scripts and data to run the example modification of the modelling pipeline

other/README.md

-Scripts and data to reproduce various plots / table from the Supporting 
-information
+Scripts and data to reproduce various plots / tables from the Supporting 
+information but also to reproduce the example modification of the modelling
+pipeline which is described in the main manuscript.
 
 1. S1 Fig: Length of modelled loops in homology modelling benchmark
 2. S1 Table: Structural coverage in default StructureDB
+3. Example modification of modelling pipeline
 
 
 S1 Fig: Length of modelled loops in homology modelling benchmark
@@ -23,3 +25,8 @@ S1 Table: Structural coverage in default StructureDB
   displayed in S1 Table. Be aware: the table reports the average values over 3 
   runs of this script. 
 
+Example modification of modelling pipeline
+------------------------------------------
+
+Scripts, data and another README are available in the *mod_pipeline* directory.
+

other/mod_pipeline/BF.sm/config

+[core]
+pdb_storage = external
+smtl_path = /scratch/smng_dbs/SMTL_2ND
+full_gmqe = False
+title = 2019-10-12_00000117_1_54
+project_type = homo
+antibody_chain = False
+
+[meld]
+last_model_id = 1
+

other/mod_pipeline/BF.sm/mdl/01/info.json

+{"templates":["1f7ee0185c027f840714313bee002b90c1645193"],"oligo":{"based_on":"prediction","res_to_mdl":69,"state":"monomer","state_bu":"homo-dimer","qs_prediction":"0.000","qs_conserved":"not conserved","chains_to_mdl":1,"state_tpl":"monomer"},"pred_lddt":0.6470000148,"chain_subprj_list":null,"creation_date":"2019-10-12","ligands":[{"description":"SUGAR (2-MER)","number":"1","reason":{"sterically_valid":false,"conserved_residues":false,"relevant":true,"bound":true},"included":false,"model_binding_residues":[],"name":["NAG","NAG"]},{"description":"SUGAR (2-MER)","number":"4","reason":{"sterically_valid":false,"conserved_residues":false,"relevant":true,"bound":true},"included":false,"model_binding_residues":[],"name":["NAG","NAG"]},{"description":"SUGAR (N-ACETYL-D-GLUCOSAMINE)","number":"2","reason":{"sterically_valid":false,"conserved_residues":false,"relevant":true,"bound":true},"included":false,"model_binding_residues":[],"name":["NAG"]},{"description":"SUGAR (N-ACETYL-D-GLUCOSAMINE)","number":"5","reason":{"sterically_valid":false,"conserved_residues":false,"relevant":true,"bound":true},"included":false,"model_binding_residues":[],"name":["NAG"]},{"description":"SUGAR (4-MER)","number":"3","reason":{"sterically_valid":false,"conserved_residues":false,"relevant":true,"bound":true},"included":false,"model_binding_residues":[],"name":["NDG","NAG","NAG","NAG"]},{"description":"SUGAR (4-MER)","number":"6","reason":{"sterically_valid":false,"conserved_residues":false,"relevant":true,"bound":true},"included":false,"model_binding_residues":[],"name":["NDG","NAG","NAG","NAG"]}],"modified_template":false,"plip":{},"residue_range":[{"chain_name":"A","residue_from":"13","residue_to":"79"}],"mdlchain_butpl_map":{"A":"4b8v.1.A"},"qmean_values":{"local_scores":{"A":[null,null,null,null,null,null,null,null,null,null,null,null,0.7595292171,0.7709733199,0.7679715335,0.6820321387,0.6794604594,0.7352636235,0.7226174383,0.7494432568,0.7677644492,0.7858676785,0.7878309719,0.6730515146,0.7086870985,0.7589610189,0.7607696096,0.7466237069,0.7449181176,0.7246933642,0.7050858737,0.7261962419,0.7584532412,0.6333229049,0.43971576,0.1634149258,0.1554763455,0.2373588915,0.318227385,0.4479396439,0.7316497638,0.7062396185,0.7575763978,0.7841259311,0.7706970752,0.7719843127,0.8095682517,0.729691249,0.8273358234,0.7909998149,0.7513066077,0.7295026071,0.6877599727,0.6585904841,0.7421009272,0.7107673751,0.6399285621,0.7359773907,0.7313914551,0.7494003413,0.76231139,0.7656656656,0.8042642126,0.7876690829,0.7929124565,0.7871559264,0.7826168183,0.7099086222,0.6682278917,0.7148507187,0.6419257498,0.6889439201,0.6746461196,0.7482797818,0.674896879,0.6848403448,0.7668447042,0.7403137208,0.6808314423]},"global_scores":{"interaction_norm_score":-0.0142020561,"qmean6_z_score":-1.469761816,"torsion_z_score":-0.7130880371,"torsion_norm_score":-0.1998463023,"ss_agreement_z_score":-0.7636034172,"acc_agreement_norm_score":0.5373134328,"cbeta_norm_score":-0.0138066274,"packing_z_score":-0.675742068,"packing_norm_score":-0.3204136162,"qmean4_z_score":-1.1247422437,"interaction_z_score":-1.1237743381,"ss_agreement_norm_score":0.4854423844,"avg_local_score":0.695602226,"cbeta_z_score":-0.4576629659,"qmean6_norm_score":0.6861979829,"qmean4_norm_score":0.7195471638,"acc_agreement_z_score":-1.676258949,"avg_local_score_error":0.108}},"major_issues":null,"mod_engine":"PROMOD3","tpl_info":{"4b8v.1.A":{"origin":"reference database","entity_id":"1","label_asym_id":"A","entity_type":"polymer"}}}
\ No newline at end of file

