- modeller_usage - salilab.org

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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How to optimize & refine the conformation of the mutant side chain along with the backbone by using modeller (mutate_model.py ) ?
by Mahesh Velusamy 06 Jun '16

06 Jun '16

Dear All, I want to know how to generate a mutant models with optimization and refinement on sidechain of mutated residue including backbone/near the residues by mutate_model.py. Kindly , Let me know how to modify this and I hope this modification needs on the following lines (139 to 153) #only optimize the selected residue (in first pass, just atoms in selected #residue, in second pass, include nonbonded neighboring atoms) #set up the mutate residue selection segment #s = selection(mdl1.chains[chain].residues[respos]) s = selection(mdl1.chains[chain].residues[respos]) mdl1.restraints.unpick_all() mdl1.restraints.pick(s) s.energy() s.randomize_xyz(deviation=4.0) mdl1.env.edat.nonbonded_sel_atoms=2 optimize(s,sched) Thanking you in advance

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[Fwd: How to optimize & refine the conformation of the mutant side chain along with the backbone by using modeller (mutate_model.py ) ?]
by Mahesh Velusamy 06 Jun '16

06 Jun '16

Dear All, I hope you all know that there is script available in modeller "mutate_model.py". To generate a mutant models and then optimize the mutated residue following refinement in sidechain alone but I want to make this process (optimization/refinement) including the backbone/near residues instead of restricting only with sidechain. So, Does anyone know how to modify the default script I hope the modification needs on the following lines (139 to 153) #only optimize the selected residue (in first pass, just atoms in selected #residue, in second pass, include nonbonded neighboring atoms) #set up the mutate residue selection segment #s = selection(mdl1.chains[chain].residues[respos]) s = selection(mdl1.chains[chain].residues[respos]) mdl1.restraints.unpick_all() mdl1.restraints.pick(s) s.energy() s.randomize_xyz(deviation=4.0) mdl1.env.edat.nonbonded_sel_atoms=2 optimize(s,sched) Thanking you in advance

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(no subject)
by Claire Smathers 26 May '16

26 May '16

Hi, I am wanting to make a homology model for the 5HT2c receptor using the dopamine D3 receptor as the template. Is there a way to make modeller use D3 as a template instead of it searching for similar protein sequences to align with? Thanks, smathersc

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fwd:problem with GluP ACe CT3 patch
by Prevost Martine 21 Apr '16

21 Apr '16

Hello, Thanks for your prompt answer. Below is the full input: from modeller import * from modeller.automodel import * # Load the automodel class env = environ() # directories for input atom files class mymodel(automodel): def special_patches(self, aln): self.patch(residue_type='ACE', residues=(self.residues['1:A'])) # self.patch(residue_type='CT3', residues=(self.residues['473:A'])) # Disable default NTER and CTER patches env.patch_default = False a = mymodel(env, alnfile = 'all.pir', knowns = ('3ob6_A','3ob6_B'), sequence = 'Can1_E184H') a.starting_model= 1 a.ending_model = 1 a.make() and the error message: modeller.error: patch___482E> Patching residue identifier not found: ACE I don't understand the argument for GLUP in noH models. If the total charge of GLUP is zero it should influence differently (compared to Glu -1) the interaction of it with surrounding residues in the construction of the model via the classical part of the force field (Coulomb term)? Thanks. Martine. Forwarded message: >From: mprevost(a)ulb.ac.be >To: modeller_usage(a)salilab.org >Cc: >Date: Wed, 20 Apr 2016 11:31:02 (CEST) >Subject: problem with GluP ACe CT3 patch > >hello, > >I am trying to patch a protonated glu as well as ACE and CT3. >Most of the documentation on patches is for DISU. >As for ACE or CT3 (which is what I tried first) I used: > >class mymodel(automodel): > def special_patches(self, aln): > self.patch(residue_type='CT3', residues=(self.residues['473:A'])) > >a = mymodel(env, alnfile = 'all.pir', > knowns = ('3ob6_A','3ob6_B'), > sequence = 'Can1_E184H') > >a.starting_model= 1 >a.ending_model = 1 > >I got the following error: > >patch___482E> Patching residue identifier not found: CT3 > >Same thing for ACE. I also tried with allhmodel but it fails as well. > >Another question for GLUP patching in no hydrogen models how can one be sure that one got indeed GLUP? > >Thanks in advance for your help, > >Martine. > > >-------------------------------------------- > Martine Prévost > Structure et Fonction des Membranes Biologiques > CP 206/2 > Université Libre de Bruxelles > Bld du Triomphe > B-1050 Bruxelles > Belgium > Phone : 32-2-650 2049 > Fax : 32-2-650 5382 > E-mail: mprevost(a)ulb.ac.be >-------------------------------------------- > > > > > > > no attachments have been sent > > -------------------------------------------- Martine Prévost Structure et Fonction des Membranes Biologiques CP 206/2 Université Libre de Bruxelles Bld du Triomphe B-1050 Bruxelles Belgium Phone : 32-2-650 2049 Fax : 32-2-650 5382 E-mail: mprevost(a)ulb.ac.be --------------------------------------------

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