- modeller_usage - salilab.org

scoring function and optimization
by sdimicco 26 Nov '12

26 Nov '12

Dear Modellers, I have three points to discuss. 1) As I changed the optimization protocol, I woul dlike to check if my set up has been done. Where could I check it? 2) I am building a multimeric protein. The DOPE and GA341 scores are developed for single chain models. How can I asses the quality of my models? The sole molpdf is sufficient? 3) I found thie messagge in the log file: Treating residue type GSH as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. I have understood that the input PDB file is the .ini, which is written during the calculation. Thus, how can I "remove the corresponding 'MODELLER BLK RESIDUE" to treat the residue flexible? Have I to define it as my own residue? Thank you in advance All the best Simone

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(no subject)
by Shota Nakamura 20 Nov '12

20 Nov '12

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Error while running compare.py
by Anogna 20 Nov '12

20 Nov '12

Dear Modeller Users, I trying simple modelling methodology to model required protein structure. Till build_profile.py everything went well. But when gave compare.py.....i am get an error as follows *Traceback (most recent call last):* * File "compare.py", line 11, in ?* * m = model(env, file=pdb, model_segment=('FIRST:'+chain, 'LAST:'+chain)) * * File "C:\Program Files\Modeller9v7\modlib\modeller\model.py", line 72, in __in* *it__* * self.read(**vars)* * File "C:\Program Files\Modeller9v7\modlib\modeller\model.py", line 117, in rea* *d* * model_format, model_segment)* *IOError: pdbnam_____E> Filename for PDB code not found: 3d3l* * Directories: .;atom_files* * Extensions : ;.atm;.pdb;.ent;.crd* * (Also tried prepending 'pdb', looking for .Z, .gz, .bz2, .7z, * * and trying PDB-style subdirectories - e.g. ab for pdb1abc.ent)* Do I need make any modifications in my compare.py file....I am attaching compare.py file which i used. Please help me with this problem. Thanking You, Anogna

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optimization protocol and HETATM flexibility
by sdimicco 20 Nov '12

20 Nov '12

Dear Modellers, I am tring to set up my script to build a multimeric model with loop refinement. The script looks like: log.verbose() class dope_loopmodel(dope_loopmodel): def special_patches(self, aln): # Rename both chains and renumber the residues in each self.rename_segments(segment_ids=['A', 'B'], renumber_residues=[1, 1]) env = environ() env.io.hetatm = True a = dope_loopmodel(env, alnfile='TvLDH-1bdm.ali', knowns='1bdm', sequence='TvLDH', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 2 # Very thorough VTFM optimization: a.library_schedule = autosched.slow a.max_var_iterations = 300 # Thorough MD optimization: a.md_level = refine.very_slow # Repeat the whole cycle 2 times and do not stop unless obj.func. > 1E6 a.repeat_optimization = 2 a.max_molpdf = 1e6 a.loop.starting_model = 1 # First loop model a.loop.ending_model = 1 # Last loop model a.loop.md_level = refine.fast # Loop model refinement level a.make() automodel.final_malign3d = True It seems that the script works but I would like to check if all optimization steps have been done. How could I check it? Please, if you note errors in the script, give me suggestions Moreover, I built a model with an HETATM residue. If I want to treat it as flexible residue: how could I do that? Thank you in advance. Bests Simone

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Modeller Help
by mario rossi 19 Nov '12

19 Nov '12

Hello everyone I'am Simone an italian student, ineed to learn to use modeller to do homology modelingbut i have some trouble. I downloaded and installed both modeller and python on my pc (windows 7). To learn what to do I tried to follow the basic tutorial but I find serious problems in giving the input. I can not even load the sequence as the file (.ali) is not recognized by python and if the command is entered manually, I get syntax error?? Can you help me to understand where is the mistake?

