March 2006 - modeller_usage

any .log indication of .md_level results?
by Mark Daniels 13 Mar '06

13 Mar '06

Hello all- Is there any way in which one can generate output from, or verify the running of, the .md_level routine in Modeller8v2? I do not see any indication in the .log that a molecular dynamics simulated- annealing routine was applied to any model generated when I specify " automodel.md_level = refine.very_fast ". thanks in advance- Mark

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File name control problem
by 서주현 13 Mar '06

13 Mar '06

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Sequence consensus
by Cassiano 13 Mar '06

13 Mar '06

Hi everybody! I have a question about sequence alignment (i known that it isn't the subject of this forum, but i'll be very glad for any help). From a alignment, i intend to extract the consensus sequence differently. I keep only the aa that are really conserved (and probably structurally important). The others, I substituted by the aa G (for example: GGGDGGGRKGGGHEGG, where the aa D,R,K,H and E are very conserved in the protein's alignment). My aim is to modeler the consensus folding to the classes of protein in my study, emphasizing only the functionally important aa. I don't known if I really have a useful structural information or not. If not, i'll be very glad for any advice. Thanks, Cassiano Carromeu.

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model.mutate problem
by Zhiqiang Ye 12 Mar '06

12 Mar '06

Hi, all I have a homodimer protein structure, it has two chains: A and B, both of whcih start from 2. I want to get the structure of the mutant K2S. So I modified the provided example: mutate_model.py to do this job, the mainly modified part is: (I want to mutate both chains) mdl.pick_atoms(aln, selection_segment=("2:A", "2:A"), selection_status='INITIALIZE', selection_search='SEGMENT', selection_from='ALL') mdl.pick_atoms(aln, selection_segment=("2:B", "2:B"), selection_status='ADD', selection_search='SEGMENT', selection_from='ALL') But in the output model, the two chains are connected as one single chain, and the residue number has changed start from 1, but I want the mutant keep the original chain ID and number. How can I get this kind of results? Thank you very much! Regards! -- Zhiqiang Ye PHD candidate

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Loop
by BiplabBose＠bits-pilani.ac.in 11 Mar '06

11 Mar '06

Hi I have modeled a dimeric protein using Modeller. Now I want to discard a small loop (~8-9 amino acids) of this initial model and want to model that region using some other PDB file. Is it possible by Modeller? I hope, yes. But how? Expecting your help With regards Biplab BITS, Pilani

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using BLAST to find templates for modelling
by Nick Fusseder 09 Mar '06

09 Mar '06

Hi all, I have been dwelling over the following problems and simply do not know how to continue. Any help would be greatly appreciated. My scenario: I am running a BLAST search against PDB sequences in order to find suitable templates to model my target protein. I have all PDB structures locally installed and the atom_files variable pointing to this directory in my .py scripts. I basically have 2 questions: 1. From what I understand the modlib/CHAINS_all.seq is used to store the sequences for the PDB structures. Now if I want to use a novel PDB structure as a template which is not included in this list, will I have to manually create the chain sequence in PIR format (with commands/make_chains.py) and append it to the modlib/CHAINS_all.seq file? ALso is there a way to create a CHAIN_all.seq file from all PDB structure files in one go? 2. Since I am already running a BLAST search to find my template structures, I won't be using search.py. In order to create the .ali alignment file which is neccessary for the computation of the final structure prediction of my target sequence, i will need to run malign.py. The problem is, malign takes a .seg file as input. I have not yet found an automated method to generate such a .seg file from a target sequence and template structures found by BLAST. Will I have to create the .seg file manually? Maybe I am just missing the point and the solution to all my problems is in fact really easy. I guess my main problem boils down to which files can be created by modeller for me and which files need to be generated or edited by hand. I would greatly appreciate any help. Regards, nick -- Echte DSL-Flatrate dauerhaft f�r 0,- Euro*! "Feel free" mit GMX DSL! http://www.gmx.net/de/go/dsl

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Advice on Modeller usage
by Nagesh Chakka 06 Mar '06

