modeller_usage

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3151 discussions

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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problem with GluP ACe CT3 patch
by Prevost Martine 20 Apr '16

20 Apr '16

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 --------------------------------------------

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ions and non-standard amino acids problem
by 程中一 04 Mar '16

04 Mar '16

Dear modeller users, I have the following problem: I have to model a metalloenzyme named nitrile hydratase with a cobalt ion as well as two oxidised Cysteines in the active site. The problems is that once the model is established, the structure of the active site is very different from that of the template. I want to figure out how to get an accurate protein model with ions or non-standard amino acids in its active site. Please suggest me any ideas to overcome this problem. Thanks in advance. Expecting reply from you guys.

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