- modeller_usage - salilab.org

problem!
by Paola D'Alessio 15 Jun '01

15 Jun '01

Dear users, I am trying to produce a chimeric model for my protein. The first thing I want to do is to check the alignment I have. When I tell Modeller to execute the "check_alignment" command, I get the following message: rdpir___E> alignment sequence not found in PDB file: 1 ./pXXXX.pdb ####################################################################################################################################### The alignment I have is: >P1;pXXXX structureX:pXXXX:.::.::::: CKPMSNFRF-GENHAIMGVAFTWVMALACAAPPLVGWS--RYIPEGMQC-SCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTH--------QGSDFGPIFMTIPAFFAKTSAVYNPVIYIMM* >P1;pAveM structure:pAveM:2::211::::: -----------VRWAKLYSLVIWGCTLLLSSPMLV-----------------------------EVFTNMLLNVVGFLLPLSVITFCTMQ---------------------ERRATVLVLVVLLLFIICWLPFQISTFLDTL----------------VITQIASFMAYSNSCLNPLVYVIV* >P1;Ali2 sequence:Ali2:::::::: VKTMSMGRMRGVRWAKLYSLVIWGCTLLLSSPMLVFRTMKEYSDEGHNVTACVISYPSL---IWEVFTNMLLNVVGFLLPLSVITFCTMQIMQVLRNNEMQKFKEIQT---ERRATVLVLVVLLLFIICWLPFQISTFLDTLHRLGILSSCQDERIIDVITQIASFMAYSNSCLNPLVYVIV* ####################################################################################################################################### Perhaps, something is wrong with file names or PDB codes.(I stored the pdb files as pXXXX.pdb) Can somebody help me? Thank you very much, Paola -- dott. Paola D'Alessio (PhD student) Universita' degli Studi di Salerno Dipartimento Scienze Farmaceutiche via Ponte Don Melillo, 84084 Fisciano (Sa), Italy tel.+39 089 962822; e-mail: pdalessio(a)unisa.it

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Re: Modeling homotrimer
by Roberto Sanchez 13 Jun '01

13 Jun '01

Hi, You can have more than one pair of segments defined trough the DEFINE_SYMMETRY command, so you can restrict the three molecules to be identical by defining, for example, three pairs. If you have three monomers A, B, and C you would define pairs A-B, B-C, and C-A, that should make all three identical. The 'defsym' routine in the TOP file would look something like this (note the values for the ADD_SYMMETRY option): SUBROUTINE ROUTINE = 'defsym' SET RES_TYPES = 'ALL' SET ATOM_TYPES = 'MNCH' SET SELECTION_STATUS = 'INITIALIZE' SET SELECTION_SEARCH = 'SEGMENT' SET SYMMETRY_WEIGHT = 0.5 PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = '1:' '102:' PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = '103:' '204:' DEFINE_SYMMETRY ADD_SYMMETRY = on off PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = '103:' '204:' PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = '205:' '306:' DEFINE_SYMMETRY ADD_SYMMETRY = on off PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = '205:' '306:' PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = '1:' '102:' DEFINE_SYMMETRY ADD_SYMMETRY = on off RETURN END_SUBROUTINE I hope this helps. Best, Roberto -- Roberto Sanchez, Assistant Professor Structural Biology Program, Department of Physiology & Biophysics and Institute for Computational Biomedicine, Mount Sinai School of Medicine Box 1677, 1425 Madison Avenue, New York, NY 10029 phone +1 (212) 659 8648, fax +1 (212) 849 2456 http://physbio.mssm.edu/~sanchez/ > ------------------------------------------------------------------------ > > Subject: Modeling homotrimer > Date: Tue, 12 Jun 2001 15:09:54 +0200 > From: "KVA (Kim Vilbour Andersen)" <kva(a)maxygen.dk> > To: "'modeller_usage(a)salilab.org'" <modeller_usage@guitar> > > Hello Modeller users > > I'm trying to model a homotrimeric molecule. > > The template is a trimer with speudosymmetry making the three molecules > identical. > > I would like to include this pseudosymmetry in the model forcing the three > molecules to be identical. > > In the manual I found the DEFINE_SYMMETRY command, but this seems to me > mainly to be for dimers. > > Any ideas will be greatly appreciated > > Best regards > > Kim Vilbour Andersen > > ------------------------------------------------------------------------ > Kim Vilbour Andersen, PhD > Principal Scientist > Maxygen > Agern Allé 1 > DK-2970 Hørsholm > Denmark > > NB! Maxygen Denmark was previously known as ProFound Pharma A/S > > Tel: +45 7020 5550 > Direct: +45 4517 8473 > Fax: +45 7020 5530 > > E-mail: kva(a)maxygen.dk > http://www.maxygen.dk/ > ------------------------------------------------------------------------

