- modeller_usage - salilab.org

Modelling of multi-domain protein from oligomeric template
by Chugunov Anton 06 Jul '11

06 Jul '11

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optimize.py
by MUSTAFA BUGHIO 06 Jul '11

06 Jul '11

Dear I am trying to do energy minimization step by running optimize.py script file but it does not execute every time i tried to run and got the following error, i will be thankful if you help me get this problem resolved. IOError: pdbnam_____E> Filename for PDB code not found: hGLR Directories: ../atom_files Extensions : :.atm:.pdb:.ent:.crd (Also tried prepending 'pdb', looking for .Z, .gz, .bz2, .7z, .xz, and trying PDB-style subdirectories - e.g. ab for pdb1abc.ent) # Example for: conjugate_gradients(), molecular_dynamics(), model.switch_trace() # This will optimize stereochemistry of a given model, including # non-bonded contacts. # non-bonded contacts. from modeller import * from modeller.scripts import complete_pdb from modeller.optimizers import conjugate_gradients, molecular_dynamics, actions env = environ() env.io.atom_files_directory = ['../atom_files'] env.edat.dynamic_sphere = True env.libs.topology.read(file='$(LIB)/top_heav.lib') env.libs.parameters.read(file='$(LIB)/par.lib') code = '*hGLR*' mdl = complete_pdb(env, code) mdl.write(file=code+'.ini') # Select all atoms: atmsel = selection(mdl) # Generate the restraints: mdl.restraints.make(atmsel, restraint_type='stereo', spline_on_site=False) mdl.restraints.write(file=code+'.rsr') mpdf = atmsel.energy() # Create optimizer objects and set defaults for all further optimizations cg = conjugate_gradients(output='REPORT') md = molecular_dynamics(output='REPORT') # Open a file to get basic stats on each optimization trcfil = file(code+'.D00000001', 'w') # Run CG on the all-atom selection; write stats every 5 steps cg.optimize(atmsel, max_iterations=20, actions=actions.trace(5, trcfil)) # Run MD; write out a PDB structure (called '1fas.D9999xxxx.pdb') every # 10 steps during the run, and write stats every 10 steps md.optimize(atmsel, temperature=300, max_iterations=50, actions=[actions.write_structure(10, code+'.D9999%04d.pdb'), actions.trace(10, trcfil)]) # Finish off with some more CG, and write stats every 5 steps cg.optimize(atmsel, max_iterations=20, actions=[actions.trace(5, trcfil)]) mpdf = atmsel.energy() mdl.write(file=code+'.B') I am trying to give the code which i have got after my pdb files are dveveloped. -- MUSTAFA BUGHIO Junior Research Fellow Lab # P-133 Computational Medicinal Chemistry and Drug Design Panjwani Center For Molecular Medicine and Drug Research, International Center for Chemical Sciences, University of Karachi, Karachi 75270 Pakistan, +923313425010

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reproduction
by Jean-Paul Armache 05 Jul '11

05 Jul '11

hi, i would like to ask for a bit of an input. you see, i have an alignment of two proteins, one is an xray structure, serves as a template. the other one is the target. the template consists of a globular domain which gets reproduced very nicely, and of an extended part, which gets somehow randomized, or differs substantially from the template. the question of mine is, how to inform modeller to reproduce this part, of just the whole protein which as little deviation as possible (ie. to closely resemble the template) ? thank you for any input, best, jean-paul

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Re: [modeller_usage] FATAL ERROR: MODINSTALL9v9 environment variable not set: incomplete MODELLER installation on Ubuntu 10.4
by R K Belew 03 Jul '11

03 Jul '11

(i'm trying to tack on to the thread closest to my experience) i've successfully installed mod9.9 on MacOS, but want to have less-mediated Python access, and so am re-installing on Ubuntu. i grabbed modeller_9.9-1_i386.deb, invoked dpkg as recommended: > sudo env KEY_MODELLER=<myCode> dpkg -i modeller_9.9-1_i386.deb and the install seemed to work fine. but then going to .../examples/ and trying to run_tests: > monk:/usr/share/doc/modeller-9.9/examples> ./run_tests > Entering directory: all-steps > #!/bin/sh -v > mod9.9 search.py > Could not find platform independent libraries <prefix> > Could not find platform dependent libraries <exec_prefix> > Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] > 'import site' failed; use -v for traceback > ... (similar errors for all other scripts) going thru the archives, you (Ben) say things like: "it needs certain environment variables set first, which python or mod9.9 take care of. " "... You don't actually need to set *any* of the environment variables you have above" regarding previous releases, and so i don't want to mess until i have to! i can also go back to the generic Unix version, but thought you must want Ubuntu's .deb option also working? thanks for your great work, rik

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Regarding Modeller model building script
by Ashish Runthala 01 Jul '11

01 Jul '11

Dear Modellers & Respected Sir Benn, If i am correct Modeller uses distance restraints from multiple templates based on alignment, Tell me the way to use one complete template during modeling and chunks from others. I tried doing that but GDT score decreased when i aligned chunks to one complete template alignment. The aligned chunks were covering target region which was unaligned by one selected complete template span. So HOW TO GENERATE FOLD BASED ALIGNMENT WHICH IMPROVES GDT SCORES BY INCREASING CONSIDERATION WEIGHT OF A SINGLE TEMPLATE AS COMPARED TO OTHERS IN MODELLING. Thanks Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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Two domains get oriented randomly although modelled from a single template
by Чугунов Антон 30 Jun '11

