- modeller_usage - salilab.org

error message
by Madhan Kumar A 27 Jun '06

27 Jun '06

Sir(s), While trying to model my protein using Modeller 8v2, I encounter the following error message in the log file: * Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 2) = ted * I have checked the ALI and ATM files. Everything seems to be alright. Pls let me know what the problem could be. Thanking you in advance. Madhan Kumar *My alignment file:* >P1;1ABC structureX:1ABC:2 :O:231 :O:::: GGSDGLQDVTIMNQDQEQIIFAFPPVLGYGLMYQNLSSRLPS-YKLCAFDFIEE-EDRLDRYADLIQKLQPEGPLTLFGYSAGCSLAFEAAKKLEGQGRIVQRIIMVDSYKKQGVSDLDGRTVESDVEALMNVNRDNEALNSEAVKHGLKQKTHAFYSYYVNLISTGQVKADIDLLTSGADFDIPEWLASWEEATTGAYRMKRGFGTHAEMLQGETLDRNAGILLEFLNTQT* >P1;ted sequence:ted: :: ::::: ------------------PVFVFHPAGGSTVVYEPLLGRLPADTPMYGFERVEGSIEERAQQYVPKLIEMQGDGPYVLVGWSLGGVLAYACAIGLRRLGKDVRFVGLIDAVRAG-----------------------------------------------------------------------------------------------------------------------* *My script file:* # 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 = '' a = automodel(env, alnfile = 'align_ted.ali', # alignment filename knowns = '1ABC', # codes of the templates sequence = 'ted') # 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 *Log file:* ** 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=['1ABC', 'ted'], atom_files=[], file='align_ted.ali', (def)remove_gaps=True, (def)alignment_format='PIR', add_sequence=True, (def)rewind_file=False, (def)close_file=True) openf___224_> Open align_ted.ali Dynamically allocated memory at amaxalignment [B,kB,MB]: 2124923 2075.120 2.026 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2126623 2076.780 2.028 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2130023 2080.101 2.031 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2136823 2086.741 2.038 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2147161 2096.837 2.048 read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 2) = ted

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question about multiple alignment tutorial
by Mike White 20 Jun '06

20 Jun '06

I have a question about the example script salign.py in the Advanced tutorial for version 8v2. I understand the logic of the script where salign is called three successive times incorporating more information each time in the form of the "weights" parameter, and one sees increase in alignment quality with each cycle. However, I am unclear of the purpose of the last call to salign after the alignment files are written. The tutorial text says that the last call is to generate a quality score, but after examining the log file the quality of the alignment after this call is worse than after the first three calls. I noticed that the rms_cutoff for the first three calls is 3.5, while that for the final call is 1.0 (presumably more stringent), and that the alignment type is "progressive" rather than "tree." Since the alignment files are already written, and this is what is used in the alignment with the sequenced to be modeled, why is this last step run? As usual, thanks for all of your help Mike White

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Restraints to apply for nucleic acid
by Charlotte Habegger-Polomat 20 Jun '06

20 Jun '06

Hello! Modeller has been quite successful at modelling my protein of interest and I am very happy with the results. I am now using Modeller to model my protein in complex with a nucelic acid (tNRA), as there is a homolog complex of known structure. The family of models I obtained is quite good but the nucleic acid seems a little out of shape. It looks like some of the base pairing and/or stacking has been lost. I have been thinking of adding restraints to the modelling process. Do you have any ideas on the best type of restraints to use (H-bonds, distance, etc.)? Thanks! -Charlotte Habegger-Polomat, Quebec

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Using template's ligand as model's ligand
by Frederico Arnoldi 19 Jun '06

19 Jun '06

Dear Modeller's users, Could I superimpose the template and the best model of this template and use the template's ligand as model's ligand? Which are the theorical problem of doing it if I used Modeller to build the model? How precise is it? Thanks for the help. Fred UNESP - Brazil

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homomultimers and symmetry
by Mike White 19 Jun '06

19 Jun '06

Hi there, I am new to hands-on experience with Modeller. I would like to create a homology model of the protein that I am interested in as a homopentamer, using known homopentamer X-ray structures of related proteins. I have run across several questions in the archives about imposing symmetry constraints in the modeling process. Is it necessary to impose such constraints if the template is already a homopentamer with 5-fold symmetry? Doesn't this by itself impose symmetry constraints? Or, is it possible that an energy-minimized structure based on a symmetric template may not retain all of the symmetry of the template and the symmetry restraints make sure that the original symmetry is forced to be retained? Finally, since model.symmetry.define() deals with pairs, does one enforce pentameric symmetry in the complex by forcing AB, BC, CD, DE, and EA symmetry, where A-E are the five individual subunits in the homopentamer? Thanks Mike White

