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What is a difference between automodel and loopmodel with respect to refining only part of the model optimization ?
by Mahesh Velusamy 07 Jul '16

07 Jul '16

Dear All, Let me explain that what I have tried: I have generated 100 models for one single point mutation sequence following optimization(loop model) on single point mutated residue along with neighbour residues(with different sphere range 1A°-10A°). Now, the observation from my out put is as following: 1. When i optimized the SPM model with the large sphere (10A°) of neighbour residues, I got bad model compared to crysal structure but DOPE score was really high(~5K). 2.When i optimized the SPM model with the less sphere (1A°) of neighbour residues, I got similar model compared to crysal structure but DOPE score was really bad(~250). So , I dont understand why I am getting less DOPE score when I have similar good models compared to crystal structure and vice versa. Then, I followed the same procedure but automodel default optimization on selceted region where i got all the models simlar to crystal structure with less difference between dope score(range ~5k to 6K) Now, I want to what is the difference between automodel and loopmodel optimization on selected region ? and what loop model optimization exactly does ? and why there is a illogical contrast between DOPE score in loop model optimization? Thanking you in advance With Regards Mahesh V

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Modeller 9.17 release
by Modeller Caretaker 06 Jul '16

06 Jul '16

The new version of Modeller, 9.17, is now available for download! Please see the download page at https://salilab.org/modeller/ for more information. If you have a license key for Modeller 8 or 9, there is no need to reregister for Modeller 9.17 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 9.17 is primarily a bugfix release relative to the last public release (9.16). Major user-visible changes include: # loopmodel-generated PDB or mmCIF files now contain extra header information, including the values of any assessment scores. # automodel-generated PDB or mmCIF files now list, for each template, the sequence identity and the range of residues modeled. # EM density maps used for purposes other than density.grid_search() (e.g. use in Flex-EM) no longer have to be cubic. # Chain breaks are now shown (if appropriate) when showing mismatches between a sequence and a structure (SequenceMismatchError). See the Modeller manual for a full change log: https://salilab.org/modeller/9.17/manual/node40.html If you encounter bugs in Modeller 9.16, please see https://salilab.org/modeller/9.17/manual/node10.html for information on how to report them. Note: you are receiving this email either because you subscribed to the modeller_usage mailing list, or you provided this address when you requested a Modeller license and you ticked the "notify me of new releases" box. In the latter case, if you no longer wish to receive announcements of new Modeller releases, simply reply to this email and let us know. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org https://salilab.org/modeller/ Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage

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is it possible run MUTATE_MODEL (optimization step alone) in multithreading / Parallel job ?
by Mahesh Velusamy 05 Jul '16

05 Jul '16

Dear All, Actually, I am using Mutate_model.py script(http://salilab.org/modeller/wiki/Mutate%20model) to generate single point mutant models for large mutation library with an optimization of selected region(~280 atoms). There is no issue on time using for mutating residues but the script takes long time to finish the optimization step alone. So, I want to put this optimization step alone as a multithreading (running on all the CPU cores)similar to a.use_parallel_job(j)# Use the job for model building If it is possible kindly some one could help me out of this would be really useful Thanking you in advance With Regards Mahesh V

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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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