- modeller_usage - salilab.org

(no subject)
by bestkarollo 10 Oct '06

10 Oct '06

> Hello, > > I am new in modelller. I have a problem. > > 1) I made an alignmnet file in PIR format - below > > >P1;1AX8 > structureX:1AX8:3 : :146 : :LEPTIN:HUMAN: 2.4: 0.215 > IQKVQDDTKT LIKTIVTRIN DI-------- ------LDFI PGLHPILTLS > KMDQTLAVYQ QILTSMPSRN VIQISNDLEN LRDLLHVLAF SKSCHLPEAS > GLETLDSLGG VLEASGYSTE VVALSRLQGS LQDMLWQLDL SPGC* > > >P1;spP41160 > sequence:spP41160:::::::: > VPIQKVQDDT KTLIKTIVTR INDISHTQSV SAKQRVTGLD FIPGLHPILS > LSKMDQTLAV YQQVLTSLPS QNVLQIANDL ENLRDLLHLL AFSKSCSLPQ > TSGLQKPESL DGVLEASLYS TEVVALSRLQ GSLQDILQQL DVSPEC* > > > 2) PDB FILE - 1AX8 > > 3) I used automodel class - default script > > # Homology modelling by the automodel class > > from modeller.automodel import * # Load the automodel class > > log.verbose() # request verbose output > env = environ() # create a new MODELLER environment to build this model in > > # directories for input atom files > env.io.atom_files_directory = './:../atom_files' > > a = automodel(env, > alnfile = 'alignment2.ali', # alignment filename > knowns = '1AX8', # codes of the templates > sequence = 'spP41160') # code of the target > 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 the actual homology modelling > > > > 4) I am always having this same error > > Read the alignment from file : alignment2.ali > Total number of alignment positions: 146 > > # Code #_Res #_Segm PDB_code Name > ------------------------------------------------------------------------------- > 1 1AX8 145 1 1AX8 LEPTIN > 2 spP41160 161 1 spP41160 > runcmd______> alignment.check() > > check_a_343_> >> BEGINNING OF COMMAND > openf5__224_> Open 11 OLD SEQUENTIAL ../atom_files\1AX8.pdb > > Dynamically allocated memory at amaxstructure [B,kB,MB]: 2437705 2380.571 2.325 > openf5__224_> Open 11 OLD SEQUENTIAL ../atom_files\1AX8.pdb > rdabrk__291E> Sequence difference between alignment and pdb : > x (mismatch at alignment position 1) > Alignment IQKVQDDTKT LIKTIVTRIN DI LDFI PGLHPILTLS KMDQTLAVYQ QIL > PDB IQKVQDDTKTLIKTIVTRINDILDFIPGLHPILTLSKMDQTLAVYQQILTSMPSRN > Match * * * > Alignment residue (UNK) does not match pdb residue I (ILE), > for align code 1AX8 (atom file 1AX8), pdb residue number "3", chain " " > > Please check your alignment file header to be sure you correctly specified > the starting and ending residue numbers and chains. The alignment sequence > must match that from the atom file exactly. > > Another possibility is that some residues in the atom file are missing, > perhaps because they could not be resolved experimentally. (Note that Modeller > reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.) > In this case, simply replace the section of your alignment corresponding > to these missing residues with gaps. > rdabrk__288W> Protein not accepted: 1 1AX8 > check_a_337E> Structure not read in (please consult the log file > for more details): 1 1AX8 > > > 5) I don't know what I did wrong. I don't understand this explanation that I have a sequence difference between alignmnet and PDB - I checked - starting residues are these same ILE - ILE. > > > - alignment file and script are in the automodel folder > - PDB is in the atom_files folder > > > I will be very grateful for any help. > > Yours sincerely, > > Karol Kaszuba

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How to calculate amino acid similarity and identity
by James T Metz 05 Oct '06

05 Oct '06

Modeller Users Group, I have two protein sequences. They have already been aligned and the lengths are identical . I have a few gaps in the alignment. How do I calculate the percent similarity or percent identity between the two sequences. I know I need to use something like the BLOSUM50 or some other substitution matrix (for similarity). How exactly do I do the math so that I end up saying "protein A and protein B are 70 % similar and 40 % identical". Please note - I want to know how to do the math, step-by-step. I am not interested in using a computer program at this point, even if it is free, because I want to write my own code, once I understand how to do the math. I have looked in several books, looked all over the Internet, BioPERL, etc, but I can not find a clear step-by-step explanation of how to do the math. I would be most grateful if someone knowledgeable could explain this. Thank you, Jim Metz James T. Metz, Ph.D. Research Investigator Chemist GPRD R46Y AP10-2 Abbott Laboratories 100 Abbott Park Road Abbott Park, IL 60064-6100 U.S.A. Office (847) 936 - 0441 FAX (847) 935 - 0548 james.metz(a)abbott.com This communication may contain information that is legally privileged, confidential, or exempt from disclosure. If you are not the intended recipient, please note that any dissemination, distribution, use, or copying of this communication is strictly prohibited. Anyone who receives this message in error should notify the sender immediately by telephone or return email and delete it from his or her computer.

