March 2015 - modeller_usage

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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