June 2001 - modeller_usage

Error using MALIGN3D
by Michael Buck 24 Jan '02

24 Jan '02

MALIGN3D Top files which worked well using Modeler 4 are giving me this error : fndatmi_284E> Beginning atom index for a residue out of bounds: 0 0 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 I am using the following script # MALIGN3D READ_ALIGNMENT FILE = 'pair.aa' SET ATOM_FILES = '1.pdb' '2.pdb' SET FIT_ATOMS = 'CA' MALIGN3D GAP_PENALTIES_3D= 0 2.0, WRITE_FIT = on, WRITE_WHOLE_PDB = off If anybody has seen this problem, please help. Thank you Michael Buck ************************************************ Michael Buck NCSU Genetics mjbuck(a)unity.ncsu.edu Phone (919)515-5759 Fax (919)515-3355 http://www4.ncsu.edu/~mjbuck *************************************************

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H Bond between GLU OE1 and ASP OD2
by Dr Nicolas Le Novere 27 Jun '01

27 Jun '01

Dear users, In a model I got with MODELLER, there is a potential hydrogen bond between oxygens of a glutamate and an aspartate (or the respective acids). However there is supposedly an important electrostatic repulsion. In the template the aspartate is replaced by a glycine. There is room for several of the glutamate conformers. Is it normal that MODELLER made the choice to keep the original conformer of the glutamate even with the unfavourable electrostatic environment? 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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Installation on Octane, problem solved
by Adam Zabell 22 Jun '01

22 Jun '01

Hi all, The problem in a nutshell was that I was trying to use pipes to run modeller: mod4 < inputfile > outputfile and the executable script 'mod4' didn't like it. So if I drop the user- supplied pipes when running the program: mod4 inputfile then it worked fine. Thanks to both Eric and Oliver for their help in pointing me in the right direction! Adam Zabell

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Installation on Octane
by Adam Zabell 21 Jun '01

21 Jun '01

Hi all! I'm in the process of installing modeller for use on an Octane R12000, and although the automated process says that it's worked, I get a file called 'mod.log' instead of my expected output file which contains the normal modeller header information and the following message: MODELLER is compiled in : single precision Job starting time : 21-Jun-01 12:42:18 ipdbnam_W> environment variable PDBENT undefined fullfn__E> file not found: mod directories : :/scratch/modeller4/bin/ extensions : .top: prefixes : nothing, pdb I'm not at all sure why it's looking for the PDBENT variable since I never defined the PDB variable in my .cshrc file. I get this error message using either the mod_r10000-IRIX6.5-1300_40 or the mod_iris4d-IRIX5.3 exectuable file. Any help would be greatly appreciated. Thanks, Adam Zabell, PhD Walther Research Fellow Purdue University/University of Notre Dame

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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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