smoe
commented
9 years ago Hello,
It seems to work from what I grasp. Nice merge. Here the results for my "621" sequence with multiple grafts for heavy and light, multi-templates on and allowing for three templates? Are the identical proposals for templates for the same loop (L1 or L2, ...) intentional?
Best,
Steffen
light template: pdb3mlw_chothia.pdb light template: pdb4d9l_chothia.pdb light template: pdb2yk1_chothia.pdb I: Queryname=heavy I: Found 600 blast results (limit 600) heavy template: pdb2xzc_chothia.pdb heavy template: pdb2xza_chothia.pdb heavy template: pdb2eks_chothia.pdb I: Queryname=L1 I: Found 33 blast results (limit 600) L1 template: pdb2xzc_chothia.pdb L1 template: pdb2xzc_chothia.pdb L1 template: pdb2xzc_chothia.pdb I: Queryname=L2 I: Found 24 blast results (limit 600) L2 template: pdb2yk1_chothia.pdb L2 template: pdb2yk1_chothia.pdb L2 template: pdb2yk1_chothia.pdb I: Queryname=L3 I: Found 11 blast results (limit 600) L3 template: pdb3n9g_chothia.pdb L3 template: pdb3n9g_chothia.pdb L3 template: pdb3n9g_chothia.pdb I: Queryname=H1 I: Found 5 blast results (limit 600) WARNING: No template avaliable for H1 after filtering! Using a random template of the same length as the query H1 template: pdb1ai1_chothia.pdb WARNING: No template avaliable for H1 after filtering! Using a random template of the same length as the query H1 template: pdb1ai1_chothia.pdb WARNING: No template avaliable for H1 after filtering! Using a random template of the same length as the query H1 template: pdb1ai1_chothia.pdb I: Queryname=H2 I: Found 245 blast results (limit 600) H2 template: pdb2xzc_chothia.pdb H2 template: pdb2xzc_chothia.pdb H2 template: pdb2xzc_chothia.pdb I: Queryname=H3 I: Found 0 blast results (limit 600) WARNING: No template avaliable for H3 after filtering! Using a random template of the same length as the query H3 template: pdb3d85_chothia.pdb WARNING: No template avaliable for H3 after filtering! Using a random template of the same length as the query H3 template: pdb3d85_chothia.pdb WARNING: No template avaliable for H3 after filtering! Using a random template of the same length as the query H3 template: pdb3d85_chothia.pdb I: Queryname=light_heavy I: Found 632 blast results (limit 600) light_heavy template: pdb2xzc_chothia.pdb light_heavy template: pdb2xzc_chothia.pdb light_heavy template: pdb2xzc_chothia.pdb
nmarze
Default behavior is still single-template grafting. Small change to naming of grafted pdb file, template pdb file names; e.g.: old: model.pdb new: model.0.pdb
Also adding additional template selection methods for light_heavy orientation; these methods require new files angles.sc, make_angle_distances.py, and comparisons.txt.