- modeller_usage - salilab.org

basic modeling problem
by Sana Bilal 10 Sep '06

10 Sep '06

Hey! I am trying to model the 3D structure of a protein sequence by using two templates namely 3cd4 and 4gcr. The resultant PDB file that I get is not properly folded. The portion of the target sequence matching template 3cd4 is correctly modeled but the portion corresponding to template 4gcr is not folded. Alignment file and resultant PDB file are attached. Please help.

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structural alignment
by Prabhakar. G. 05 Sep '06

05 Sep '06

Dear Modellers, we are building a dimer model from two dimer templates one template having 392 residues(1UZG) other having 495 residues(1P58, Calpha coordinates is only available), Both the templates are of the same protein (E protein, Dengue virus type 2), want to use the first 392 residues from 1UZG and the last 400-495 from the 1P58 to build the model of our query sequence. To make a initial structural alignment of the two templates and we used salign_multiple.py how to specify the the two chains(A & B) of the two templates to get structurally aligned in the below script? =================================================================================================== # Illustrates the SALIGN multiple structure/sequence alignment log.verbose() env = environ() env.io.atom_files_directory = './:../atom_files/' aln = alignment(env) for (code, chain) in (('1p58', 'A'), ('1uzg', 'A')): mdl = model(env, file=code, model_segment=('FIRST:'+chain, 'LAST:'+chain)) aln.append_model(mdl, atom_files=code, align_codes=code+chain) for (weights, write_fit, whole) in (((1., 0., 0., 0., 1., 0.), False, True), ((1., 0.5, 1., 1., 1., 0.), False, True), ((1., 1., 1., 1., 1., 0.), True, False)): aln.salign(rms_cutoffs=(3.5, 6., 60, 60, 15, 60, 60, 60, 60, 60, 60), normalize_pp_scores=False, rr_file='$(LIB)/as1.sim.mat', overhang=30, gap_penalties_1d=(-450, -50), gap_penalties_3d=(0, 3), gap_gap_score=0, gap_residue_score=0, dendrogram_file='1is3A.tree', alignment_type='tree', # If 'progresive', the tree is not # computed and all structues will be # aligned sequentially to the first #ext_tree=True, # Tree building can be avoided if the tree # is input #input_weights_file='1is3A_exmat.mtx', feature_weights=weights, # For a multiple sequence alignment only # the first feature needs to be non-zero improve_alignment=True, fit=True, write_fit=write_fit, write_whole_pdb=whole, output='ALIGNMENT QUALITY') aln.write(file='1p58-1uzgABnew3.pap', alignment_format='PAP') aln.write(file='1p58-1uzgABnew3.ali', alignment_format='PIR') # The number of equivalent positions at different RMS_CUTOFF values can be # computed by changing the RMS value and keeping all feature weights = 0 aln.salign(rms_cutoffs=(1.0, 6., 60, 60, 15, 60, 60, 60, 60, 60, 60), normalize_pp_scores=False, rr_file='$(LIB)/as1.sim.mat', overhang=30, gap_penalties_1d=(-450, -50), gap_penalties_3d=(0, 3), gap_gap_score=0, gap_residue_score=0, dendrogram_file='1is3A.tree ', alignment_type='progressive', feature_weights=[0]*6, improve_alignment=False, fit=False, write_fit=True, write_whole_pdb=False, output='QUALITY') ========================================================================================================== subsequently are to make a alignment with the query sequence using salign_align2d.py and build models using mod-def.py or model-fast.py. Thanks in advance prabhakar

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pdb output
by yalini.pathy＠yale.edu 02 Sep '06

02 Sep '06

Hi, I ran a test modeller script to generate 2 models. From running this script, I only got the Dxxxxx files and not the PDB output files. The log file didn't contain any error messages for generating PDB files - might anyone be able to suggest a solution please? Thanks, Yalini

