- modeller_usage - salilab.org

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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3-10 alpha-helix restraints
by Alexey Orlov 27 Jan '16

27 Jan '16

Hi, Is there anyway to make 3-10 alpha-helix restraints? I've searched the archives but haven't found anything connected with it. Best regards, Alexey.

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homo-dimer problem
by Anouk 21 Jan '16

21 Jan '16

Dear modeller users, I have the following problem: I have to model a homo-dimer. There is no template of dimer (there are several templates that cover just some parts of the monomer and thus I do use multiple templates to get a descent model of the monomer). I have an alignment file that looks something like this: >P1;proteintomodel A—AABB-BC—CC / A—AABB-BC—CC* >P1;template1_1 ———BB-BC-CC / ————————* >P1;template1_2 ———————— / ———BB-BC-CC* >P1;template2_1 A-AABB———— / ————————* >P1;template2_2 ———————— / A-AABB————* On the positive side I have a list of constraints, so I want to rely on the constraints when I model the dimer interface. The problems is that since the templates for each of the monomers have the same coordinates (modelling each of the monomers of my dimer) i do obtain a model of my dimer with the 2 monomer chains basically inter-twisted (so there is no any kind of interface in between the chains because the chains are nested one in another). Also i can’t understand why, but one of the chains has secondary structure while the other doesn’t. I hoped the constraints file will push and orient the chains in the right possible way but it doesn’t seem the case. Please suggest me any ideas to overcome this problem. Thanks in advance. Expecting reply from you guys.

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my mail address
by vidya george 21 Jan '16

21 Jan '16

vidyapgb06(a)gmail.com

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Modeller 9.16 release
by Modeller Caretaker 12 Jan '16

12 Jan '16

The new version of Modeller, 9.16, is now available for download! Please see the download page at http://salilab.org/modeller/ for more information. If you have a license key for Modeller 8 or 9, there is no need to reregister for Modeller 9.16 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 9.16 is primarily a bugfix release relative to the last public release (9.15). Major user-visible changes include: # alignment.check_sequence_structure() no longer erroneously warns about the potentially large CA-CA distances between residues in different chains. # Add Python 3.5 support. # Bundled version of HDF5 updated to 1.8.14. See the Modeller manual for a full change log: http://salilab.org/modeller/9.16/manual/node40.html If you encounter bugs in Modeller 9.16, please see http://salilab.org/modeller/9.16/manual/node10.html for information on how to report them. Note: you are receiving this email either because you subscribed to the modeller_usage mailing list, or you provided this address when you requested a Modeller license and you ticked the "notify me of new releases" box. In the latter case, if you no longer wish to receive announcements of new Modeller releases, simply reply to this email and let us know. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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