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Questions on loop modelling
by hori koshii 16 Jun '06

16 Jun '06

My target sequence has two insertions at 2 loop regions (14aa, 9aa) when compare to my template structure. I have three questions: 1. Since 12aa is the limit of loop modelling, is that viable to build a "model" with the "template sequence plus 2 aa of the "target" insertion, then use this "template +2aa" model as template for building the model of the target???? 2. The residues flanking the insertions also belong to the loop regions (of the template), so, my question is, when we do loop modelling, do we need to model the whole piece of loop for accuracy?? 3. When we generate loop models, do you model one loop and then the other? Since I have two loop regions, I wonder if I should build (~500) models for one regions and then another set for the other region? Does one loop region actually affect the conformation of the other loop? Do you think it's necessary to build them both at the same time? Thank you very much for answering the questions. Have a great day. Sincerely, Jasmine --------------------------------- Do you Yahoo!? Next-gen email? Have it all with the all-new Yahoo! Mail Beta.

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alignment using multiple templates
by Mike White 15 Jun '06

15 Jun '06

HI there, I am working my way through the tutorials, playing with the Python scripts to get a better understanding of how things work. I have successfully done a multiple structural alignment using a modified version of the salign.py script in the advanced tutorial aligning multiple sequences for a protein from several different species using the pdb files as input. The protein is a homopentamer, and using the example script, I aligned the "A" chains and everything worked fine. Since I really want to work on modeling a homopentamer, I then tried to do the alignment on the pentamers. I receive the following error: ************************************************************************* linux:/home/mike/Modeller_files/Modelling_projects/Test_run/Mult_align # mod8v2 salignPentamer.py Traceback (most recent call last): File "salignPentamer.py", line 11, in ? mdl = model(env, file=code, model_segment=('FIRST:@, LAST:')) File "/usr/bin/modeller8v2/modlib/modeller/model.py", line 23, in __init__ self.read(io, aln, libs, **vars) File "/usr/bin/modeller8v2/modlib/modeller/model.py", line 40, in read io=io.modpt, libs=libs.modpt, **vars) File "/usr/bin/modeller8v2/modlib/modeller/util/top.py", line 189, in read_model return _modeller.read_model(mdl, aln, io, libs, *args) ValueError: Expected a sequence for model_segment ************************************************************************* I assume that the problem is in reading the pdb files and getting the information.The pdb files do contain the chain ID's (A-E). Here is the Python script I used, which is essentially a slightly modified version of the example script: ********************************************************************* from modeller import * log.verbose() env = environ() env.io.atom_files_directory = './:../atom_files/' aln = alignment(env) for (code, chain) in (('1i9b', 'A'), ('2br7', 'A'), ('2bj0', 'A')): mdl = model(env, file=code, model_segment=('FIRST:@, LAST:')) 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='$(LIB)/as1.sim.mat', overhang=30, gap_penalties_1d=(-450, -50), gap_penalties_3d=(0, 3), gap_gap_score=0, gap_residue_score=0, dendrogram_file='fm00495.tree', alignment_type='tree', # If 'progresive', the tree is not # computed and all structues will be # aligned sequentially to the first feature_weights=weights, # For a multiple sequence alignment only # the first feature needs to be non-zero improve_alignment=True, fit=True, write_fit=write_fit, write_whole_pdb=whole, output='ALIGNMENT QUALITY') aln.write(file='achbpsPentamer.pap', alignment_format='PAP') aln.write(file='achbpsPentamer.ali', alignment_format='PIR') aln.salign(rms_cutoffs=(1.0, 6., 60, 60, 15, 60, 60, 60, 60, 60, 60), normalize_pp_scores=False, rr_file='$(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') ********************************************************************************** the only change that I made from the script that worked on the single subunits was to change the "model_segment" parameters from "('FIRST:'+chain, 'LAST:'+chain)" to "('FIRST:@, LAST:'))". I couldn't find anything in the Online manual concerning the arguments on the line before (for (code,chain) in.....)- should I have replaced chain "A" with something else to read the entire set of chains? Thanks for whatever help you can provide. I am sure that as I get deeper into things that I'll have more questions- hopefully not so basic. Mike White

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Modeling a Chimera
by Toty Santos 14 Jun '06

