November 2016 - modeller_usage

MUTATE MODEL [OPTIMIZATION]
by Mahesh Velusamy 28 Nov '16

28 Nov '16

Dear All, I have a couple of questions regarding optimization step of mutate_model script. As mentioned in the script there is some optimization steps performed on mutated residue (the conformation of the mutant sidechain is optimized by conjugate gradient and refined using some MD). Here my question is: can we include some neighbor residues (residues that are located around the mutated residue) for optimization ? If yes,what is the reasonable size of neighbor residue region that we can use it for optimization? ( for ex: neighbor residues that are within 5Å/10Å of mutated residue) Thanking you in advance With Regards Mahesh V

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Issue in selected atoms optimization
by Mahesh Velusamy 24 Nov '16

24 Nov '16

Dear All, I have a small issue in getting correct models after optimizing selected atoms. Instead I am getting models with distorted atoms in some residues. Actually, what I have done is as follows: I tried to build a models for single mutant with separate optimization on neighbor residues ( residues that are located with in 15Å of mutated residue) by using mutate_model.py where I used the default optimize ,refine and restraints with random deviation equal to 4 but I didnt get that which parameters that leads atom distortion in optimized models. So kindly give me some suggestion about the parameters that I can tune to resolve the atom distortion. def optimize(atmsel, sched): for step in sched: step.optimize(atmsel, max_iterations=200, min_atom_shift=0.001) refine(atmsel) 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) s.randomize_xyz(deviation=4.0) Thanking you in advance With Regards Mahesh V

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Partial structure alignment
by Parker de Waal 21 Nov '16

21 Nov '16

Hello modeller list, Does anyone know if it is possible to perform a 3d alignment between two proteins while only moving the selected atoms? (i.e. leaving the unselected atoms for the alignment unmoved?) Best, Parker

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my email address
by sara20＠mail.ustc.edu.cn 18 Nov '16

18 Nov '16

sara20(a)mail.ustc.edu.cn

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Including Non-Protein Residue to the Model
by Fadhila Balqis N 17 Nov '16

17 Nov '16

Dear All, I wanted to make a model of human flavin-containing monooxydase 3 (FMO3) enzyme from the template FMO of *Saccharomyces pombe*. This enzyme has FAD residue that is important to the project I'm working on. But of all the model output, none came with this FAD residue. I have tried simple usage automodelling provided in the manual and modelling with the guide from basic modelling tutorial (provided here: https://salilab.org/modeller/tutorial/basic.html) Lastly, I also have tried to use the script for including water molecules, HETATM residues, and hydrogen atoms to the model (described in here: https://salilab.org/modeller/manual/node18.html) The FAD residue was not present and I ran out of ideas on how to make this work. The FAD binding site is highly conserved in FMOs across species, so I don't see why it was excluded from the model. In the last try the script gave me this: read_pd_459W> Residue type FAD not recognized. 'automodel' model building will treat this residue as a rigid body. To use real parameters, add the residue type to ${LIB}/restyp.lib, its topology to ${LIB}/top_*.lib, and suitable forcefield parameters to ${LIB}/par.lib. What should I do? Your inputs are so much wanted and appreciated Fadhila Balqis Nurfitria

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ALIGN CODES NOT FOUND
by Fadhila Balqis N 14 Nov '16

14 Nov '16

Dear All, I want to make a model by using this specific template "2GVC" and I try to include HETATM residues to my model. But then this happened: openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL9v17}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL9v17}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 191566 187.076 0.183 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 192094 187.592 0.183 openf___224_> Open ${MODINSTALL9v17}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 240694 235.053 0.230 rdrdih__263_> Number of dihedral angle types : 9 Maximal number of dihedral angle optima: 3 Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5 openf___224_> Open ${MODINSTALL9v17}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041 0.242 openf___224_> Open ${MODINSTALL9v17}/modlib/radii14.lib openf___224_> Open ${MODINSTALL9v17}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL9v17}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL9v17}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL9v17}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL9v17}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL9v17}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 openf___224_> Open align-ligand.ali Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 265487 259.265 0.253 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 266937 260.681 0.255 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 269837 263.513 0.257 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 275637 269.177 0.263 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 287237 280.505 0.274 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 310437 303.161 0.296 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 325013 317.396 0.310 read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 2) = P31513 I used this script: # Comparative modeling with ligand transfer from the template from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] # Read in HETATM records from template PDBs env.io.hetatm = True a = automodel(env, alnfile = 'align-ligand.ali', # alignment filename knowns = '2gvc', # codes of the templates sequence = 'P31513') # code of the target a.starting_model= 4 # index of the first model a.ending_model = 4 # index of the last model # (determines how many models to calculate) a.make() # do the actual comparative modeling and used this alignment format: >P1;2gvc structureX:2gvc:5: :575: :flavin-containing monooxidase:saccharomyces pombe: : MCLPTIRKIAIIGAGPSGLVTAKALLAEKAFDQVTLFERRGSPGGVWNYTSTLSNKLPVP STNPILTTEPIVGPAALPVYPSPLYRDLQTNTPIELMGYCDQSFKPQTLQFPHRHTIQEY QRIYAQ--PLLPFIKLATDVLDIE-----KKDGSWVVTYKGTKAGSPISKDIFDAVSICNGHYEVPYIPNI-- KGLDEYAKAVPGSVLHSSLFREPELFVGESVLVVGGASSANDLVRHLTPVAKHPIYQSLL GG--------------------------------------------------------- GDIQNES--------------LQQVPEITKFDPTTREIYLKGGKVLSNIDR VIYCTGYLYSVPFPSLAKLKSPETKLIDDGSHVHNVYQHIFYIPDPTLAFVGLALH- VVPFPTSQAQAAFLARVWSGRLKLPSKEEQLKWQDELMFSLSGANNMYHSLDYPKD---ATYINKLH--------- DWCKQATPVLEEE-FP------------SPYWGEKERSIRENMWSIRAK----- FFGI-EPPK-----------------------..* >P1;P31513 sequence:P31513:0:.:0:.:flavin-containing monooxidase 3:homo sapiens: : ----MGKKVAIIGAGVSGLASIRSCLEEGL--EPTCFEKSNDIGGLWKFSDHAEEGR----- -------------------ASIYKSVFSNSSKEMMCFPDFPFPDDFPNF MHNSKIQEYIIAFAKEKNLLKYIQFKTFVSSVNKHPDFATTGQWDVTTER--- DGKKESAVFDAVMVCSGHHVYPNLPKESFPGLN----HFKGKCFHSRDYKEPGVFNGKRVLVVGLGN SGCDIATELSRTAEQVMISSRSGSWVMSRVWDNGYPWDMLLVTRFGTFLKNNLPTAISDW LYVKQMNARFKHENYGLMPLNGVLRKEPVFNDELPASILCGIVSVKPNVKEF-- TETSAIFEDGTIFEGIDCVIFATGYSFAYPFLDESIIKSRNNEIILFKG----VFPPL-- LEKSTIAVIGFVQSLGAAIPTVDLQSRWAAQVIKGTCTLPSMEDMMNDINEKMEKK---RKWFG- KSETIQTDYIVYMDELSSFIGAKPNIPWLFLTDPKLAMEVYFGPCSPYQFRLVGPGQWPGARNAI- LTQWDRSLKPMQTRVVGRLQKPCFFFHWLKLFAIPILLIAVFLVLT..* Please point out my mistakes. Your help is so much appreciated. Thanks in advance Fadhila Balqis Nurfitria

