- modeller_usage - salilab.org

Re: [modeller_usage] DOPE score based model selection
by Mouses Stamboulian 16 Apr '15

16 Apr '15

then driven from what score I choose the best model from a set of produced models? DOPE? GA341? mol-pdf? ________________________________ From: Min-yi Shen <minyishen(a)gmail.com> Sent: Thursday, April 16, 2015 4:57 PM To: Mouses Stamboulian Cc: vipul(a)nccs.res.in; modeller_usage(a)salilab.org Subject: Re: [modeller_usage] DOPE score based model selection Dope has the tendency to pick the most compactly packed model because it favors contacts. For disordered regions of proteins this may or may not be a good thing. On Thursday, April 16, 2015, Mouses Stamboulian <mouses.stamboulian(a)lau.edu<mailto:mouses.stamboulian@lau.edu>> wrote: the DOPE score is not a correct indication from my experience. Ive modelled proteins of already known structures, then calculated their RMSD by aligning my computed models through modeller with the structure found in PDB. it has shown that not always the model with the lowest DOPE or nomralized DOPE for that matter has the best RMSD results with the PDB structure. ________________________________________ From: modeller_usage-bounces(a)salilab.org <modeller_usage-bounces(a)salilab.org> on behalf of vipul(a)nccs.res.in <vipul(a)nccs.res.in> Sent: Thursday, April 16, 2015 4:31 PM To: modeller_usage(a)salilab.org Subject: [modeller_usage] DOPE score based model selection Dear Modeller_usage members, Is it necessary to select the best protein model based on DOPE scores? I have made 100 models of a ~260 residue protein (enzyme) using Modeller. Then I chose the best model based on the DOPE Score and did loop refinement on a 16-residue long loop (50 refined models created) located at active site cleft. In loop-refined model the loop occludes the active site cleft, but in another loop-refined model (with intermediate DOPE score) it is alright. Can I use this loop-refined model? Also, is it essential to refine the loop even when some initial Models have good conformations of the loop? Any suggestions would be very helpful. Thanks in advance, Vipul _______________________________________________ modeller_usage mailing list modeller_usage(a)salilab.org https://salilab.org/mailman/listinfo/modeller_usage _______________________________________________ modeller_usage mailing list modeller_usage(a)salilab.org https://salilab.org/mailman/listinfo/modeller_usage

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how to build a collagen microfibril?
by Ming Tang 13 Apr '15

13 Apr '15

Dear all, I want to build the collagen I microfibril structure. I have the tough structure 3HR2 from PDB, which contains only the Carbon and rattus norvegicus, and the amino acid sequences of bovine. I learnt from the literature that homology modelling can be used to achieve this goal. I am totally new in Modeller. Where should I start? Is there any examples for me to follow? Thanks inadvance, Ming

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Silencing all Modeller output
by David Menéndez Hurtado 25 Mar '15

25 Mar '15

Hi, I wonder if there is a way to silence all output when running automodel. I have set modeller.log.none() at the beginning of the script, but I still get a bunch of output: 0 atoms in HETATM/BLK residues constrained to protein atoms within 2.30 angstroms and protein CA atoms within 10.00 angstroms 0 atoms in residues without defined topology constrained to be rigid bodies >> Model assessment by DOPE potential DOPE score : -13973.771484 >> Model assessment by DOPE-HR potential DOPE-HR score : -7906.894043 >> Model assessment by DOPE potential DOPE score : -13973.771484 >> Normalized DOPE z score: -0.645 [...] >> Summary of successfully produced models: Filename molpdf DOPE score DOPE-HR score GA341 score Normalized DOPE score ----------------------------------------------------------------------------------------------------------- MODEL.B999910001.pdb 12623.23730 -13973.77148 -7906.89404 1.00000 -0.64460 MODEL.B999910002.pdb 12689.78906 -13755.89648 -7777.28760 1.00000 -0.54034 [...] I have also tried to redirect stdout to /dev/null from Python while Modeller runs, without effect, so I guess this must be coming from a compiled printf. Is there any other way I am overlooking? In my case I have several processes running in parallel, and all my output is cluttered by this. Thank you, David.

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Is energy minimization possible in MODELLER?
by Arijit Ghosh 16 Mar '15

16 Mar '15

Hi dear MODELLER users, I made a good homology model with MODELLER, it's showing good credibility in all the programs in SAVES server, but I want to do an energy minimization before I go for docking some small ligands onto it. Please let me know if it is possible in MODELLER? Regards, Arijit -- *Arijit Ghosh* *4th Year Integrated MSc.* *School of Biological Sciences* *National Institute of Science Education and Research* *Bhubaneswar, Orissa-751005, India* *Alternate electronic contact: arijitghosh2009(a)gmail.com <arijitghosh2009(a)gmail.com>* *Handheld: +91-986-171-9393*

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native overlap of pdb structures
by Mouses Stamboulian 10 Mar '15

