- modeller_usage - salilab.org

Report of final energy
by 서주현 14 Mar '06

14 Mar '06

2 1

Dope Vs PROSA2003
by jo hanna 14 Mar '06

14 Mar '06

Hi If am trying to model loops within my protein model that seem to correspond to regions of high energy in both DOPE and PROSA analysis. why should it be that aftre modelling the loop with a lower DOPE energy shoud actaully increase in the region of loop modelling with reference to the original model and PROSA analysis? Any advice much appreciated Do people generally prefer DOPE or use PROSA and DOPE to complement each other? Thanks Jo

1 0

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

2 1

File name control problem
by 서주현 13 Mar '06

13 Mar '06

2 1

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.

1 0

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

2 2

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

1 0

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

2 1

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

2 1

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 ****************************************************

2 1