March 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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Multiple heteroatoms
by Thorsten Schweikardt 31 Mar '00

31 Mar '00

Hi there, I am trying to model a protein containing 2 copper atoms. I took the advice you gave Michel Giorgi (5-2-99) and pretended that copper is zinc. But the models I receive only have one zinc atom, not two. I tried several changes in the command syntax (/z*) to get the second copper/zinc modelled, e.g. /zz* or / z-z*, but any change results in the error: forrtl: severe (61): format/variable-type mismatch, unit 6, file stdout. I did not find anything about it in the manual. Can anyone tell me how to model the second zinc/copper atom into the structure ? Are there updated libraries available, where copper is parametrized ? Thanks for your help, Thorsten Schweikardt Molekulare Biophysik Universitat Mainz Germany

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Linux huge version and multiple and not overlapping templates
by Xiao-Ping Zhang 28 Mar '00

28 Mar '00

Hi, I would like to ask a few questions: 1. I wonder if somebody succeeded with modelling of a protein with "multiple and not overlapping templates" (sorry for asking an old question) with Modeller. I have two situations about this issue: (1) model a two domain protein from two separate pdb files, there is a gap about 10 residues between them; and (2) model a two subunits protein from one pdb file which contains many subunits. I would appreciate very much if I can share your experience (How the top file is and how the alignment file should be?). Which program is the best for these kinds of modeling? 2. Has anybody compiled a linux huge version? I would like to try on the above examples. 3. Does anybody know a modeling program in which you can do ab initio modeling for short peptide (30-60 residues)? Thank you very much for your kind attention. Sincerely yours, Xiao-Ping Zhang ------------------------------------------------ Xiao-Ping Zhang Department of Biochemistry Stockholm University 106 91 Stockholm Sweden Phone: 46-08-162582 / 162472 Fax: 46-08-153679 e-mail: zhang(a)biokemi.su.se

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Re: [Crystallographic Symmetry] for the record
by Andras Fiser 15 Mar '00

15 Mar '00

> Subject: Re: Crystallographic Symmetry > Date: Tue, 14 Mar 2000 08:28:48 -0500 (EST) > From: sali(a)rockvax.rockefeller.edu > To: derek(a)ysbl.york.ac.uk (Derek Smith) > CC: sali(a)bass.rockefeller.edu (Andrej Sali) > > Hi, > > The "expensive" way is the only way, though one remotely relevant tool > is DEFINE_SYMMETRY. > > Best wishes, Andrej > > > Dear Modellers, > > > > Is it possible to incorporate crystallographic symmetry in Modeller in > > order to generate models of monomer proteins that form large multimers? > > > > I guess it is probably easier to generate the other protein segments of > > a structure to be modelled, and model a homologous sequence for all > > segments, although this would be computationally expensive. > > > > If it is possible - how would it be done? > > > > Yours, > > > > Derek Smith > > > > -- > > ************************************************************************ > > Derek Smith, Structural Biology Laboratory, Department of Chemistry, > > University of York, Heslington, York. YO10 5DD, United Kingdom. > > phone: (01904) 432550 fax: (01904) 410519 email: derek(a)yorvic.york.ac.uk > > ************************************************************************ > > > > -- > -- > Andrej Sali, Associate 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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Crystallographic Symmetry
by Derek Smith 14 Mar '00

14 Mar '00

Dear Modellers, Is it possible to incorporate crystallographic symmetry in Modeller in order to generate models of monomer proteins that form large multimers? I guess it is probably easier to generate the other protein segments of a structure to be modelled, and model a homologous sequence for all segments, although this would be computationally expensive. If it is possible - how would it be done? Yours, Derek Smith -- ************************************************************************ Derek Smith, Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York. YO10 5DD, United Kingdom. phone: (01904) 432550 fax: (01904) 410519 email: derek(a)yorvic.york.ac.uk ************************************************************************

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RTF format
by Fabio Zuccotto 13 Mar '00

13 Mar '00

Dear All, I'm trying to define a new ligand for inclusion in the Modeller topology library (top.lib). I usually generate this starting with a RTF file from Quanta. Unfortunately I don't have access to that program anymore. Is there any other way I can use to generate the appropriate topology for inclusion (perhaps with minor changes) into top.lib? Than you very much. Fabio ***************************** Fabio Zuccotto, PhD Biological NMR Centre Medical Sciences Building University Road Leicester LE1 9HN ENGLAND (UK) Tel. +44 (0)116 252 3620/3071

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desperation
by Duccio Calamandrei 13 Mar '00

13 Mar '00

Hi everybody, I' m tempting invane to model a sequence with three template structures. Unfortunately during a preliminary step using only one template, I get the error message reported within the .log file. what can I do? p.s. I enclose .ali .log and .pdb files Thank you for your kindness Duccio.

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