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Modeling homotrimer
by KVA (Kim Vilbour Andersen) 12 Jun '01

12 Jun '01

Hello Modeller users I'm trying to model a homotrimeric molecule. The template is a trimer with speudosymmetry making the three molecules identical. I would like to include this pseudosymmetry in the model forcing the three molecules to be identical. In the manual I found the DEFINE_SYMMETRY command, but this seems to me mainly to be for dimers. Any ideas will be greatly appreciated Best regards Kim Vilbour Andersen ------------------------------------------------------------------------ Kim Vilbour Andersen, PhD Principal Scientist Maxygen Agern Allé 1 DK-2970 Hørsholm Denmark NB! Maxygen Denmark was previously known as ProFound Pharma A/S Tel: +45 7020 5550 Direct: +45 4517 8473 Fax: +45 7020 5530 E-mail: kva(a)maxygen.dk http://www.maxygen.dk/ ------------------------------------------------------------------------

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Re: COMPARE scripts
by Troy Wymore 01 Jun '01

01 Jun '01

Hello Eric and Modellers, Thanks to Eric Feyfant, my compare script now works. My main problem was that I needed to have the sequence of my model in the alignment file... could not just use the sequence for the actual structure. So after adding the sequence for my model and naming it something different than the actual xray structure code, which is already present and making a few minor changes, it works. Regards, Troy Wymore

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COMPARE scripts
by Troy Wymore 30 May '01

30 May '01

Hello Modellers, I have built a protein structure using MODELLER and would like to compare it with the actual crystal structure using the COMPARE routines. The MODELLER protein and XRAY protein have the same sequence but the MODELLER protein is numbered from 1-494 and the XRAY protein is numbered from 7-500 and contains multiple chains. So MODELLER complains: sequence difference between alignment and pdb compare_W> some residues are without DISTANCE_ATOMS[1] atom So is there something simple I can do to make this compare script work? I am thinking that I can delete the other chains and renumber the residues in the xray structure file to make it look similar to the MODELLER produced file but was hoping there was something easier to do. Any help would be much appreciated. Troy Wymore

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by Orbital casino 25 May '01

25 May '01

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HETATM
by Bessie 23 May '01

23 May '01

Dear users, I am having problem with adding heteroatoms to my model. My template is a dimer with each having one inhibitor and one cofactor. I use '.' for HETATM and 'w' for water molecule in my alignment file. But each time I run, the .log file told me there are " too many non-bonded pairs. Increase MPAIRS". What does it mean? What should I do? By the way, what should the comment line be with 2 chains and 4 HETATM and one H2O all together? The last several letters of the alignment file is: DHYRY/....w* Is it right? Best Bessie

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oligomers
by Dr Nicolas Le Novere 21 May '01

21 May '01

Dear modellers, My template is a homooligomer. I would like to model similar oligomers either with N times the same sequence, or with different homologous sequences. What is the best format for the alignment and/or top (How to force MODELLER to model the sequence X on the chain A and the sequence Y on the chaine B?) Regards, -- Dr Nicolas Le Novère http://www-alt.pasteur.fr/~lenov Dpt of Zoology, Univ of Cambridge, Downing street, Cambridge CB2 3EJ, UK tel: +44 1223 336623 fax: +44 1223 336676 e-mail: nl223(a)cus.cam.ac.uk

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can't get disulfides bonds
by Dr Nicolas Le Novere 21 May '01

21 May '01

Dear modellers, [modeller6a] My template contains two disulfides bonds, and the cysteines are conserved in the protein I want to model. Hence, PATCH_SS_TEMPLATE, automatically run by the routine 'model' is suppose to take care of the bonds. It doesn't. Hence my first question: How MODELLER detect SS bonds in templates: SSBOND in the HEADER or CONECT at the end of the PDB file? Then I decided to patch the disulfides manually with INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ALNFILE = 'a7ggmono2.ali' # alignment filename SET KNOWNS = 'mono2' # codes of the templates SET SEQUENCE = 'a7gg' # code of the target SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model # (determines how many models to calculate) CALL ROUTINE = 'model' # do homology modelling STOP SUBROUTINE ROUTINE = 'special_patches' PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '127' '141' PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '189' '190' RETURN END_SUBROUTINE It did not work either. Any ideas? -- Dr Nicolas Le Novère http://www-alt.pasteur.fr/~lenov Dpt of Zoology, Univ of Cambridge, Downing street, Cambridge CB2 3EJ, UK tel: +44 1223 336623 fax: +44 1223 336676 e-mail: nl223(a)cus.cam.ac.uk

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3d staff
by Joshua Bleeth 06 May '01

06 May '01

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