- modeller_usage - salilab.org

Changing dir and printing hydrogens
by Manoj Singh 02 Apr '14

02 Apr '14

Hi I am using mutate_model.py for making mutations. I have two questions. 1. How can I read the original pdb from different directory and put output structure in current directory. 2. How can I read and print hydrogen of original pdb in mutated pdb structure (except of mutated residue)

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Question
by Francisco garcia 02 Apr '14

02 Apr '14

Hi! I tried to generate a theoretical alpha-helix with the example from Modeller's Manual, but just don't work, because rasmol not identified as helix (my sequence is longer than example). I use more iterations ( 1x10^9) and get a better result but is not enough. Somebody know a better way to generate a perfect alpha helix?? I really need a theoretical helix for my work, please help me. This is the example: # Example for model.build_sequence(), secondary_structure.alpha() from modeller import * from modeller.optimizers import conjugate_gradients # Set up environment e = environ() e.libs.topology.read('${LIB}/top_heav.lib') e.libs.parameters.read('${LIB}/par.lib') # Build an extended chain model from primary sequence, and write it out m = model(e) m.build_sequence('GSCASVCGV') m.write(file='extended-chain.pdb') # Make stereochemical restraints on all atoms allatoms = selection(m) m.restraints.make(allatoms, restraint_type='STEREO', spline_on_site=False) # Constrain all residues to be alpha-helical # (Could also use m.residue_range() rather than m.residues here.) m.restraints.add(secondary_structure.alpha(m.residues)) # Get an optimized structure with CG, and write it out cg = conjugate_gradients() cg.optimize(allatoms, max_iterations=100) m.write(file='alpha-helix.pdb') P.D. I apologize for my English, i hope you understand me. Thanks!

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PYTHONPATH on Windows 7
by chris.wood＠stfc.ac.uk 01 Apr '14

01 Apr '14

Hello, I’ve got Python 2.7.3 on Windows 7: Python 2.7.3 |EPD 7.3-2 (64-bit)| (default, Apr 12 2012, 15:20:16) [MSC v.1500 64 bit (AMD64)] on win32 Type "copyright", "credits" or "license()" for more information. I’ve installed Modeller 9.12; but typing from modeller import * results in the “ImportError: No module named modeller” error, even though I've got modeller in my python path: >>> sys.path ['', 'C:\\Python27\\Lib\\idlelib', 'C:\\Program Files (x86)\\Modeller9.12\\modlib\\modeller', 'C:\\Program Files (x86)\\Modeller9.12\\modlib\\python2.7', 'C:\\Python27\\python27.zip', 'C:\\Python27\\DLLs', 'C:\\Python27\\lib', 'C:\\Python27\\lib\\plat-win', 'C:\\Python27\\lib\\lib-tk', 'C:\\Python27', 'C:\\Python27\\lib\\site-packages', 'C:\\Python27\\lib\\site-packages\\PIL', 'C:\\Python27\\lib\\site-packages\\win32', 'C:\\Python27\\lib\\site-packages\\win32\\lib', 'C:\\Python27\\lib\\site-packages\\Pythonwin'] >>> import modeller Traceback (most recent call last): File "<pyshell#5>", line 1, in <module> import modeller ImportError: No module named modeller I'm sure I've missed something obvious, but can't see it! Cheers, Chris ------------------- Dr Chris Wood STFC Rutherford Appleton Laboratory Didcot OX11 0QX chris.wood(a)stfc.ac.uk www.ccpem.ac.uk Tel: +44(0)1235 567864 Tel: +44(0)7909 586624 Fax: +44(0)1235 567801 Skype: chris_c_wood<callto://chris_c_wood/> -- Scanned by iCritical.

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How to override the build_seq() command in loopmodel class
by Abhijit Muley 21 Mar '14

21 Mar '14

I am having knots in my structure, same problem as this person had- http://salilab.org/archives/modeller_usage/2005/msg00394.html I went through the manual but could not find any specific part where such instructions have been mentioned (althought they could have been in some section I have missed). Can anyone please direct me to the appropriate resources to solve this problem?

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(no subject)
by Ankita Nagpal 17 Mar '14

17 Mar '14

hi I have just started using modeller with the help of tutorial example.In the aligning step when iam aligning 1bdm with TvLDH IAM getting error only 317 residue out of 318 contain atom of type CA .Can you plz help me out what is going wro <http://wrong.it/>ng

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Use some local alignments
by fakharian 15 Mar '14

15 Mar '14

Hi I want to build a model for my target protein base on a known template structure. And I have some target-template local alignments. I want to use(and force) these local alignments on known regions; and align other regions of target by MODELLER alignment functions such as align2d or salign. Can anyone suggest a method to perform this? Thank you.

