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DanielP520 / sequence_logo_project

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basic curiosities #2

Open Yogesh1-11 opened 1 year ago

Yogesh1-11 commented 1 year ago
  1. sequence logos are on the basis of MSA or number of PDB files.
  2. The energy section in example PDB files is required?

    All scores below are weighted scores, not raw scores.

    BEGIN_POSE_ENERGIES_TABLE 2p9h_98712-clean-2_both_hydrated_0001.pdb

    label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega fa_dun p_aa_pp yhh_planarity ref rama_prepro total weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA if yes, how to generate these?

DanielP520 commented 1 year ago

  1. The are based on the number of PDB uploaded.

  2. No, the energy function part is not required, the examples come from a Rosetta Design and thats why they have an energy section, but when processing the PDB files this section is ignored.

Yogesh1-11 commented 1 year ago

It will be great if we can add mmseq homology search here. It's impractical to bind ligand in multiple protein homologs. It will be better if user can supply pdb file along with mmseq alignment. Alignment should be used for logo. 👌

On Thu, 3 Aug, 2023, 12:53 am Daniel Pineda, @.***> wrote:

1.

The are based on the number of PDB uploaded. 2.

No, the energy function part is not required, the examples come from a Rosetta Design and thats why they have an energy section, but when processing the PDB files this section is ignored.

— Reply to this email directly, view it on GitHub https://github.com/DanielP520/sequence_logo_project/issues/2#issuecomment-1662850430, or unsubscribe https://github.com/notifications/unsubscribe-auth/AZNDTOQPW6AZ6BYHOFR7GD3XTKSLJANCNFSM6AAAAAA25ACKB4 . You are receiving this because you authored the thread.Message ID: @.***>