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PDB problem
by deepak kumar 02 Nov '16

02 Nov '16

Hi, Thanks for your previous kind reply. I came across a problem which is quite strange to me: When running modeller to model a sequence on a template pdb 4QTA (obtained from BLAST, pdbaa database), I figured out that the sequence of the pdb from blast output is different from the original pdb sequence, Please see below the error I get from modeller because of this issue: Alignment sequence: MAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKIL LRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDL KPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNR PIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHK RIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS PDB sequence matching range provided in alignment: GPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENII GINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNT TCDLKICDFGLARVADTRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPS QEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEP IAEAPFKFDMELDDLPKEKLKELIFEETARFQPGY Traceback (most recent call last): File "modified-comp-align.py", line 11, in <module> a.auto_align() # get an automatic alignment File "/data/deepak-protein-modeling/modlib/modeller/automodel/automodel.py", line 146, in auto_align self.sequence, matrix_file, overhang, write_fit) File "/data/deepak-protein-modeling/modlib/modeller/scripts/align_strs_seq.py", line 8, in align_strs_seq aln = alignment(env, file=segfile, align_codes=knowns) File "/data/deepak-protein-modeling/modlib/modeller/alignment.py", line 20, in __init__ self.append(**vars) File "/data/deepak-protein-modeling/modlib/modeller/alignment.py", line 79, in append allow_alternates) _modeller.SequenceMismatchError: get_ran_648E> Alignment sequence does not match that in PDB file: 1 ./4QTA.pdb (You didn't specify the starting and ending residue numbers and chain IDs in the alignment, so Modeller tried to guess these from the PDB file.) Suggestion: put in the residue numbers and chain IDs (see the manual) and run again for more detailed diagnostics. You could also try running with allow_alternates=True to accept alternate one-letter code matches (e.g. B to N, Z to Q). when checking the alignment file, I see that the alignment (obtained from BLAST result) and modified to PIR format is fine: >P1;NP_002736.3.35214 sequence:NP_002736.3.35214:1 : :360 : :::-1.00:-1.00 MAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS* >P1;4QTA structure:4QTA: :A : :A :::-1.00:-1.00 MAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS* The problem is arising because the original PDB file 4QTA has different chain A sequence than the chain A sequence obtained from BLAST. May I please ask your comments and solution to how this problem can be solved? , and please let me know why is this problem occurring? Thanks much, Deepak On Sun, Oct 30, 2016 at 4:18 AM, Modeller Caretaker < modeller-care(a)salilab.org> wrote: > On 10/28/16 9:33 AM, deepak kumar wrote: > >> However, does not >> mentioning the "start" and "end" residue of the PDB file influence the >> quality of the structure? or influence the model any way? >> > > No. > > Am I right, if I say, that modeller by default takes the residues of >> chain "B", finds the corresponding residues in chain B and correctly >> models the sequence as per the alignment. >> > > That's correct. > > > 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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energy of interface between selections
by David De Sancho 02 Nov '16

02 Nov '16

Hi I’m handling a problem where it is important to evaluate energies of interfacial residues (e.g. interface residues between two helices in a protein). In order to carry out this energy evaluation with Modeller, I start by producing a model for the protein. Then I generate two selections (e.g. one for each helix). Would it be possible to calculate the energy for residues in the interface between both selections? Thanks, David

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