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top to python (+ symmetry restraints)
by yalini.pathy＠yale.edu 30 Aug '06

30 Aug '06

Hi, I have a top file from Modeller v6.0 (or possibly older). The top script defines a tetramer and then applies alpha-helical restraints to the same residue range in each monomer. I have been trying to convert this to use with the newest version of Modeller. I've been unsuccessful so far - might someone be able to help please? The top script is attached to this e-mail; Many thanks in advance! Yalini

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Re: [modeller_usage] CHARMM atom type is out of range
by Modeller Caretaker 29 Aug '06

29 Aug '06

zzj wrote: > Hi, the problem was solved by deleting "inifile = 'mgl.pdb'" in my > script. mgl.pdb is my template pdb file, without any further change. If > you still think this is not normal, I'll send the input files towrrow > when I get to lab. If you specify an "inifile" it needs to be a set of coordinates of your model (usually from a previous optimization), not a template. If you leave out "inifile", then Modeller will automatically build an initial model (with a .ini file extension) based on your template(s) and the alignment. This is usually what you want, although sometimes the .ini file has such a bad structure (e.g. knots in the sequence or other bad clashes) that the optimization is unable to recover, and you may be able to manually tweak the initial model to correct this. Unfortunately, Modeller does very little checking on a user-provided initial model, and expects it to match the .ini file (i.e. same residue and atom order, just with different coordinates). So you can get weird errors if this is not the case. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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Hello,everyone, what are CA CB atoms?
by li bai 29 Aug '06

29 Aug '06

Hello,everyone! Today I study manual of modeller.I found a question! It says:"non-hydrogen mainchain (N, C,CA,O)and CB atoms" what are CA and CB atoms? How analyse CA and CB atoms? Sincerely！ --------------------------------- 抢注雅虎免费邮箱-3.5G容量，20M附件！

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CHARMM atom type is out of range
by zzj 28 Aug '06

28 Aug '06

Hellow everyone, I am learning how to use Modeller. It gives me the following infor in the log file: ..... preppdf_203E> CHARMM atom type is out of range; Probably because model.generate_topology() was not called. Atom index, atom type: 0 >> Summary of failed models: hgl.B99990001.pdb preppdf_203E> CHARMM atom type is out of range; Probably because model.generate_topology() was not called. Atom index, atom type: 0 Dynamically allocated memory at finish [B,kB,MB]: 4148015 4050.796 3.956 Starting time : 2006/08/28 16:17:29.348 Closing time : 2006/08/28 16:17:48.589 Total CPU time [seconds] : 17.68 I believe my alignment is ok. Here's my script: # Modeling using a provided initial structure file (inifile) from modeller.automodel import * # Load the automodel class log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = './:../atom_files' a = automodel(env, alnfile = 'alignment.ali', # alignment filename knowns = 'mgl', # codes of the templates sequence = 'hgl', # code of the target inifile = 'mgl.pdb') # use 'my' initial structure a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) a.make() # do homology modelling Can somebody give me a hint? Thanks alot. JOE -- _________________________________________ Joe (zhaocai) Zhou Department of Pathology & Laboratory Medicine University of Pennsylvania, School of Medicine 252 John Morgan Building 36th Street & Hamilton Walk Philadelphia, PA 19104-6082 Tel: 215-898-2870 Fax:215-898-2401 Cell:781-330-2409 -------------------------------------------------------------

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Assess model quality with multi chains
by bmbbl＠leeds.ac.uk 23 Aug '06

23 Aug '06

Dear all, I have remodelled a loop on a tetramer model, and kicked out 40 of 100 loops which had bad objective functions. As pointed out in the manual, either DOPE or GA341 function is recommended to assess a model with multi chains. So how to assess the 60 loop models? Many thnx. Binbin

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dope energy of template
by caj 18 Aug '06

18 Aug '06

Hi all, The evaluate-model.py was used for a few of my models but I would like to compare the DOPE energies to my template and where do I find that data-set? Hope it is not too obvious.... Best wishes Caroline

