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Doubts regrading implementing parallel job on mutate_model.py optimization step
by Mahesh Velusamy 05 Jul '16

05 Jul '16

Dear All, I have tried to implement parallel job on mutate model optimization steps where I selected 457 atoms for optimization (I am doing this because of implement our own objective) and to do this I added the following lines in Mutate_Model.py: from modeller.parallel import * j = job() j.append(local_slave()) j.append(local_slave()) j.append(local_slave()) j.append(local_slave()) j.queue_task(optimize(s,sched)) j.queue_task(refine(atmsel)) j.run_all_tasks() I am not sure I am doing this in correct way but I am getting the following errors: Running 4 tasks on 4 slaves /usr/bin/python2.7 /usr/lib/modeller9.14/bin/modslave.py -slave 172.16.35.74:48622:0:TPLDZNFC >& mutate_model.slave0 /usr/bin/python2.7 /usr/lib/modeller9.14/bin/modslave.py -slave 172.16.35.74:48622:1:INNJBKXG >& mutate_model.slave1 /usr/bin/python2.7 /usr/lib/modeller9.14/bin/modslave.py -slave 172.16.35.74:48622:2:XZYKJCXC >& mutate_model.slave2 /usr/bin/python2.7 /usr/lib/modeller9.14/bin/modslave.py -slave 172.16.35.74:48622:3:XJXTJMBR >& mutate_model.slave3 Traceback (most recent call last): File "/comptes/invite-u/PycharmProjects/untitled/3O26_050716_144858/R12H_A102C_F104A/mutate_model.py", line 104, in <module> j.run_all_tasks() File "/usr/lib/python2.7/dist-packages/modeller/parallel/job.py", line 156, in run_all_tasks for task in self._finish_all_tasks(): File "/usr/lib/python2.7/dist-packages/modeller/parallel/job.py", line 189, in _finish_all_tasks task = self._process_event(obj, s) File "/usr/lib/python2.7/dist-packages/modeller/parallel/job.py", line 201, in _process_event slave.run_task(self.tasks.pop(0)) File "/usr/lib/python2.7/dist-packages/modeller/parallel/slave.py", line 52, in run_task for transfer in task.input_files: AttributeError: 'NoneType' object has no attribute 'input_files' Identified slave <Slave on localhost> My SCRIPT: ---------- import sys import os from modeller import * from modeller.optimizers import molecular_dynamics, conjugate_gradients from modeller.automodel import autosched from modeller.parallel import * # Use 4 CPUs in a parallel job on this machine j = job() j.append(local_slave()) j.append(local_slave()) j.append(local_slave()) j.append(local_slave()) def optimize(atmsel, sched): for step in sched: step.optimize(atmsel, max_iterations=200, min_atom_shift=0.001) ########################################### j.queue_task(refine(atmsel)) ############################################## #refine.use_parallel_job(j) cg = conjugate_gradients() cg.optimize(atmsel, max_iterations=200, min_atom_shift=0.001) def refine(atmsel): md = molecular_dynamics(cap_atom_shift=0.39, md_time_step=4.0, md_return='FINAL') init_vel = True for (its, equil, temps) in ((200, 20, (150.0, 250.0, 400.0, 700.0, 1000.0)), (200, 600, (1000.0, 800.0, 600.0, 500.0, 400.0, 300.0))): for temp in temps: md.optimize(atmsel, init_velocities=init_vel, temperature=temp, max_iterations=its, equilibrate=equil) init_vel = False def make_restraints(mdl1, aln): rsr = mdl1.restraints rsr.clear() s = selection(mdl1) for typ in ('stereo', 'phi-psi_binormal'): rsr.make(s, restraint_type=typ, aln=aln, spline_on_site=True) for typ in ('omega', 'chi1', 'chi2', 'chi3', 'chi4'): rsr.make(s, restraint_type=typ+'_dihedral', spline_range=4.0, spline_dx=0.3, spline_min_points = 5, aln=aln, spline_on_site=True) log.verbose() env = environ(rand_seed=int(-4000)) env.io.hetatm = True env.edat.dynamic_sphere=False env.edat.dynamic_lennard=True env.edat.contact_shell = 4.0 env.edat.update_dynamic = 0.39 env.libs.topology.read(file='$(LIB)/top_heav.lib') env.libs.parameters.read(file='$(LIB)/par.lib') mdl1 = model(env, file = "3O26") ali = alignment(env) ali.append_model(mdl1, atom_files= "3O26.pdb", align_codes= "3O26") s1=selection(mdl1.chains['A'].residues['104']) s1.mutate(residue_type='ALA') s2=selection(mdl1.chains['A'].residues['102']) s2.mutate(residue_type='CYS') s3=selection(mdl1.chains['A'].residues['12']) s3.mutate(residue_type='HIS') ali.append_model(mdl1, align_codes="3O26") mdl1.clear_topology() mdl1.generate_topology(ali[-1]) mdl1.transfer_xyz(ali) mdl1.build(initialize_xyz=False, build_method='INTERNAL_COORDINATES') mdl2 = model(env, file="3O26.pdb") mdl1.res_num_from(mdl2,ali) mdl1.write(file="3O26"+'ALA'+'104'+'CYS'+'102'+'HIS'+'12'+"A"+'.tmp') mdl1.read(file="3O26"+'ALA'+'104'+'CYS'+'102'+'HIS'+'12'+"A"+'.tmp') make_restraints(mdl1, ali) mdl1.env.edat.nonbonded_sel_atoms=1 sched = autosched.loop.make_for_model(mdl1) s = selection(mdl1.atoms['CA:'+'104'+':'+'A'].select_sphere(10),mdl1.atoms['CA:'+'102'+':'+'A'].select_sphere(10),mdl1.atoms['CA:'+'12'+':'+'A'].select_sphere(10)).by_residue() mdl1.restraints.unpick_all() mdl1.restraints.pick(s) s.energy() s.randomize_xyz(deviation=100) mdl1.env.edat.nonbonded_sel_atoms=2 ####################################### j.queue_task(optimize(s,sched)) ####################################### mdl1.env.edat.nonbonded_sel_atoms=1 ######################################### j.queue_task(optimize(s,sched)) ######################################### s.energy() ####################################### j.run_all_tasks() ####################################"" atmsel = selection(mdl1.chains["A"]) score = atmsel.assess_dope() mdl1.write(file="/comptes/invite-u/PycharmProjects/untitled/3O26_050716_144858/R12H_A102C_F104A/R12H_A102C_F104A.MM9999.pdb") os.remove("3O26"+'ALA'+'104'+'CYS'+'102'+'HIS'+'12'+"A"+'.tmp') Kindly correct me If I am wrong and let me know that how to do this in correct way. Thanking you in advance

