February 2000 - 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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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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by netspirit＠asean-export.com 19 Feb '00

19 Feb '00

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MAXSPL ???
by Aldo Jongejan 18 Feb '00

18 Feb '00

Hi All, I encountered a problem using 10 template structures to model a long loop structure. The alignment is very minimal, so maybe I should break it down in smaller parts. Modeller checks the alignment and suggest setting the 'MAXSPL' value to a bigger (?) value. What is this MAXSPL value and how can I set this? I thought it had something to do with the SPLINE's setting, so I turned SPLINE_ON_SITE off. This resulted in a 'repetition: incomprehensible list input' error. What does this mean? And, most important' how can I prevent this from happening ! :-) thnaks, aldo jongejan

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None
by Prevost Martine 16 Feb '00

16 Feb '00

Hello, I would like to introduce a restrained distance between two atoms when generating a model with Modeller. Unfortunately when the two atoms for which I would like to retrain the distance are specified in my top file, the program seems to interpret this as all atoms between these two are concerned by possible restraints ?? I believe that when one wants to introduce restraints from NMR data that's what one wishes to do, i.e. specify pairs of atoms (one or many more) for which the distance should be within a certain range. Could somebody explain to me how the Modeller input should be modified so as to introduce such restraints ? Thank you very much. Martine. -------------------------------------------- Martine Prevost Ingenierie Biomoleculaire, CP 165/64 Universite Libre de Bruxelles 50 avenue Franklin Roosevelt B-1050 Bruxelles Belgium Phone : 32-2-650 2049 Fax : 32-2-650 3606 E-mail: mprevost(a)ulb.ac.be --------------------------------------------

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Thanks for the clarification of versions...
by T. .R. Dafforn 01 Feb '00

01 Feb '00

Dear all Thanks for the clarifcation.. However I still seem to be having core dump problems which seem to be linked to a memory problem.. I have about 100Mb of memory and a Virtual Swap of 1Gb... But still it dies... andy Ideas? cheers Tim -- Tim Dafforn Structural Medicine Department of Haematology CIMR University of Cambridge Wellcome-MRC Building (Level6) Hills Road Cambridge CB2 2XY Tel. (01223) 336829 Fax. (01223) 336827 http://smokeroom.cimr.cam.ac.uk/

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Confused about versions!
by T. .R. Dafforn 01 Feb '00

01 Feb '00

Sorry all, The header line on the modeller output i have reads: MODELLER 5o, August 18, 1998 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS v Copyright(c) 1989-1998 Andrej Sali All Rights Reserved v Written by A. Sali, A. Badretdinov, R. Sanchez, A. Fiser & E. Feyfant Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK What version is this? 5, 4, or 50? Cheers Tim -- Tim Dafforn Structural Medicine Department of Haematology CIMR University of Cambridge Wellcome-MRC Building (Level6) Hills Road Cambridge CB2 2XY Tel. (01223) 336829 Fax. (01223) 336827 http://smokeroom.cimr.cam.ac.uk/

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Re: article reprint
by sali＠rockvax 01 Feb '00

01 Feb '00

Well, I was as surprised as you. It must have been a mistake on the sender's part. But it will be out shortly. Thanks, Andrej > Dear Dr Sali > > I just saw a mail on the Modeller usage list about modeller 5.0. I had a > look at the webpage but couldn't see anything about it. Is it yet > available for general distribution? Where can I get information on the > new features? > > Thanks very much in advance > > Daniel Rigden > > > +-------------------------------------------------------------------------+ > | Dr Daniel John Rigden | > | CENARGEN/EMBRAPA | e-mail: daniel(a)cenargen.embrapa.br | > | S.A.I.N. Parque Rural, Final W5 | http://www.cenargen.embrapa.br | > | Asa Norte | Phone: +55 (61)348-4741 | > | 70770-900, Brasilia-D.F.-BRAZIL | Fax: +55 (61)340-3624 | > +-------------------------------------------------------------------------+ > > > -- -- Andrej Sali, Assistant Professor The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399 tel +1 212 327 7550; lab +1 212 327 7206 ; fax +1 212 327 7540 e-mail sali(a)rockefeller.edu; http://salilab.org

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core dumps
by T. .R. Dafforn 01 Feb '00

01 Feb '00

Dear All, I have just installed modeller V5.0 and have found that when I run my old scripts the program gets as far as TOP______> 40 40 SET TOPLIB = '${LIB}/top_heav.lib' TOP______> 41 41 SET TOPOLO and then Core dumps... Does any one have any ideas or previous experience of this? Cheers tim -- Tim Dafforn Structural Medicine Department of Haematology CIMR University of Cambridge Wellcome-MRC Building (Level6) Hills Road Cambridge CB2 2XY Tel. (01223) 336829 Fax. (01223) 336827 http://smokeroom.cimr.cam.ac.uk/

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