September 2006 - modeller_usage

protein 3 D structure alignment
by drugdesign 02 Oct '06

02 Oct '06

Dear modeller users, I have a series of 3D structures built by MODELLER. I need top make 3D alignment of these structures because I need to see the differences between these protein stuctures (they are from one family of proteins) and the RMSD from RMS coordinates of the proteins. Which scrip is better to use for it? There are 2 MODELLER scripts below. Where in these scripts I need to put my PDB files. Fpr example I have prot1.pdb, rpot2.pdb and prot3.pdb and 1-3.ali file. How such script must look with these files? Respectively yours, Andrew ------------------------------------ # 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 (('1is4', 'A'), ('1uld', 'D'), ('1ulf', 'B'), ('1ulg', 'B'), ('1is5', '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='$(LIB)/as1.sim.mat', overhang=30, gap_penalties_1d=(-450, -50), gap_penalties_3d=(0, 3), gap_gap_score=0, gap_residue_score=0, dendrogram_file='1is3A.tree', alignment_type='tree', # If 'progresive', the tree is not # computed and all structues will be # aligned sequentially to the first #ext_tree=True, # Tree building can be avoided if the tree # is input #input_weights_file='1is3A_exmat.mtx', feature_weights=weights, # For a multiple sequence alignment only # the first feature needs to be non-zero improve_alignment=True, fit=True, write_fit=write_fit, write_whole_pdb=whole, output='ALIGNMENT QUALITY') aln.write(file='1is3A.pap', alignment_format='PAP') aln.write(file='1is3A.ali', alignment_format='PIR') # The number of equivalent positions at different RMS_CUTOFF values can be # computed by changing the RMS value and keeping all feature weights = 0 aln.salign(rms_cutoffs=(1.0, 6., 60, 60, 15, 60, 60, 60, 60, 60, 60), normalize_pp_scores=False, rr_file='$(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')

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minimum size of loop for refinement?
by Mike White 28 Sep '06

28 Sep '06

Hi I have searched the archives for the converse of the "how big is too big for loop modeling?" issue but haven't come across anything. I have modeled a protein that has two 1-residue and one 2-residue insertions relative to the templates. If the insertions were larger, I know that I could use loop modeling to further refine the model, but would much be gained by loop refinement of such a small region (would 1 residue even count as a loop?)? Would extending the "loop" by several residues on either side of the insertion be appropriate in this case, even if it means allowing residues with corresponding positions in the template structure to move? Thanks! MIke White

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DOPE calculation for multiple models
by yalini.pathy＠yale.edu 28 Sep '06

28 Sep '06

Hi all, I am trying to calculate the DOPE energy terms for multiple models. I know very little about python and I'm not sure how to tell modeller to calculate the energy for *each* model. I've attached my script to this e-mail - it's the last 4 lines of the script that I'm having difficulties with. I'd be very grateful if someone could point me in the right direction please? Many thanks, Yalini -- Yalini Arinaminpathy, DPhil (Oxon) Department of Molecular Biophysics and Biochemistry Bass 426, 266 Whitney Avenue Yale University New Haven, CT 06520 (o): +1-203-432-8771 (f): +1-203-432-6946 (w): http://homes.gersteinlab.org/people/yalini/

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The number of sequences in CHAINS_all.seq
by Zhiqiang Ye 28 Sep '06

28 Sep '06

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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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