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Modelling trans-membrane (TM) regions
by Sushil Mishra 29 Jun '16

29 Jun '16

Dear all: I am quite new to MODELLER and I would like to know if it is possible to to models a protein having with few trans-membrane (TM) regions. Are there such an example or tutorial available? I tried to search archive but, unfortunately, there was nothing that can help me. Is it possible to assign a few TM regions (in the form of restrain or something like that) which would be modeled in a plane. Any suggestions/inputs related to modelling enzyme having TM regions will be appreciated. My system has very poor similarity (< 20 %) in PDB, and also no similarity between TM regions of query and TM regions of proteins in PDB. Best, SK

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Is it possible to rum model_single.py in multiple nodes ?
by Mahesh Velusamy 27 Jun '16

27 Jun '16

Dear All, I know there is a option to run modeller in multiple cores but How can run model_single.py in multiple nodes (My wish is to rum 44 nodes where each node has 16 PROCESSOR). If it is possible could you provide me a examples / scripts. Thanking you in advance With Reagrds Mahesh VELUSMAY

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Is it possible to do single residue optimization for automodels ?
by Mahesh Velusamy 27 Jun '16

27 Jun '16

Dear All, Since, My main objective is to get a better conformational sample for a particular single point mutation, I have generated a 100 number of SPM models through automodel but Since, Automodel uses the distance restraints from the template target structure alignment there is not much variations when comparing with the original structure. So I thought to relax the restrains by doing additional optimization on mutated position alone like we see in mutate_model.py http://salilab.org/modeller/wiki/Mutate%20model. Then, I try to modified the automodel script as same like mutate_model.py but I endup in lot of confusions that 1.what shoud I keep for : #conjugate gradient for step in sched: step.optimize(atmsel, max_iterations=200, min_atom_shift=0.001 2.Whether should I include make restraints function ? 3. Is it Ok If I do only optimize and refine step ? def optimize(atmsel, sched): #conjugate gradient for step in sched: step.optimize(atmsel, max_iterations=200, min_atom_shift=0.001) #md refine(atmsel) cg = conjugate_gradients() cg.optimize(atmsel, max_iterations=200, min_atom_shift=0.001) #molecular dynamics def refine(atmsel): # at T=1000, max_atom_shift for 4fs is cca 0.15 A. md = molecular_dynamics(cap_atom_shift=0.39, md_time_step=4.0, md_return='FINAL') init_vel = True for (its, equil, temps) in ((200, 20, (150.0, 250.0, 400.0, 700.0, 1000.0)), (200, 600, (1000.0, 800.0, 600.0, 500.0, 400.0, 300.0))): for temp in temps: md.optimize(atmsel, init_velocities=init_vel, temperature=temp, max_iterations=its, equilibrate=equil) init_vel = False #use homologs and dihedral library for dihedral angle restraints def make_restraints(mdl1, aln): rsr = mdl1.restraints rsr.clear() s = selection(mdl1) for typ in ('stereo', 'phi-psi_binormal'): rsr.make(s, restraint_type=typ, aln=aln, spline_on_site=True) for typ in ('omega', 'chi1', 'chi2', 'chi3', 'chi4'): rsr.make(s, restraint_type=typ+'_dihedral', spline_range=4.0, spline_dx=0.3, spline_min_points = 5, aln=aln, spline_on_site=True) a = MyModel(env, alnfile=current_file, knowns='3O26', sequence='R1Y', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 1 a.make() So , Could you guide me on single residue optimization on automodel structures ? Thanking you in advance

