- modeller_usage - salilab.org

ERROR IN MODELS ASSESSMENT
by Mahesh Velusamy 12 Dec '16

12 Dec '16

Dear All, This is to inform you that I have introduced new residue type called BGC which has a Glycosidic linkage between ASP and Beta-D-GLUCOSE as mentioned in the following protocol https://salilab.org/modeller/6v2/FAQ.html#2. I can access this newly introduced residue successfully throughout the modeling but after the models generation I get the following warning message for the single models assessment. >> Model assessment by DOPE potential iatmcls_286W> MODEL atom not classified: BGC:N BGC iatmcls_286W> MODEL atom not classified: BGC:CA BGC iatmcls_286W> MODEL atom not classified: BGC:CB BGC iatmcls_286W> MODEL atom not classified: BGC:CG BGC iatmcls_286W> MODEL atom not classified: BGC:OD1 BGC iatmcls_286W> MODEL atom not classified: BGC:OD2 BGC iatmcls_286W> MODEL atom not classified: BGC:C BGC iatmcls_286W> MODEL atom not classified: BGC:O BGC iatmcls_286W> MODEL atom not classified: BGC:C1 BGC iatmcls_286W> MODEL atom not classified: BGC:O5 BGC iatmcls_286W> MODEL atom not classified: BGC:C5 BGC iatmcls_286W> MODEL atom not classified: BGC:C2 BGC iatmcls_286W> MODEL atom not classified: BGC:O2 BGC iatmcls_286W> MODEL atom not classified: BGC:C3 BGC iatmcls_286W> MODEL atom not classified: BGC:O3 BGC iatmcls_286W> MODEL atom not classified: BGC:C4 BGC iatmcls_286W> MODEL atom not classified: BGC:O4 BGC iatmcls_286W> MODEL atom not classified: BGC:C6 BGC iatmcls_286W> MODEL atom not classified: BGC:O6 BGC iatmcls_286W> MODEL atom not classified: ALA:OXT ALA preppdf_453W> No fixed restraints selected; there may be some dynamic ones. preppdf_454W> Restraints file was probably not read; use restraints.append(). Here, I just want to know what does these statements implies "No fixed restraints selected; there may be some dynamic ones. Restraints file was probably not read; use restraints.append()" Even, I added all these "BGC" atoms in "/atmcls-mf.lib" file but still I am getting this warning. So, Kindly let me know that is it necessary to worry about this warning ? If not can you guide me how to append this "BGG new residue" restraints? Thanking you

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Is it possible to control atom movements of specific residue during optimization?
by Mahesh Velusamy 07 Dec '16

07 Dec '16

Dear All, I have been doing separate optimization steps on selected region where i experienced that certain residue(ARG,LYS,TYR) atoms get distorted (like bonds between two atoms were distorted). So is their anyway to control the random deviation of certain residues atoms. Thanking you in advance With Regards Mahesh V

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Modeling loop using template from PDB file
by Markus Heller 07 Dec '16

07 Dec '16

Hello, I have a structure (A) which is missing a stretch of a dozen or so residues. I also have the structure of the protein from a different organism which has said stretch of residues resolved (B). Now I'd like to take the coordinates of A and model the missing residues using the relevant coordinates (i.e. for these residues only) from B. How would I go about doing this? Thanks Markus

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using crosslinking information as restrain
by ncuspywangxuedong 07 Dec '16

07 Dec '16

Hey all, I was using modeller in order to obtain a model satisfying crosslink restrains. Now I know the crosslinked sites, but I do not know how to add crosslink restrains. Could you tell me how to do it? It is best If you can give specific examples to me! thanks a lot!!!! Su Mu

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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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