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Select and remove atoms from automodel
by Ignacio Ibarra 04 Mar '14

04 Mar '14

Hello, Currently I am generating nucleic acid models using the MODELLER suite. I would like to remove the initial phosphate group declared in the first residue of each nucleic acid chain. Those atoms should not be present in real structures. I would like to do it without writing new text in the .lib files that are into the modlib folder I read about a pick_atoms() method in an older version of MODELLER, but it is not commented in the 9v11 manual ( http://binf.gmu.edu/software/MODELLER/node131.html) Is there something similar currently available for removing atoms from the model in the automodel or another class? Regards, Ignacio

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Alignment missing
by Paul Zair Leyva Miranda 25 Feb '14

25 Feb '14

Dear Modeller team, I need your quick suggestions and corrections on my scripts that I have been using to run on multiple computers. I am not getting any errors when I run the script3.py. But, when I compare the files .pap and .ali with other alignment servers like muscle, there are aminoacids missing in the alignment with Modeller. I don`t know where is the problem, if it is related to the alignmet with Modeller or if there is a problem in the script.py. Best regards. Paul Zair Leyva Miranda Laboratory of Molecular Modeling ESM-IPN

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Best workflow to modeling a disordered loop in a complicated structure
by Zachary W Carpenter 19 Feb '14