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How to print/write the selected (atoms/residues) from selction?
by Mahesh Velusamy 23 Jun '16

23 Jun '16

Dear All, I selected some set of atoms and the residues with the following two commends: s=selection(mdl1.atoms['CA:102:A].select_sphere(10)) s=selection(mdl1.atoms['CA:102:A].select_sphere(10)).by_residue() And, When I try to print the selected atoms/residues Its just giving the counts not the atoms/residues. So could you tell me how to do the same. Thanking you in advance

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How to select rigid restraints with certain residues ?
by Mahesh Velusamy 23 Jun '16

23 Jun '16

Dear All, Actually, I try to do optimization on set of selected atoms with random deviation 100 . Then later I realized that I cant keep random deviation more than 0.5 for following these residue (HIS,TRY,TYR,PHE) and I have PHE and HIS in my selected set. So , I decided to keep the atoms of HIS,PHE as rigid by following these commends: s=selection(mdl1.atoms['CA:'+respos+':'+chain].select_sphere(10))#selected set for optimization r = rigid_body(selection(s).only_residue_types('HIS,TYR,TRP,PHE'))# By this I select atoms of HIS,PHE from selected set to keep rigid mdl.restraints.rigid_bodies.append(r) But, This doesn't work So could you tell me how to select atoms of (HIS,TYR,TRP,PHE) residues from selection to make rigid ? Thanking you in advance

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Need some example and commend arguments for (selection.extend_by_residue())
by Mahesh Velusamy 23 Jun '16

23 Jun '16

Dear All, If anyone knows how to use this two commends . Could you tell me the arguments to pass and some example which would be really helpful. selection.extend_by_residue() -- extend selection by residue selection.by_residue() -- make sure all residues are fully selected For example: I selected particular region of atoms for optimization following this commend: sI=selection(mdl1.atoms['CA:'+respos+':'+chain].select_sphere(10)) Then , I selected the residues which has single atom in selction through this commend. s = sI.extend_by_residue(pick_hot_cutoff=12) And , I want to do the same with selection.extend_by_residue() but I got stuck with arguments for this commend. Thanking you in advance

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Is it possible to pick all the neigbour residues atoms/residues within mentioned A° of the 'CA' atom is some resudue?
by Mahesh Velusamy 23 Jun '16

23 Jun '16

Dear All, As I can see this from the following link: https://salilab.org/modeller/9v2/manual/node220.html. We can able to pick all the atoms within mentioned A° by this following commend: # Pick and superpose all atoms within 6 angstroms of the 'CA' atom in residue '10:': atmsel = mdl.atoms['CA:10'].select_sphere(6.0) atmsel.superpose(mdl2, aln) Where, What I have understood is: It picks atoms that comes within mentioned A° and not all the atoms of matched residues that comes in the mentioned A° So, Here I want to know that Is it possible to pick all the neigbour residues atoms within mentioned A° of the 'CA' atom is some resudue? I hope its understandable. Thanking you in advance

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ERROR: CHARMM residue type 'A' unrecognized (in mutate_model.py execution)
by Mahesh Velusamy 21 Jun '16

21 Jun '16

Dear All, When I try to make a mutate models by using mutate_model.py , I am getting error like below: Traceback (most recent call last): File "mutate_model.py", line 95, in <module> s.mutate(residue_type=restyp) File "/usr/local/opt/apps/pkg/modeller/9.16/modlib/modeller/selection.py", line 492, in mutate inds, residue_type) _modeller.ModellerError: mutate_mod_E> CHARMM residue type 'v' unrecognized and this " type 'v' " arise for all the residues. Thanking you in advance With Regards Mahesh V

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How to generate a model with double mutant, combination of mutants by using mutate_model.py ?]
by Mahesh Velusamy 06 Jun '16

06 Jun '16

Dear All, As you all know that current mutate_model.py works only for single mutants but I want to make it for double and combination of mutants. So , Kindly do let me know that Is it possible ? Thanking you in advance

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