modeller_usage

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modeller_usage@salilab.org

March 1999

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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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ANNOUNCEMENT: ModBase database of comparative protein structure models
by sali＠rockvax.rockefeller.edu 16 Mar '99

16 Mar '99

ModBase database of comparative protein structure models Roberto Sanchez and Andrej Sali http://salilab.org/modbase/ ModBase is a queryable database of many annotated comparative protein structure models. The models consist of coordinates for all non-hydrogen atoms in the modeled part of a protein. They are derived by an automated modeling pipeline relying mainly on the program MODELLER. The database currently contains 3D models for substantial segments of 15-23% of proteins in the genomes of M. genitalium, M. jannaschii, E. coli, S. cerevisiae, and C. elegans. In total, there are models for 3,732 proteins. The database also includes fold assignments and alignments on which the models were based. In addition, special care is taken to assess the overall quality of the models and their accuracy at the residue level. In the future, ModBase will grow to reflect (i) the growth of the sequence databases, (ii) the growth of the database of known protein structures, (iii) and improvements in the software for calculating the models. It is expected that the Swiss-Prot+TrEMBL protein sequence database will be processed by the end of 1999. ModBase is introduced in R. Sanchez & A. Sali. Proc. Natl. Acad. Sci. USA 95, 13597-13602, 1998.

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