinate set(s) were parsed in 0.03s.
Visualizations and results¶
Original Structure Visualization¶
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@> 827 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> 808 atoms and 1 coordinate set(s) were parsed in 0.03s.
3m1bF_TEMP Blue:3lowA Red:3m1bF
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AlphaFold predictions¶
Best AF prediction to fold 1¶
No max_af_pdb1
Best AF prediction to fold 2¶
@> 836 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> 808 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> 836 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> 808 atoms and 1 coordinate set(s) were parsed in 0.03s.
3m1bF_TEMP
Blue:ShallowMsa_035_unrelaxed_rank_004_alphafold2_ptm_model_2_seed_000 Red:3m1bF
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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¶
@> 808 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> 836 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> 808 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> 836 atoms and 1 coordinate set(s) were parsed in 0.03s.
reference and target coordinate arrays must have same number of atoms 0.96655 ShallowMsa_008_4_TEMP
Blue:3m1bF Red:ShallowMsa_008_4
3Dmol.js failed to load for some reason. Please check your browser console for error messages.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 14210 | 3lowA_3m1bF | ShallowMsa_008_4.pdb | 0.56539 | 0.96655 | 008 | 0.472291 | 0.759877 | 10 | 0 | 1 | 0 | 1 |
| 14412 | 3lowA_3m1bF | ShallowMsa_029_8.pdb | 0.56539 | 0.96655 | 029 | 0.460839 | 0.787307 | 10 | 0 | 1 | 0 | 1 |
| 14385 | 3lowA_3m1bF | ShallowMsa_026_0.pdb | 0.56539 | 0.96655 | 026 | 0.460087 | 0.729159 | 10 | 0 | 1 | 0 | 1 |
| 14485 | 3lowA_3m1bF | ShallowMsa_036_1.pdb | 0.56539 | 0.96655 | 036 | 0.399432 | 0.727963 | 10 | 0 | 1 | 0 | 1 |
| 14675 | 3lowA_3m1bF | ShallowMsa_055_2.pdb | 0.56539 | 0.96655 | 055 | 0.445765 | 0.769200 | 10 | 0 | 1 | 0 | 1 |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 14243 | 3lowA_3m1bF | ShallowMsa_012_9.pdb | 0.46064 | 0.62532 | 012 | 0.454150 | 0.651158 | 10 | 0 | 1 | 0 | 1 |
| 14749 | 3lowA_3m1bF | ShallowMsa_062_5.pdb | 0.34066 | 0.62419 | 062 | 0.417943 | 0.723247 | 10 | 0 | 1 | 0 | 1 |
| 14743 | 3lowA_3m1bF | ShallowMsa_062_0.pdb | 0.34334 | 0.61211 | 062 | 0.417943 | 0.723247 | 10 | 0 | 1 | 0 | 1 |
| 14196 | 3lowA_3m1bF | ShallowMsa_007_2.pdb | 0.42492 | 0.60123 | 007 | 0.447634 | 0.650151 | 10 | 0 | 1 | 0 | 1 |
| 14238 | 3lowA_3m1bF | ShallowMsa_011_6.pdb | 0.41696 | 0.47881 | 011 | 0.441395 | 0.711689 | 10 | 0 | 1 | 0 | 1 |
630 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)