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enforcing symmetry in loop refinement
by Mike White 10 Aug '06

10 Aug '06

I have modeled a homopentamer using automodel with enforcing pentameric symmetry, and everything looks fine. There are two regions of each subunit that have 3 and 5 residue long loops that aren't in the templates. When I do loop modeling of all 10 of these loops at the same time using a script based on the one in the Advanced tutorial, I get a set of models where the loops are no longer symmetric. I then introduced the same symmetry constraints in the loop modeling that I used in the original model, and it produced models with the appropriate symmetry. However, it took much longer (765 seconds of cpu time to generate 5 loop models without the symmetry , but 8629 seconds to generate 2 loop models with symmetry). I don't mind letting things run overnight to generate models, but the hugh increase in computational time suggests that I might not be doing this right. Below is the python script: ******************************************************************* # Loop refinement of an existing model of the receptor from modeller import * from modeller.automodel import * log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = './:../atom_files' def defsym(mdl, aln, seg1, seg2): for (set,seg) in [(2,seg1), (3,seg2)]: mdl.pick_atoms(aln, pick_atoms_set=set,selection_segment=seg, atom_types='ALL',selection_status='INITIALIZE', selection_search='SEGMENT') mdl.symmetry.define(symmetry_weight=1.0,add_symmetry=(True,False)) segsize = 217 #number of residues per chain # 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): # 4 residue insertion in Loop C in each subunit self.pick_atoms(selection_segment=('198:', '201:'), selection_status='INITIALIZE') self.pick_atoms(selection_segment=('415:', '418:'), selection_status='ADD') self.pick_atoms(selection_segment=('632:', '635:'), selection_status='ADD') self.pick_atoms(selection_segment=('849:', '852:'), selection_status='ADD') self.pick_atoms(selection_segment=('1066:', '1069:'), selection_status='ADD') # 3 residue insertion in Loop F in each subunit self.pick_atoms(selection_segment=('162:', '164:'), selection_status='ADD') self.pick_atoms(selection_segment=('379:', '381:'), selection_status='ADD') self.pick_atoms(selection_segment=('596:', '598:'), selection_status='ADD') self.pick_atoms(selection_segment=('813:', '815:'), selection_status='ADD') self.pick_atoms(selection_segment=('1030:', '1032:'), selection_status='ADD') def special_restraints(self, aln): #identify the seqments to maintain symmetry: A-B, B-C, C-D, D-E defsym(self,aln,seg1=('1',str(segsize)), seg2=(str(segsize+1),str(2*segsize))) defsym(self,aln,seg1=(str(segsize+1),str(2*segsize)), seg2=(str(2*segsize+1),str(3*segsize))) defsym(self,aln,seg1=(str(2*segsize+1),str(3*segsize)), seg2=(str(3*segsize+1),str(4*segsize))) defsym(self,aln,seg1=(str(3*segsize+1),str(4*segsize)), seg2=(str(4*segsize+1),str(5*segsize))) m = myloop(env, inimodel='ReceptorBEST.pdb', # initial model of the target sequence='Receptor') # code of the target m.loop.starting_model= 11 # index of the first loop model m.loop.ending_model = 12 # index of the last loop model m.loop.md_level = refine.very_fast # loop refinement method m.make() ******************************************************************************** The only difference between the two scripts is the inclusion of the definition of the defsym operation and the mdl.symmetry.define operation and the "def special_restraints" block. The cutting and pasting into this message screwed up the indentation, but the "mdl.symmetry.define" command is lined up with the "for (set, seg).." line. Have I done this right? I'm still at the "copying other scripts and trying to adapt them to my needs stage." There was an earlier post about this topic (http://salilab.org/archives/modeller_usage/2005/msg00381.html )but I didn't quite understand how this was to be implemented in loop modeling. Thanks! Mike White

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