10 Mar '15

Dear Ben, I'm working on a project similar to the work you and Andrej Sali did in 2003 (comparative protein structure modeling by iterative alignment, model building and model assessment), Except that I'm using Scatter Search Heuristics rather than Genetic Algorithms. after running my algorithm and comparing the 3D structures obtained with the ones found in PDB, the results are showing good RMSD values, however using the superpose method of Modeller: from modeller import * env = environ() env.io.atom_files_directory = [''] mdl = model(env, file='3HLA') mdl2 = model(env, file='3HLA.B99991001') aln = alignment(env, file='superpose_alignment.ali', align_codes=('3HLA', 'ABCD')) atmsel = selection(mdl).only_atom_types('CA') r = atmsel.superpose(mdl2, aln, rms_cutoff =5, reference_distance = 10, refine_local=False, superpose_refine=False) rms = r.rms drms = r.drms print("%d equivalent positions" % r.num_equiv_pos) mdl2.write(file='superpose_alignment.txt') I'm not getting such good overlaps within 5 angstroms. my question is that is there a way to refine my final comparative Model so that I'll get better (higher) native overlap values? Thank you.

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Re: [modeller_usage] The results of your email commands
by Mouses Stamboulian 10 Mar '15

10 Mar '15

Sorry I didn't get that. what kind of modeling should I use? like automodel class...? ________________________________________ From: modeller_usage-bounces(a)salilab.org <modeller_usage-bounces(a)salilab.org> Sent: Tuesday, March 10, 2015 7:37 PM To: Mouses Stamboulian Subject: The results of your email commands The results of your email command are provided below. Attached is your original message. - Results: Ignoring non-text/plain MIME parts - Unprocessed: How can I obtain the best comparative model given a target-template alignment and 3D model of the template. I want to get a comparative model, with native overlap with 5 angstroms cutoff between the calculated model and that of the actual structure found in pdb, as high as possible given the alignment. the native overlap is calculated by the superpose method of modeller. Thank you. - Done.

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native overlap
by Mouses Stamboulian 10 Mar '15

10 Mar '15

Hi, How can I obtain the best comparative model given a target-template alignment and 3D model of the template. I want to get a comparative model, with native overlap with 5 angstroms cutoff between the calculated model and that of the actual structure found in pdb, as high as possible given the alignment. the native overlap is calculated by the superpose method of modeller. Thank you.

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Is my model a good one based on these values?
by Arijit Ghosh 03 Mar '15

03 Mar '15

>> Summary of successfully produced models: Filename molpdf DOPE score GA341 score ---------------------------------------------------------------------- qseq1.B99990001.pdb 42902.98828 -324037.96875 1.00000 qseq1.B99990002.pdb 46528.09375 -324130.28125 1.00000 qseq1.B99990003.pdb 48212.83203 -322118.65625 1.00000 qseq1.B99990004.pdb 46319.42969 -321580.65625 1.00000 qseq1.B99990005.pdb 46323.31250 -323706.06250 1.00000 -- *Arijit Ghosh* *4th Year Integrated MSc.* *School of Biological Sciences* *National Institute of Science Education and Research* *Bhubaneswar, Orissa-751005, India* *Alternate electronic contact: arijitghosh2009(a)gmail.com <arijitghosh2009(a)gmail.com>* *Handheld: +91-986-171-9393*

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Problem with tetramer modelling
by Arijit Ghosh 25 Feb '15

25 Feb '15

Hi, I am using the following code for a tetramer modelling: from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() class MyModel(automodel): def special_restraints(self, aln): s1 = selection(self.chains['A']).only_atom_types('CA') s2 = selection(self.chains['B']).only_atom_types('CA') s3 = selection(self.chains['C']).only_atom_types('CA') s4 = selection(self.chains['D']).only_atom_types('CA') self.restraints.symmetry.append(symmetry(s1, s2, s3, s4)) def user_after_single_model(self): self.restraints.symmetry.report(1.0) env = environ() env.io.atom_files_directory = ['.', '../atom_files'] a = MyModel(env, alnfile = 'qseq1-tseq1.ali' , # my alignment filename knowns = 'tseq1', # code of the tetramer template sequence = 'qseq1') # code of the monomer made with modeller a.starting_model= 1 a.ending_model = 1 a.make() but after running it, the console is showing "raise KeyError <"No such chain: %s" % indx> KeyError: 'No such chain: A'" Please help me. Regards, Arijit Ghosh -- *Arijit Ghosh* *4th Year Integrated MSc.* *School of Biological Sciences* *National Institute of Science Education and Research* *Bhubaneswar, Orissa-751005, India* *Alternate electronic contact: arijitghosh2009(a)gmail.com <arijitghosh2009(a)gmail.com>* *Handheld: +91-986-171-9393*

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Homology modelling a loop
by Anjela Manandhar 24 Feb '15

24 Feb '15

Hello, I need to model a missing loop for my protein. I used the sequence of missing loop and aligned with its homologous sequence. Then I modeled my loop from the alignment. Now the problem is my modeled loop is very far away from the place where it needs to be ( due to the template i used). So how can I stitch my loop into the protein. Also, is there a way to homology model the loop such that its position is within the protein. I am attaching my script and alignment files. Sincerely, Anjela Manandhar Graduate Student Biochemistry Program Graduate Center, City University of New York 365 Fifth Avenue, NY-10016, USA

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