30 Jun '11

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loop_refine.py parallel error
by 刘吉元 30 Jun '11

30 Jun '11

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segfault writing alignment file
by Meesters, Christian 22 Jun '11

22 Jun '11

Hi, I'm using modeller v9.9 in a Linux environment (Ubuntu 11.04) with Python 2.7. When running a script like the build_profile.py from the tutorial, everything works fine, except for the last line: aln.write(file='build_profile.ali', alignment_format='PIR') which results in: openf___224_> Open build_profile.ali Segmentation fault The file is created, but nothing gets written to it. Writing to Python file objects with a simple x = open('test', 'w') x.write('test') x.close() works. So I dare to conclude this is no permissions thing. Although running modeller only via Python, I thought perhaps this is of interest, too: $ ldd mod9.9_x86_64-intel8 linux-vdso.so.1 => (0x00007fff643ff000) libmodeller.so.5 => /home/cm/bin/modeller9.9/lib/x86_64-intel8/libmodeller.so.5 (0x00007f709af77000) libglib-2.0.so.0 => /lib/x86_64-linux-gnu/libglib-2.0.so.0 (0x00007f709ac62000) libpython2.3.so.1.0 => /home/cm/bin/modeller9.9/lib/x86_64-intel8/libpython2.3.so.1.0 (0x00007f709aa37000) libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f709a6a3000) libifcore.so.5 => /home/cm/bin/modeller9.9/lib/x86_64-intel8/libifcore.so.5 (0x00007f709a493000) libsvml.so => /home/cm/bin/modeller9.9/lib/x86_64-intel8/libsvml.so (0x00007f709a308000) libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f709a104000) libhdf5.so.6 => /home/cm/bin/modeller9.9/lib/x86_64-intel8/libhdf5.so.6 (0x00007f7099c69000) libhdf5_hl.so.6 => /home/cm/bin/modeller9.9/lib/x86_64-intel8/libhdf5_hl.so.6 (0x00007f7099a3d000) libsaxs.so => /home/cm/bin/modeller9.9/lib/x86_64-intel8/libsaxs.so (0x00007f709983c000) libpcre.so.3 => /lib/x86_64-linux-gnu/libpcre.so.3 (0x00007f70995ff000) librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f70993f7000) libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f70991d9000) libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007f7098fd5000) libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f7098d50000) /lib64/ld-linux-x86-64.so.2 (0x00007f709b52b000) libimf.so => /home/cm/bin/modeller9.9/lib/x86_64-intel8/libimf.so (0x00007f70989ec000) libintlc.so.5 => /home/cm/bin/modeller9.9/lib/x86_64-intel8/libintlc.so.5 (0x00007f70988ae000) So, no missing libraries, but perhaps a wrong version? Any ideas on what might trigger this segfault? TIA Christian

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how to download
by Victor 20 Jun '11

20 Jun '11

Hi, How to download Modeller?

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Restrain problem
by flavio seixas 18 Jun '11

18 Jun '11

Hi, I had sucessfull modelled a protein without restrains. However, when I put alpha helix restrains in the script below I face this problem: File "model-restriction-single.py", line 21 rsr.add(secondary_structure.alpha(self.residue_range('47:', '57:'))) ^ IndentationError: unindent does not match any outer indentation level I saw the script too many times and I am not able to see where the problem is. Could anyone help-me? from modeller import * from modeller.automodel import * log.verbose() env = environ() env.io.hetatm = True # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms # Add some restraints from a file: # Residues 47 through 57 should be an alpha helix: rsr.add(secondary_structure.alpha(self.residue_range('47:', '57:'))) # Residues 130 through 140 should be an alpha helix: rsr.add(secondary_structure.alpha(self.residue_range('130:', '140:'))) # Residues 182 through 184 should be an alpha helix: rsr.add(secondary_structure.alpha(self.residue_range('182:', '184:'))) # Residues 191 through 195 should be an alpha helix: rsr.add(secondary_structure.alpha(self.residue_range('191:', '195:'))) a = MyModel(env, alnfile='MODEL-TemplateA.ali', knowns='TemplateA', sequence='MODEL', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 5 0 a.make() # Get a list of all successfully built models from a.outputs ok_models = filter(lambda x: x['failure'] is None, a.outputs) # Rank the models by DOPE score key = 'DOPE score' ok_models.sort(lambda a,b: cmp(a[key], b[key])) # Get top model m = ok_models[0] print "Top model 1: %s (DOPE score %.3f)" % (m['name'], m[key]) m = ok_models[1] print "Top model 2: %s (DOPE score %.3f)" % (m['name'], m[key]) m = ok_models[2] print "Top model 3: %s (DOPE score %.3f)" % (m['name'], m[key]) m = ok_models[3] print "Top model 4: %s (DOPE score %.3f)" % (m['name'], m[key]) m = ok_models[4] print "Top model 5: %s (DOPE score %.3f)" % (m['name'], m[key])

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