August 2008 - modeller_usage

side chains turned inside out
by Josmar R. da Rocha 08 Aug '08

08 Aug '08

Hi modellers, I'm trying to build a homology model of a multi-chain heteromeric protein (with model-default.py script) using as template a homomeric protein as showed in the following example: #begin of "ali" file >P1;pdb structureX:pdb:1:A:10::::: AAAAAAAAAA/ AAAAAAAAAA/ AAAAAAAAAA/ AAAAAAAAAA/ AAAAAAAAAA* >P1;ABBAB sequence::::::::: AAAAAAAAAA/ BBBBBBBBBB/ BBBBBBBBBB/ AAAAAAAAAA/ BBBBBBBBBB* #End of "ali" file The model is built normally. However, I noticed that many residues in the active site (which is localized in the interface between each pair of monomers) that are supposed to exposed are turned inside out. I tried to model just as homomeric and so all important side chains in the active site kept the template position. Is there anything I can do to make the modeled residues to adopt the same position as in the template? Would it be reasonable? I'd appreciate any help! Best regards, Josmar Rocha Novos endereços, o Yahoo! que você conhece. Crie um email novo com a sua cara @ymail.com ou @rocketmail.com. http://br.new.mail.yahoo.com/addresses

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question about a mix model
by Jesica MLM 08 Aug '08

08 Aug '08

Hi All, this is the first time i write, i am from Argentina, and I would like to create an model of a short protein ( 96 amino acids) mixing or emsamblin two models, because the protein has two domains very well modeled but with diferet proteins and with diferent cordinates, so i have two models, hte first from 2 to 90 aa, and the second from 91-96 aa. how can i make a one model from these two? thank you very much Jesica Levingston Mac leod Animal Virology Center Milstein Center Buenos Aires Argentina ____________________________________________________________________________________ ¡Buscá desde tu celular! Yahoo! oneSEARCH ahora está en Claro http://ar.mobile.yahoo.com/onesearch

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modeling an oligomer
by Douglas Kojetin 07 Aug '08

07 Aug '08

Hi All, I would like to create an oligomeric (hexamer) model. I have a Ca- only hexameric model (chains A-F) to use for the template and an experimentally determined monomer structure I would like to use for the target. Essentially, I would like to map six of the monomer target structures to chains A-F of the template. I've attempted to do this using the "model-myini.py" script as described here: http://www.salilab.org/modeller/manual/node26.html and here: http://www.salilab.org/modeller/examples/automodel/model-myini.py but my output hexamer structure ends up looking like spaghetti. Am I using the proper modeling script for this task? If so, what should the alignment and target PDB files look like to map the monomer structure to the hexamer structure? Thanks, Doug

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GPCR modeling
by Sharangdhar S. Phatak 07 Aug '08

07 Aug '08

Hello, I was wondering if anyone could help me address the issue of flipped residues. I am modeling a 7-TM GPCR and in one of the TM the residues are flipped. Is there a way to fix this? Thank you Sharang

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new to modeller
by Chinwe Ekenna 02 Aug '08

02 Aug '08

good day sir, pls i'm new to modeller and do not know where to start .i have read the manual but it get all confusing . i have not put in any input file cos i don't know where to start. i tried running the modeller mod9v3 model-default.py and it gives me import site failed cannot open file or directory . please help. if i can know the very first thing to do i think i can take it from there. thank you in advance chinwe

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Oligomer Modelling
by Manjunatha Karpenahalli 31 Jul '08

31 Jul '08

Dear All, Is it possible to model home-tetramer using modeller? Thank you very much in advance. Download prohibited? No problem. CHAT from any browser, without download. Go to http://in.webmessenger.yahoo.com/

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