Commit a90a9630 authored by Studer Gabriel's avatar Studer Gabriel
Browse files

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

parent 886477e6
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.
[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
{"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
This diff is collapsed.
{"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
{"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
slurmstepd: error: task/cgroup: unable to add task[pid=12709] to memory cg '(null)'
__smng_slurm_plugin_after_cmd 0
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
13839@dhi05.scicore-dmz.lan COMPLETED
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
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
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
12924@dhi05.scicore-dmz.lan COMPLETED
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