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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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Protein not accepted
by Giacomo Bastianelli 02 Oct '06

02 Oct '06

I had to do an automodelling of a protein based on a template. I first ran the seqcheck and use the sequences that I got for the alignment (using tcoffee). I prepared the alignment file as follow: >P1;1GNS sequence:1GNS: 4 :A: 275 :A:undefined:undefined:-1.00:-1.00 GPYGVSQIKAP-ALHSQGYTGSNVKVAVIDSGID------SSHPALKVAGGASFVPSETN PFQDNNSHGTHVAGTVLA-------VAPSASLYAVKVLGADGS--GQYSWIINGIEWAIA NNMDVINMSLGGPSGSAALKAA---VDKAVASGVVVVAAAGNEGTSGSSSTVGYPGKYPS VIAVGAV-----------DSSNQRASFSSVGP------ELDVMAPGVSIWSTL------- -----PGNKYGAKSGT-MASPHVAGAAALI------------------------------ -------------LSKHPNWTNTQVRSSLE------------------------------ -----------------NTTTKLGDSFYYG--------------------KGLINVEAAA ---------------Q* >P1;1WMD structureX:1WMD: 1 :A: 434 :A:undefined:undefined:-1.00:-1.00 NDVARGIVKADVAQSSYGLYGQGQIVAVADTGLDTGRNDSSMHEAFRGKITALYALGRTN NANDTNGHGTHVAGSVLGNGSTNKGMAPQANLVFQSIMDSGGGLGGLPSNLQTLFSQAYS AGARIHTNSWGAAVNGAYTTDSRNVDDYVRKNDMTILFAAGNEGPNGG--TISAPGTAKN AITVGATENLRPSFGSYADNINHVAQFSSRGPTKDGRIKPDVMAPGTFILSARSSLAPDS SFWANHDSKYAYMGGTSMATPIVAGNVAQLREHFVKNRGITPKPSLLKAALIAGAADIGL GYPNGNQGWGRVTLDKSLNVAYVNESSSLSTSQKATYSFTATAGKPLKISLVWSDAPAST TASVTLVNDLDLVITAPNGTQYVGNDFTSPYNDNWDGRNNVENVFINAPQSGTYTIEVQA YNVPVGPQTFSLAIVN* this is my script for the automodelling: # Homology modelling by the automodel class from modeller.automodel import * # Load the automodel class log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = './:../home/Bis/gbastian/Documents/Data/ExcerciseModeling/SUBTILISIN BPN/Structure files/' a = automodel(env, alnfile = 'alignedsequences.ali', # alignment filename knowns = '1WMD', # codes of the templates sequence = '1GNS') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 10 # index of the last model # (determines how many models to calculate) a.make() # do the actual homology modelling and this is what I got after running it: openf5__224_> Open 11 OLD SEQUENTIAL $(LIB)/restyp.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/resdih.lib rdrdih__263_> Number of dihedral angle types : 9 Maximal number of dihedral angle optima: 3 Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/radii.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/radii14.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/mnch1.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/mnch2.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/mnch3.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 runcmd______> alignment.append(align_codes=['1WMD', '1GNS'], atom_files=[], file='alignedsequences.ali', (def)remove_gaps=True, (def)alignment_format='PIR', add_sequence=True, (def)rewind_file=False, (def)close_file=True) openf___224_> Open alignedsequences.ali Dynamically allocated memory at amaxalignment [B,kB,MB]: 2270569 2217.353 2.165 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2293501 2239.747 2.187 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2316901 2262.599 2.210 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2363701 2308.302 2.254 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2457301 2399.708 2.343 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2644501 2582.521 2.522 Read the alignment from file : alignedsequences.ali Total number of alignment positions: 436 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1WMD 434 1 1WMD undefined 2 1GNS 262 1 1GNS undefined runcmd______> alignment.check() check_a_343_> >> BEGINNING OF COMMAND pdbnam__217W> Filename for PDB code not found: 1WMD Directories: ./:../home/Bis/gbastian/Documents/Data/ExcerciseModeling/SUBTILISIN BPN/Structure files/ Extensions : :.atm:.pdb:.ent:.crd rdabrk__288W> Protein not accepted: 1 1WMD check_a_337E> Structure not read in (please consult the log file for more details): 1 1WMD What's wrong with my PDB?? I checked the name reference and they are all right. Thanks a lot Giacomo

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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/

2 1

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

28 Sep '06

2 2

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

1 0

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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