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multimeric model and loop refinement
by sdimicco 16 Nov '12

16 Nov '12

Dear Member, I am trying to built a multimeric model. I would like to if I have to use restraints symmetry to model it. Moreover, i would like to built a model with all hydrogens and to refine loop automatically. How can I do that? I am trying to use allh model and loop model in the same script, but without success. Thank you in advance Simone

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Re: [modeller_usage] Introduction of Zinc restraints
by flavio seixas 06 Nov '12

06 Nov '12

Hi Mehdi I never used the restrains you listed before. I can not say if it is right or not. You may try to modeller and see the results by overlaying model and template (SSM superpose) in a graphic software like Coot. My suggestion was more simple. I suggest you modify your alignment file. You may have a lot of identical residues in the alignment of zinc finger region. Try to modeller them as rigid bodies, replacing then in your sequence by dots "." This will copy the restrains of your template to your model. Another suggestion is to do as Ben advised. Regards, Flavio --- On Tue, 11/6/12, Mehdi Talebzadeh Farooji <mahditzf(a)yahoo.com> wrote: From: Mehdi Talebzadeh Farooji <mahditzf(a)yahoo.com> Subject: Re: [modeller_usage] Introduction of Zinc restraints To: "flavio seixas" <oivalf_nix(a)yahoo.com> Date: Tuesday, November 6, 2012, 2:29 AM Hi Flavio Thank you for your reply. I have to sets of restraints, the distance between SG of Cysteins and Zn 2.3 A, ND1 of his and Zn 2.0 A. I intruduced these restraints in MyModel.py class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints for ids in (('SG:204:B', 'ZN:238:B'), ('SG:207:B', 'ZN:238:B'), ('SG:225:B', 'ZN:238:B'), ('ND1:228:B', 'ZN:238:B')): atoms = [self.atoms[i] for i in ids] rsr.add(forms.upper_bound(group=physical.upper_distance, feature=features.distance(*atoms), mean=2.3, stdev=0.03) I am not sure if I am doing right thing. Regards, Mehdi From: flavio seixas <oivalf_nix(a)yahoo.com> To: mahditzf(a)yahoo.com Sent: Sunday, November 4, 2012 9:07:58 PM Subject: Re: [modeller_usage] Introduction of Zinc restraints Hi. try to build identical residues of zinc finger as well zinc atom as rigid bodies "." and modeler only the different residues. Regards flavio ------------------------------ Em sex, 2 de nov de 2012 18:41 GMT Mehdi Talebzadeh Farooji escreveu: >Dear Users, > >I am trying to build a model of a Zinc finger protein, I am having problem with zinc coordination. Since the Zinc coordination residues of the model (CCCH) are slightly different from that of the template (CCCD), in the built model, the distances between atoms of the coordination residues and zinc do not match the standard zinc coordination. I was wondering if I could introduce the Zinc coordination restraints of the model in calculation. Any idea or help would be appreciated. > >Mehdi

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Introduction of Zinc restraints
by Mehdi Talebzadeh Farooji 06 Nov '12

06 Nov '12

Dear Users, I am trying to build a model of a Zinc finger protein, I am having problem with zinc coordination. Since the Zinc coordination residues of the model (CCCH) are slightly different from that of the template (CCCD), in the built model, the distances between atoms of the coordination residues and zinc do not match the standard zinc coordination. I was wondering if I could introduce the Zinc coordination restraints of the model in calculation. Any idea or help would be appreciated. Mehdi

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Force B-hairpin loop when modelling
by Rienk Doetjes 26 Oct '12

26 Oct '12

Hi all! I am working with a structure that, according to all available information I have, contains a beta hairpin loop. Whenever I use modeller to produce a homology model, this beta-hairpin will not be formed. Is there a way I can force modeller to actually generate this feature I want? Forcing the standard secondary structure does not seem to work. Thanks, Rienk

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Protein-complex
by Mehdi Talebzadeh Farooji 22 Oct '12

22 Oct '12

Dear Modeller users, I have a template complex (A1:B1); I would like to create a model of A2:B1 complex, A1 and A2 are similar about 50% and the structure of the A2 is known. I want to use the known structure (not the template structure of A1 subunit from complex) for modelling and refinement. I was wondering if it I could do it with modeller and how? Thanks in advance, Mehdi

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