other/mod_pipeline/BF.sm/mdl/01/report.json

+{"modelling":{"comment":"e_value=5.39014e-12, bit_score=59.6918, score=143","short_method":"X-ray","pred_lddt":0.6409999728,"trg_seq":"ARNPITITPQFDCGATNSQQYVARSGDTLTKIAQEIYHDVVGVCDIARANNLADPNRIDAGTPYTIPINCQTYDRNSCL","ProMod":null,"id":"1f7ee0185c027f840714313bee002b90c1645193","QMean":{"local_scores":{"A":[null,null,null,null,null,null,null,null,null,null,null,null,0.7595292171,0.7709733199,0.7679715335,0.6820321387,0.6794604594,0.7352636235,0.7226174383,0.7494432568,0.7677644492,0.7858676785,0.7878309719,0.6730515146,0.7086870985,0.7589610189,0.7607696096,0.7466237069,0.7449181176,0.7246933642,0.7050858737,0.7261962419,0.7584532412,0.6333229049,0.43971576,0.1634149258,0.1554763455,0.2373588915,0.318227385,0.4479396439,0.7316497638,0.7062396185,0.7575763978,0.7841259311,0.7706970752,0.7719843127,0.8095682517,0.729691249,0.8273358234,0.7909998149,0.7513066077,0.7295026071,0.6877599727,0.6585904841,0.7421009272,0.7107673751,0.6399285621,0.7359773907,0.7313914551,0.7494003413,0.76231139,0.7656656656,0.8042642126,0.7876690829,0.7929124565,0.7871559264,0.7826168183,0.7099086222,0.6682278917,0.7148507187,0.6419257498,0.6889439201,0.6746461196,0.7482797818,0.674896879,0.6848403448,0.7668447042,0.7403137208,0.6808314423]},"global_scores":{"interaction_norm_score":-0.0142020561,"qmean6_z_score":-1.469761816,"torsion_z_score":-0.7130880371,"torsion_norm_score":-0.1998463023,"ss_agreement_z_score":-0.7636034172,"acc_agreement_norm_score":0.5373134328,"cbeta_norm_score":-0.0138066274,"packing_z_score":-0.675742068,"packing_norm_score":-0.3204136162,"qmean4_z_score":-1.1247422437,"interaction_z_score":-1.1237743381,"ss_agreement_norm_score":0.4854423844,"avg_local_score":0.695602226,"cbeta_z_score":-0.4576629659,"qmean6_norm_score":0.6861979829,"qmean4_norm_score":0.7195471638,"acc_agreement_z_score":-1.676258949,"avg_local_score_error":0.108}},"chain":"A","assembly_id":1,"seq_id":43.4782600403,"SPDBV":null,"pdb_id":"4b8v","score":1.4957641363,"MODELLER":null,"method":"X-RAY DIFFRACTION","description":"EXTRACELLULAR PROTEIN 6","seq_sim":0.4202957451,"tpl_seq":"-------TKATDCGSTSNIKYTVVKGDTLTSIAKKFKS---GICNIVSVNKLANPNLIELGATLIIPENCSNPDNKSCV","oligo_state":"monomer","coverage":0.8734177351,"offset":30,"found_by":"BLAST","endtime":"12-10-19 (11:13:03)","mod_engine":["ProMod3"],"title":"Modelling","ProMod3":{"version":"2.0.0"},"starttime":"12-10-19 (11:12:56)","resolution":1.5900000334}}
\ No newline at end of file

