May 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 *************************************************

2 1

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

2 1

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 | +-------------------------------------------------------------------------+

2 1

"STARTING_MODEL" and "ENDING_MODEL"
by Xiao-Ping Zhang 23 May '00

23 May '00

Hi, Sorry, I have noticed that someone already asked the following question two years ago and Azat Badretdinov had answered the it. But I still don't understand the meaning behind the STARTING_MODEL" and "ENDING_MODEL. > > > >What exactly is the meaning behind setting "STARTING_MODEL" and > >"ENDING_MODEL"? Does setting the former to 1 and the latter to, say, > >7 result in seven models being built with the 7th model being the most > >refined? >No, it does not. STARTING and ENDING will determine the range of indeces >in .B???? file names of the models I am modeling a very short peptide with modeller4. If I set STARTING_MODEL=1, ENDING_MODEL=10, I get 10 models which have different orientations and spatial location. If I would like to get a model which can overlap with the original model (maximum uses the template coordinates), how to do it? And is it possible to keep the backbone in the same conformation of original peptide ? All suggestions are highly appreciated. Thank you for your help. ****************************** Xiao-Ping Zhang Department of Biochemistry Arrhenius Laboratories of Natural Sciences Stockholm Universities 106 91 Stockholm Sweden Phone: 046-08-162472 /162582 Fax: 046-08-153679 e-mail: zhang(a)biokemi.su.se

2 3

Segmantation fault
by Humberto Muniz 23 May '00

23 May '00

I was running MODELLER on Atlhon with Mandrake 7.02. The benchmarks runs well, but when i try modelling my protein the program returns the following message: /usr/local/bin/modeller4/bin/mod4: line 39: 2793 Segmentation fault /usr/local/bin/modeller4/bin/${EXECUTABLE} $STEERF >$LOGF Whats wrong??? Thanks in advance Hmuniz.

1 0