06 Mar '06

Hi, I am trying to use Modeller to obtain a model using the structure 1XU0. I have created the three files needed for Modeller Atom file http://www.rcsb.org/pdb/navbarsearch.do?newSearch=yes&isAuthorSearch=no&rad… Alignment file >P1;1XU0 structureX:1XU0:125:A:226:A:::: IGGYMLGNAVGRMSYQFNNPMESRYYNDYYNQMPNRVYRPMYRGEEYVSEDRFVRDCYNM SVTEYIIKPAEGKNNSELNQLDTTVKSQIIREMCITEYRRGS * >P1;XlPrP2 sequence:XlPrP2:1::134::::: IGGYMLGNAVGRMNHHFDNPMESRYYNDYYNQMPDRVYRPMYRSEEYVSEDRFVTDCYNM SVTEYIIKPSEGKNGSDVNQLDTVVKSKIIREMCITEYRRGS Top file INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 1 SET ALNFILE = 'inputAlignment_files/prp2StructAli.txt' SET KNOWNS = '1XU0' SET SEQUENCE = 'XlPrP2' SET ATOM_FILES_DIRECTORY = '/home/nagesh/modelling/structure' SET STARTING_MODEL = 1 SET ENDING_MODEL = 4 CALL ROUTINE = 'model' In doing so, the final model XlPrP2.B99990004 does not contain all the atoms for a particular residue. For example, the following is the part of the model for one amino acid ATOM 1 N ILE 1 14.910 4.779 7.839 1.00 41.08 1SG 2 ATOM 2 CA ILE 1 13.848 4.061 8.581 1.00 41.08 1SG 3 ATOM 3 CB ILE 1 12.918 3.371 7.630 1.00 41.08 1SG 4 ATOM 4 CG2 ILE 1 11.924 2.529 8.447 1.00 41.08 1SG 5 ATOM 5 CG1 ILE 1 12.242 4.416 6.730 1.00 41.08 1SG 6 ATOM 6 CD1 ILE 1 11.473 3.813 5.557 1.00 41.08 1SG 7 ATOM 7 C ILE 1 14.422 3.050 9.510 1.00 41.08 1SG 8 ATOM 8 O ILE 1 15.261 2.235 9.128 1.00 41.08 1SG 9 Atoms from the structure file ATOM 1 N ILE A 125 15.197 -5.772 -0.208 1.00 0.00 N ATOM 2 CA ILE A 125 14.432 -5.479 0.993 1.00 0.00 C ATOM 3 C ILE A 125 14.890 -6.453 2.086 1.00 0.00 C ATOM 4 O ILE A 125 14.874 -7.667 1.884 1.00 0.00 O ATOM 5 CB ILE A 125 12.922 -5.586 0.661 1.00 0.00 C ATOM 6 CG1 ILE A 125 12.526 -4.523 -0.390 1.00 0.00 C ATOM 7 CG2 ILE A 125 12.073 -5.416 1.930 1.00 0.00 C ATOM 8 CD1 ILE A 125 11.131 -4.703 -1.000 1.00 0.00 C ATOM 9 H ILE A 125 14.783 -6.386 -0.892 1.00 0.00 H ATOM 10 HA ILE A 125 14.656 -4.459 1.305 1.00 0.00 H ATOM 11 HB ILE A 125 12.723 -6.575 0.246 1.00 0.00 H ATOM 12 1HG1 ILE A 125 12.591 -3.543 0.075 1.00 0.00 H ATOM 13 2HG1 ILE A 125 13.228 -4.540 -1.223 1.00 0.00 H ATOM 14 1HG2 ILE A 125 12.338 -4.494 2.447 1.00 0.00 H ATOM 15 2HG2 ILE A 125 11.014 -5.400 1.691 1.00 0.00 H ATOM 16 3HG2 ILE A 125 12.237 -6.268 2.586 1.00 0.00 H ATOM 17 1HD1 ILE A 125 10.989 -3.972 -1.797 1.00 0.00 H ATOM 18 2HD1 ILE A 125 11.032 -5.707 -1.414 1.00 0.00 H ATOM 19 3HD1 ILE A 125 10.362 -4.542 -0.250 1.00 0.00 H What is the reason for the loss of the atoms and how can I fix this. Thank you very much in advance Nagesh

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symmetry on mod8v2 - part 2
by Giovanni Grazioso 03 Mar '06