other/mod_pipeline/BF.sm/report.json

+{"template_search":{"pdbrelease":"2019-10-04","target":["ARNPITITPQFDCGATNSQQYVARSGDTLTKIAQEIYHDVVGVCDIARANNLADPNRIDAGTPYTIPINCQTYDRNSCL"],"title":"Template Search","smtlupdate":"2019-10-09","starttime":"12-10-19 (11:11:38)","endtime":"12-10-19 (11:12:48)","subsection":{"blast_search":{"parameters":"BLOSUM62 (gap_open=11, gap_ext=1)","title":"BLAST Search","starttime":"12-10-19 (11:12:11)","blast_num_tpls":1,"blast_num_hits":8,"endtime":"12-10-19 (11:12:11)"},"hhblits":{"hhblits_command":"\/scicore\/soft\/apps\/HH-suite\/2.0.16-goolf-1.7.20-Boost-1.53.0-Python-2.7.11\/bin\/hhblits -mact 0.35 -cpu 1 -n 1 -e 0.001 -Z 10000 -B 10000 -i \/scicore\/web\/swissmodel\/smng-beta\/GT\/cameo-server-54\/work\/projects\/mY\/Td\/BF.sm\/tpl\/hhm\/query_hhblits.a3m -o \/scicore\/web\/swissmodel\/smng-beta\/GT\/cameo-server-54\/work\/projects\/mY\/Td\/BF.sm\/tpl\/hhm\/hhm100query_hhblits_mact0.35_cpu1_n1.hhr -d \/scratch\/smng_dbs\/SMTL_2ND\/hhblits\/db\/smtl_uniq","hhblits_num_hits":58,"title":"HHblits","starttime":"12-10-19 (11:11:41)","endtime":"12-10-19 (11:12:04)","hhblits_num_tpls":108}}},"template_selection":{"ranked_templates":[{"id":"1f7ee0185c027f840714313bee002b90c1645193","predicted_lddt":0.6409999728}],"endtime":"12-10-19 (11:13:04)","starttime":"12-10-19 (11:11:34)"},"modelling":{"ranked_models":[{"struct_score":0.5899411283,"id":1,"predicted_lddt":0.6470000148}]}}
\ No newline at end of file

other/mod_pipeline/BF.sm/status/auto-model

+16407292@JOB COMPLETED

other/mod_pipeline/BF.sm/status/auto-model.stderr

+slurmstepd: error: task/cgroup: unable to add task[pid=12709] to memory cg '(null)'
+__smng_slurm_plugin_after_cmd 0

other/mod_pipeline/BF.sm/status/auto-model.stdout

+Building models for all unique templates found for the target. This disables any '--num-models' setting.
+----------------------------------------------------------------------
+this is automodel for CAMEO
+project name:    : mYTdBF
+sending emails to: sd-m__2019-10-12_00000117__1-54@proteinmodelportal.org
+----------------------------------------------------------------------
+searching templates with BLAST and HHblits
+template search finished successfully
+templates chosen for modelling:
+   1. 4b8v.1.A (1f7ee0) gmqe=0.64, qs_val=0.00, is_full_bu=0, acov=0.81, scov=0.87
+
+building models for selected templates
+building model 1 for 4b8v.1.A (1f7ee0) with ProMod3
+ranked models with QMEAN (top-1)
+   1 4b8v.1.A (1f7ee0) pred=0.647, qmn=0.720, c=0.810
+ranked models with QMEANDisCo (top-1)
+   1 4b8v.1.A (1f7ee0) score=0.590, gmqe=0.647

other/mod_pipeline/BF.sm/status/meld01

+13839@dhi05.scicore-dmz.lan COMPLETED

other/mod_pipeline/BF.sm/status/meld01.stderr

+Model QS: monomer decided by prediction
+Trying to build monomer from homo-dimer
+imported 1 chains, 189 residues, 1387 atoms; with 0 helices and 0 strands
+imported 1 chains, 14 residues, 198 atoms; with 0 helices and 0 strands
+imported 1 chains, 67 residues, 509 atoms; with 0 helices and 0 strands

other/mod_pipeline/BF.sm/status/meld01.stdout

+ProMod3: ======================================================================
+ProMod3: Version 2.0.0
+ProMod3: module-path /scicore/web/swissmodel/smng-beta/GT/ProMod3/build/stage/lib64/python2.7/site-packages/promod3/__init__.pyc
+ProMod3: share-path /scicore/web/swissmodel/smng-beta/GT/ProMod3/build/stage/share/promod3
+ProMod3: Starting modelling based on a raw model.
+ProMod3: Removed 1 terminal gap(s).
+ProMod3: Trying to close small deletions (no. of gap(s): 1).
+ProMod3: Initialized default backbone scoring for modelling.
+ProMod3: Trying to fill 1 gap(s) by database.
+ProMod3: Resolved A.HIS38-(DVV)-A.GLY42 by filling A.GLN34-(EIYHDVV)-A.GLY42 (83 candidates, BB_DB)
+ProMod3: Rebuilding sidechains.
+ProMod3: Minimize energy.
+ProMod3: Perform energy minimization (iteration 1, energy: 1.18274e+18)
+ProMod3: Perform energy minimization (iteration 2, energy: 1220.89)
+ProMod3: No more stereo-chemical problems -> final energy: 607.857
+ProMod3: ======================================================================
+ranked models with QMEAN (top-1)
+   1 4b8v.1.A (1f7ee0) pred=0.647, qmn=0.720, c=0.810

other/mod_pipeline/BF.sm/status/progress.txt

+running HHblits against SMTL
+obtaining multiple sequence alignment for target sequence with HHblits
+predicting residue burial status with ACCpro
+searching PDB profile database with previously built query profile
+running BLAST against SMTL
+extracting distance constraints from 108 templates
+filtering list of templates
+structurally superpose templates
+predicting oligomeric state conservation
+select templates for modelling
+building model 1
+assessing model quality of model 1 with QMEAN

other/mod_pipeline/BF.sm/status/tplsearch

+12924@dhi05.scicore-dmz.lan COMPLETED