14 Jun '06

Hi dears, I am a starting model buiter and i´d like to know how i can make a model like this : I have a bifuncional enzime with two domains. But in the PDB i have as a model different structures : One for domain A and other to domain B. And i´d like to build a model with this two domains together. It is not a dimer, it a single enzime with two diferente domains. And i´d like to know tto, what i will do with the linker resudues between this both domains !! I anybody can help me, please be detalist cause i am a start user i am using Modeller 8v0 thanks a Lot Marcos Tadeu dos Santos Undergratuated Student UNICAMP - BRAZIL _________________________________________________________________ COPA 2006: (¯`·._.·[ Ooooooola ]·._.·´¯) e + frases para seu MSN Clique aqui! http://copa.br.msn.com/extra/frases/

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rdpir___648E> Alignment sequence not found in PDB file
by Michael Mazanetz 14 Jun '06

14 Jun '06

Dear MODELLER users, I get this error message " rdpir___648E> Alignment sequence not found in PDB file: 1 ../atom_files\1ba4.pdb " in my log file when I try and run a homology model. When I reduce the number of residues in the sequence to just four the model runs OK. What is wrong, can anyone suggest anything?? I've enclosed my files :screen output, B04_2742_111_002.ali, Loop-005.py and Loop-005.log And the -v command always gives an error too?? regards and thanks in advance. Mike The screen output is: C:\Program Files\Modeller8v2\examples\automodel>mod8v2 loop-005.py -v 'import site' failed; use -v for traceback Traceback (most recent call last): File "loop-005.py", line 24, in ? a.make() # do the actual homology modelling File "C:\Program Files\Modeller8v2\modlib\modeller\automodel\loopmodel.py", line 28, in make automodel.make(self, exit_stage) File "C:\Program Files\Modeller8v2\modlib\modeller\automodel\automodel.py", line 100, in make self.homcsr(exit_stage) File "C:\Program Files\Modeller8v2\modlib\modeller\automodel\automodel.py", line 318, in homcsr aln = self.read_alignment() File "C:\Program Files\Modeller8v2\modlib\modeller\automodel\automodel.py", line 312, in read_alignment aln.append(file=self.alnfile, align_codes=self.knowns+[self.sequence]) File "C:\Program Files\Modeller8v2\modlib\modeller\alignment.py", line 36, in append return self.__int_append('alignment.append', io, libs, vars) File "C:\Program Files\Modeller8v2\modlib\modeller\alignment.py", line 68, in__int_append libs=libs.modpt, **vars) File "C:\Program Files\Modeller8v2\modlib\modeller\util\top.py", line 33, in read_alignment return _modeller.read_alignment(aln, io, libs, *args) _modeller.error: rdpir___648E> Alignment sequence not found in PDB file:1 ../atom_files\1ba4.pdb B04_2742_111_002.ali file >P1;1ba4 structureX:1ba4:.:.:.:.: MENFQKVEKI GEGTYGVVYK ARNKLTGEVV ALKKIRXDTE TEGVPSTAIR EISLLKELNH PNIVKLLDVI HTENKLYLVF EFLHQDLKKF MDAS------* >P1;1M8Qb structureX:1M8Qb:.:.:.:.: ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ----KQPRQY* >P1;1bb2 sequence:1ba2:.:.:.:. MEDYTKIEKI GEGTYGVVYK GRHKTTGQVV AMKKIRLESE EEGVPSTAIR EISLLKELRH PNIVSLQDVL MQDSRLYLIF EFLSMDLKKY LD-SIPPGQY* Loop-005.py file # 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 = loopmodel(env, alnfile = 'B04_2742_111_002.ali', # alignment filename knowns = ('1ba4','1M8Qb'), # codes of the templates sequence = '1ba2') # 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.md_level = None # No refinement of model a.loop.starting_model = 1 # First loop model a.loop.ending_model = 1 # Last loop model a.loop.md_level = refine.fast # Loop model refinement level a.make() # do the actual homology modelling Loop-005.log file rdpir___648E> Alignment sequence not found in PDB file: 1 ../atom_files\1ba4.pdb This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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Modeling a Chimera
by Toty Santos 14 Jun '06

14 Jun '06

Hi dears, I am a starting model buiter and i´d like to know how i can make a model like this : I have a bifuncional enzime with two domains. But in the PDB i have as a model different structures : One for domain A and other to domain B. And i´d like to build a model with this two domains together. It is not a dimer, it a single enzime with two diferente domains. And i´d like to know tto, what i will do with the linker resudues between this both domains !! I anybody can help me, please be detalist cause i am a start user i am using Modeller 8v0 thanks a Lot Marcos Tadeu dos Santos Undergratuated Student UNICAMP - BRAZIL _________________________________________________________________ Você sabe em qual Copa o Pelé vestiu a camisa 10 pela 1a. vez? http://copa.br.msn.com/extra/curiosidades/1958/

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