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dina-lab3D / CombFold

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implementing crosslinks #16

Open jimfeng9705 opened 2 months ago

jimfeng9705 commented 2 months ago

Your example files contain a crosslink folder. How to run CombFold with enabling the crosslink restraints?

ben-shor commented 2 months ago

Hi, You can supply a path to crosslinks file as the 4th argument to run_on_pdbs.py. Notice that the format of each line in the crosslinks file should be:

The weight can simply be 1 if you are unsure. Let me know if you encounter issues
jimfeng9705 commented 2 months ago

Thanks for your response!

Can you help check the crosslink list in your example data? CombFold/example/example_xlinks /crosslinks.txt

Aren't some of them not the chain_ID? 94 2 651 C 0 30 0.85 149 2 651 C 0 30 0.92 280 2 196 A 0 30 0.96 789 C 159 T 0 30 0.67 40 T 27 b 0 30 0.86 424 2 206 A 0 30 0.55 351 2 29 T 0 30 0.84 149 2 196 A 0 30 0.93 761 C 304 T 0 30 0.95 152 2 651 C 0 30 0.94 351 2 832 C 0 30 0.87 206 A 645 C 0 30 0.75 832 C 40 T 0 30 0.85 424 2 23 b 0 30 0.75

jimfeng9705 commented 2 months ago

How to supply the crosslinks path as the 4th argument in the Run cell of Colab?

ben-shor commented 2 months ago

Regarding the example, it is a bit confusing, but in the example "2" is one of the chain_ids (the chain ids are 2,A,C,T,b).

Regarding the Colab. I have added support in supplying crosslinks. simply also include in your input folder a file named "crosslinks.txt" that is formatted as described.

Good luck!

jimfeng9705 commented 2 months ago

I ran the Colab with this folder directing to crosslinks: /content/CombFold-master/example/example_xlinks

How can I be sure that the crosslinks restraints are applied? I did not really see such information in the log below?

--- Searching for subunits in supplied PDB files found full A0 in AFM_A0_A0_G0_unrelaxed_rank_1_model_1.pdb chain B found full A0 in AFM_A0_A0_G0_unrelaxed_rank_1_model_1.pdb chain C found full G0 in AFM_A0_A0_G0_unrelaxed_rank_1_model_1.pdb chain D found full A0 in AFM_A0_G0_unrelaxed_rank_1_model_2.pdb chain B found full G0 in AFM_A0_G0_unrelaxed_rank_1_model_2.pdb chain C found full A0 in AFM_A0_A0_A0_unrelaxed_rank_1_model_3.pdb chain B found full A0 in AFM_A0_A0_A0_unrelaxed_rank_1_model_3.pdb chain C found full A0 in AFM_A0_A0_A0_unrelaxed_rank_1_model_3.pdb chain D found full A0 in AFM_A0_A0_A0_unrelaxed_rank_2_model_1.pdb chain B found full A0 in AFM_A0_A0_A0_unrelaxed_rank_2_model_1.pdb chain C found full A0 in AFM_A0_A0_A0_unrelaxed_rank_2_model_1.pdb chain D found full A0 in AFM_A0_A0_unrelaxed_rank_1_model_1.pdb chain B found full A0 in AFM_A0_A0_unrelaxed_rank_1_model_1.pdb chain C found full A0 in AFM_A0_G0_unrelaxed_rank_2_model_3.pdb chain B found full G0 in AFM_A0_G0_unrelaxed_rank_2_model_3.pdb chain C found full G0 in AFM_G0_G0_unrelaxed_rank_1_model_4.pdb chain B found full G0 in AFM_G0_G0_unrelaxed_rank_1_model_4.pdb chain C found full G0 in AFM_G0_G0_unrelaxed_rank_2_model_5.pdb chain B found full G0 in AFM_G0_G0_unrelaxed_rank_2_model_5.pdb chain C found full A0 in AFM_A0_A0_unrelaxed_rank_2_model_4.pdb chain B found full A0 in AFM_A0_A0_unrelaxed_rank_2_model_4.pdb chain C found full A0 in AFM_A0_A0_G0_unrelaxed_rank_2_model_3.pdb chain B found full A0 in AFM_A0_A0_G0_unrelaxed_rank_2_model_3.pdb chain C found full G0 in AFM_A0_A0_G0_unrelaxed_rank_2_model_3.pdb chain D --- Extracting representative subunits (for each subunit, its best scored model in the PDBs folder) rep A0 has plddt score 96.00915686274507 rep G0 has plddt score 89.0577211394304 --- Extracting pairwise transformations between subunits (from each PDB file with 2 or more subunits)