19 Feb '14

Hello, I have used modeller to attempt to model a loop region in a tetrameric structure. To speed up computational time I've started with just the dimer ( which I think also makes sense biologically ) and ran the following script with an .ali file I created. The region of interest is a disordered loop AA~399-417. Following this I used the evaluate model script to pick the best model, which I then used as the template input for the loop.py script. I run the loop.py script at many iterations and then when it finishes I take the top 20 models (out of 1000) by DOPE score and attempt to analyze them. Any advice on how I could improve my method would be great.. I really am at the edge of my understanding here. I've edited the name of the protein. I can include it as soon as I can verify that this can stay anonymous. Thanks!!! Scripts +files : First )using a template pdb and .ali file I made myself of the Dimer (BIO_headers in chimera and deletion of one dimer of the tetramer) Input : >P1;ABCD structureX:ABCD.pdb: 3 :A:+990:B:::-1.00:-1.00 --TSWSDRLQNAADMPANMDKHALKKYRREAYHRVFVNRSLAMEKIKCFGFNMDYTLAVYKSPEYESLGFELTVE RLVSIGYPQELLSFAYDSTFPTRGLVFDTLYGNLLKVDAYGNLLVCAHGFNFIRGPETREQYPNKFIQRDDTERF YILNTLFNLPETYLLACLVDFFTNCPRYTSCETGFKDGDLFMSYRSMFQDVRDAVDWVHYKGSLKEKTVENLEKY VVKDGKLPLLLSRMKEVGKVFLATNSDYKYTDKIMTYLFDFPHGPKPGSSHRPWQSYFDLILVDARKPLFFGEGT VLRQVDTKTGKLKIGTYTGPLQHGIVYSGGSSDTICDLLGAKGKDILYIGDHIFGDILKSKKRQGWRTFLVIPEL AQELHVWTDKSSLFEELQSLDIFLAS----------------SIQRRIKKVTHDMDMCYGMMGSLFRSGSRQTLF ASQVMRYADLYAASFINLLYYPFSYLFRAAHVLMPHES/--TSWSDRLQNAADMPANMDKHALKKYRREAYHRVFVNRSLAMEKIKCFGFNMDYTLAVYKSPEYESLGFELTVE RLVSIGYPQELLSFAYDSTFPTRGLVFDTLYGNLLKVDAYGNLLVCAHGFNFIRGPETREQYPNKFIQRDDTERF YILNTLFNLPETYLLACLVDFFTNCPRYTSCETGFKDGDLFMSYRSMFQDVRDAVDWVHYKGSLKEKTVENLEKY VVKDGKLPLLLSRMKEVGKVFLATNSDYKYTDKIMTYLFDFPHGPKPGSSHRPWQSYFDLILVDARKPLFFGEGT VLRQVDTKTGKLKIGTYTGPLQHGIVYSGGSSDTICDLLGAKGKDILYIGDHIFGDILKSKKRQGWRTFLVIPEL AQELHVWTDKSSLFEELQSLDIFLAS----------------SIQRRIKKVTHDMDMCYGMMGSLFRSGSRQTLF ASQVMRYADLYAASFINLLYYPFSYLFRAAHVLMPHES* >P1;X sequence:ABCD: : : : ::: 0.00: 0.00 MSTSWSDRLQNAADMPANMDKHALKKYRREAYHRVFVNRSLAMEKIKCFGFDMDYTLAVYKSPEYESLGFELTVE RLVSIGYPQELLSFAYDSTFPTRGLVFDTLYGNLLKVDAYGNLLVCAHGFNFIRGPETREQYPNKFIQRDDTERF YILNTLFNLPETYLLACLVDFFTNCPRYTSCETGFKDGDLFMSYRSMFQDVRDAVDWVHYKGSLKEKTVENLEKY VVKDGKLPLLLSRMKEVGKVFLATNSDYKYTDKIMTYLFDFPHGPKPGSSHRPWQSYFDLILVDARKPLFFGEGT VLRQVDTKTGKLKIGTYTGPLQHGIVYSGGSSDTICDLLGAKGKDILYIGDHIFGDILKSKKRQGWRTFLVIPEF AQELHVWTDKSSLFEELQSLDIFLAELYKHLDSSSNERPDISSIQRRIKKVTHDMDMCYGMMGSLFRSGSRQTLF ASQVMRYADLYAASFINLLYYPFSYLFRAAHVLMPHES/MSTSWSDRLQNAADMPANMDKHALKKYRREAYHRVFVNRSLAMEKIKCFGFDMDYTLAVYKSPEYESLGFELTVE RLVSIGYPQELLSFAYDSTFPTRGLVFDTLYGNLLKVDAYGNLLVCAHGFNFIRGPETREQYPNKFIQRDDTERF YILNTLFNLPETYLLACLVDFFTNCPRYTSCETGFKDGDLFMSYRSMFQDVRDAVDWVHYKGSLKEKTVENLEKY VVKDGKLPLLLSRMKEVGKVFLATNSDYKYTDKIMTYLFDFPHGPKPGSSHRPWQSYFDLILVDARKPLFFGEGT VLRQVDTKTGKLKIGTYTGPLQHGIVYSGGSSDTICDLLGAKGKDILYIGDHIFGDILKSKKRQGWRTFLVIPEF AQELHVWTDKSSLFEELQSLDIFLAELYKHLDSSSNERPDISSIQRRIKKVTHDMDMCYGMMGSLFRSGSRQTLF ASQVMRYADLYAASFINLLYYPFSYLFRAAHVLMPHES* # Homology modeling by the automodel class # # Demonstrates how to build multi-chain models, and symmetry restraints # from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() # Override the 'special_restraints' and 'user_after_single_model' methods: class MyModel(automodel): def special_restraints(self, aln): # Constrain the A, B, C and D chains to be identical s1 = selection(self.chains['A']).only_atom_types('CA') s2 = selection(self.chains['B']).only_atom_types('CA') self.restraints.symmetry.append(symmetry(s1, s2, 1)) def user_after_single_model(self): # Report on symmetry violations greater than 1A after building # each model: self.restraints.symmetry.report(1) env = environ() # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] # Be sure to use 'MyModel' rather than 'automodel' here! a = MyModel(env, alnfile = 'WT_dimer_NoCterm.ali' , # alignment filename knowns = 'ABCD', # codes of the templates sequence = 'ABCD') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 20 # index of the last model # (determines how many models to calculate) a.make() # do homology modeling # # class MyModel(automodel): 2nd) Run eval model and pick top model to use as input for the loop.py script below ---> # Loop refinement of an existing model from modeller import * from modeller.automodel import * log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = './:../atom_files' # Create a new class based on 'loopmodel' so that we can redefine # select_loop_atoms (necessary) class MyLoop(loopmodel): # This routine picks the residues to be refined by loop modeling def select_loop_atoms(self): # 10 residue insertion return selection(self.residue_range('399:A', '417:A')) m = MyLoop(env, inimodel='ABCD_Top_Model.pdb', # initial model of the target sequence='ABCD') # code of the target m.loop.starting_model= 1 # index of the first loop model m.loop.ending_model = 1000 # index of the last loop model m.loop.md_level = refine.slow # loop refinement method; this yields # models quickly but of low quality; # use refine.slow for better models m.make() 3rd) Run model_energies script Then I rank them using this perl one liner ( just cats and displays the dope and the file ) can run in any unix terminal. cat model*.log |perl -lane' print if /DOPE\ score/ || /ABCD.BL/'| perl -pe 's/ +/\t/g'|perl -pe 's/:\t//g' |cut -f3,4|perl -pe 's/\n/\t/'|perl -pe 's/(\d)\t(ABCD)/$1\n$2/g'|sort -k2,2n|head -20 4) Take top 20 models and analyze Any help with where I'm doing things wrong or how I can improve would be awesome. How many models in loop.py would you recommend to get a good answer? Is there away to interpret the models created as a whole ....for example say something like "60% of the time residue A is next to residue B and 20% of the time its over in this pocket , therefor".... etc My major aim is to compare different ligand bound crystal states, or mutation states, and show that the models created are different between them. Then use this to design wet lab experiments to test. Thanks again

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Run Modeller on multiple cpu
by Lalith Kumar 17 Feb '14

17 Feb '14

Dear Modeller team, I need your quick suggestions and corrections on my scripts that I have been using to run on multiple cpus. I am not getting any errors, when I run the script parallel-task.py with python. But it is not utilizing multiple cpus. Can you please look in to the attached scripts and let me know where I might have went wrong. Please... Thank you lot Regards, Lalith

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