June 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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a problem
by Matteo Dal Peraro 16 Jun '00

16 Jun '00

in a modelling run I have this error during: 109 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi1_dihedral' ADD_RES; TRAINTS = ON Restraint type to be calculated: chi1_dihedral getpdf__E> your library requires all bins zero; nbinx: 4 what does it mean, I didn't find informations about it how can I resolve it? thanks matteo

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Average Coordinates
by giovannibottegoni＠libero.it 13 Jun '00

13 Jun '00

Dear Modeller users, I'd like to know if it's possible to give different weights to the templates when calculating the average coordinates to assign to the target sequence (TRANSFER_XYZ). Thank you in advance. Best regards, Giovanni ********************************** Giovanni Bottegoni Dip.Scienze Farmaceutiche Facoltà di Farmacia Università degli Studi di Bologna **********************************

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Segmentation fault
by Rafael Avila de Espindola 09 Jun '00

09 Jun '00

when I try to run the example of the tutorial in a Debian 2.2 system i get a segmentation fault, how do make it work?. Obs: I am runing the TINY version of modeller4

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libf2c.so.0
by Rafael Avila de Espindola 07 Jun '00

07 Jun '00

I want to use modeller with Debian GNU/Linux 2.2 but it needs libf2c.so.0 and Debian comes with libf2c.so.0, is there a moduller version compiled against this new version or should I get the old lib? >From where can I get one of then?

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transfer of side chain conformations
by Daniel John Rigden 02 Jun '00

02 Jun '00

Hi everyone Is it possible to get MODELLER to transfer side chain conformations to a new backbone? I have some backbone traces derived from dynamic studies. I'd like to transfer the side chains from the original structure prior to refinement and further studies. Any help much appreciated. Thanks Daniel Rigden +-------------------------------------------------------------------------+ | Dr Daniel John Rigden | | CENARGEN/EMBRAPA | e-mail: daniel(a)cenargen.embrapa.br | | Parque Estacao Biologica | http://www.cenargen.embrapa.br | | PqEB - Final - Av. W3 Norte | Phone: +55 (61)448-4741 | | 70770-900, Brasilia-D.F.-BRAZIL | Fax: +55 (61)340-3624 | +-------------------------------------------------------------------------+

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