- modeller_usage - salilab.org

Distance restraint violations
by Albers, Thomas 04 Jan '17

04 Jan '17

Hello! I'm trying to model a certain membrane protein. There are two template structures with decent sequence similariry (~ 40 %) and not-so-great resolution (~ 3 angstrom). When building a model against either template nothing in particular sticks out in the logfile, but when building a model model against both templates combined there are lots of distance violations (CA-CA and N-O) in the log, however this model gives the lowest DOPE score. What gives? Thomas

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EXTREME BOND LENGTHS IN OPTIMIZED MODELS
by Mahesh Velusamy 19 Dec '16

19 Dec '16

Dear All, I have tried to do build single point mutant models (n=100) along with separate optimization step on the neighbor residues around the mutated residue.I can able to get 98 models without any issue out of 100 models but in some models, the bond lengths of longer residues(ARG,LYS,TYR) became extreme than original value. For example: IN ARG residue, the distance between (CZ & NH1) or (CZ & NH2) was extreme (3.4Å) than the original value (1.5Å ) which makes the bonds disappear. I really don't understand that what makes these issue and I use the default MD&SA parameters which used in mutate_model.py with Lenard-Jones potential. *I don't get this issue if I change the restraint from Lenard-Jones into soft-sphere potential. So, kindly give me some suggestion about the parameters that I can tune to resolve this issue. Thanking you in advance With Regards Mahesh V

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Difference between dynamic_sphere and lennard-jones potential restraints ?
by Mahesh Velusamy 12 Dec '16

12 Dec '16

Dear All, This might be very basic question and also I have read this from the manual https://salilab.org/modeller/9v8/manual/node102.html but still I am curious to know the answer for the following questions: 1.what is the difference between these two restraints in terms (when to use) usage ? 2.Which one do we need to prefer with respect to mutate_model.py? 3.Why dynamic_sphere kept as False in this script https://salilab.org/modeller/wiki/Mutate%20model ? 4.Is it good idea if I use dynamic_sphere in mutate_model.py ? Thanking you in advance With Regards Mahesh V

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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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