03 Mar '06

Thanks for your last reply, now the script (concerning the symmetry models) works well but after a few minutes the calculation ends with the following message on the log file: << end of ENERGY. runcmd______> restraints.make((def)residue_span_range=(0, 99999), (def)residue_grouping=1, restraint_type='stereo', (def)restraint_sel_atoms=1, (def)restraint_group=26, (def)basis_pdf_weight='LOCAL', (def)distance_rsr_model=1, (def)maximal_distance=999.0, (def)basis_relative_weight=0.050000000000000003, spline_on_site=False, (def)residue_span_sign=True, (def)intersegment=True, add_restraints=True, (def)dih_lib_only=False, (def)spline_dx=0.5, (def)spline_min_points=5, (def)spline_range=4.0, (def)mnch_lib=1, (def)accessibility_type=8, (def)restraint_stdev=(0.0, 1.0), (def)restraint_stdev2=(0.0, 0.0, 0.0), (def)sheet_h_bonds=7, (def)surftyp=1, (def)restraint_parameters=(3, 1, 3, 3, 4, 2, 0, 0.0, 0.086999999999999994), (def)distance_atoms=('CA', 'CA'), (def)atom_ids=('',), (def)residue_ids='') make_re_417_> Restraint type to be calculated: stereo r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 1810 2472 2851 788 Total number of restraints before, now : 0 7921 make_re_422_> Number of previous, current restraints : 0 7921 make_re_423_> Number of previous, current selected restraints: 0 7921 runcmd______> model.randomize_xyz(deviation=3.0) randomi_498_> Atoms,selected atoms,random_seed,amplitude: 1757 1757 1 3.0000 randomi_496_> Amplitude is > 0; randomization is done. runcmd______> model.optimize(optimization_method=1, (def)init_velocities=True, (def)temperature=293.0, (def)md_time_step=4.0, (def)min_atom_shift=0.01, (def)cap_atom_shift=0.20000000000000001, (def)write_all_atoms=True, (def)no_ter=False, (def)trace_output=0, (def)equilibrate=999999, max_iterations=300, (def)residue_span_range=(0, 99999), md_return='FINAL', output='REPORT', (def)id2=1, (def)root_name='undf', (def)file_id='default', (def)file_ext='', (def)output_directory='') pair2___215E> Dynamic memory allocation failed. Routine, variable, status: icat1 Mod8v2 generates the: .ini define_symmetry-1.atm define_symmetry-2.atm .pdb files. When mod8v2 was released I used it but the result does not changed. Where is the trouble? I attached here my new2.py. I'm building a model of a homopentamer with 1055 amino acids, is it too big for the software requirements? Thanks in advance. Giovanni **************************************************** Dr. Giovanni GRAZIOSO Istituto di Chimica Farmaceutica e Tossicologica Viale Abruzzi, 42 - 20131 Milano (Italy) Phone: 02/50317570 Fax: 02/50317565 e-mail: giovanni.grazioso(a)unimi.it Web site: http://users.unimi.it/demicheli/gg1.htm ****************************************************

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SET DEVIATION
by Adam C Marko 02 Mar '06

02 Mar '06

Hello all, I am using modeller 8v1 and trying to build a set of models that all differ from one another. I cannot figure out the equivalent command in 8v1 to the command: 'SET DEVIATION = 4.0 # Amount of randomization between models' in 6v2. Thank you for your help, Adam Adam C. Marko National Resource for Biomedical Supercomputing Pittsburgh Supercomputing Center Pittsburgh, PA 15213 www.psc.edu/~marko

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nselat__596E> Atom index is out of range (iatm, natm)
by MGiò 01 Mar '06

01 Mar '06

Hi! I'm trying and model a 7-helix trans-membrane receptor, as I don't like the way MODELLER models my helices, while I highly appreciate its loop modelling, I've been using the "model-myini.py" input script to model my receptor starting from a initial.pdb containing the 7 helices already modelled. Every MODELLER run ends with the "nselat__596E> Atom index is out of range" error. Considering that this error changes the couple of atoms referring to any time I delete the corresponding residue in order to by-pass the error. I've attached to the mail the input files I used and the log file. Can you help me? best regards, MG

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