August 1999 - modeller_usage

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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Model Refinement
by Derek Smith 12 Aug '99

12 Aug '99

Dear Modellers I have a manually constructed model protein, which I would like to refine using the MODELLER default schedule. I have attempted this using the protocol based on question 12 in the MODELLER FAQ. However, I find that MODELLER reads the model.ini file, and then extracts restraints from the templates, which are then used in the optimization of the model. I would like to refine my model based only upon my initial conformation. Is this possible do do, and if so, how should I go about it? Thanks in advance, Derek Smith. ************************************************************************* Derek Smith phone: (01904) 432550 Structural Biology Laboratory email: derek(a)yorvic.york.ac.uk Department of Chemistry fax: (01904) 410519 University of York, Heslington, York. YO10 5DD United Kingdom. *************************************************************************

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refinement of initial structure
by Derek Smith 09 Aug '99

09 Aug '99

Dear Modellers, I have a manually constructed model and I would like to use the MODELLER optimisation protocol. I have attempted to follow the FAQ question 12, but I find that although MODELLER reads in the 'model.ini' file I give it, it then extracts restraints from the templates to refine the model. Is there a way of presenting MODELLER with a model (minus any other details) and using the program purely as a structure refinement tool? Any help would be appreciated, Derek Smith -- ************************************************************************* Derek Smith phone: (01904) 432550 Structural Biology Laboratory email: derek(a)yorvic.york.ac.uk Department of Chemistry fax: (01904) 410519 University of York, Heslington, York. YO10 5DD United Kingdom. *************************************************************************

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