August 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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SEQUENCE_SEARCH
by Troy Wymore 27 Sep '00

27 Sep '00

Hello MODELLERs, Could someone inform me on how MODELLER performs the search for templates given a sequence? I could not tell from the manual what algorithm it was using to do this. Thanks, Troy Wymore

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Re: Protein:DNA complexes in Modeller
by Andrej Sali 24 Aug '00

24 Aug '00

Mike Sierk wrote: > > Dr. Sali, > > We do not have Modeller installed here, and I was wondering how it does > modelling DNA-binding proteins. I have a structure of a protein:DNA > complex and would like to make a model of a related protein. Would it > work to just use the protein structure as a template, ignoring the DNA? Yes. > Could it model the unknown protein on the known DNA structure? Yes, but not with the default protocol. > Would it > model the unknown protein:DNA complex(with a different DNA sequence) > using the known complex? Yes, but not with the default protocol. The results are not likely to be overwhelming. Best, Andrej > > I found only two questions about DNA in the archive, with no answers to > either. > > Thank you, > Michael Sierk > > -- > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > Michael Sierk email: mls5w(a)virginia.edu > Pharmacology Dept./Biophysics Program Phone(W): (804) 243-6725/924-1953 > Box 800735, Health Sciences Center (H): (804) 970-2268 > University of Virginia Fax: (804) 924-9057 > http://www.people.virginia.edu/~mls5w > GBS Homepage: http://www.med.virginia.edu/ed-programs/gpo/gbs/ > Grad Council Homepage: http://www.student.virginia.edu/~gsasc/ > ------------------------------------------------------------------------ > "If at first you do succeed, try not to act surprised." > - Anonymous. > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ -- 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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IRIX 6.5 problems; install patch 3371
by Andrej Sali 21 Aug '00

21 Aug '00

Problems with Modeller under Irix6.5: Patch 3371 is absolutely necessary. -- 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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