- modeller_usage - salilab.org

DOPE applied to multichains
by DimitryASuplatov 02 Nov '07

02 Nov '07

Hello, In 9v2 manual (as in all previous) it is insistently recomended to use .assess_dope() for single chains only. What exactly does it mean? 1/ Could I possibly apply dope to multichain proteins? 2/ How should I use dope on multichains? Should I split each chain to single pdb and apply dope for each one sepparately? Would this be correct? Should`t dope include chain-chain interactions? Thankyou very much for the program and for the answers!

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Re: [modeller_usage] validation with procheck
by Michael Sadowski 01 Nov '07

01 Nov '07

Dear Adriana, I believe this website still works, although I've not tried it since July of this year. It runs Procheck and whatcheck. http://biotech.ebi.ac.uk:8400/cgi-bin/sendquery Regards, Michael ---------------------------------------------------------------------- Message: 1 Date: Mon, 29 Oct 2007 17:33:56 -0300 From: "Adriana Esteves" <aesteves(a)fcien.edu.uy> Subject: [modeller_usage] validation with procheck To: "Modeller lista" <modeller_usage(a)salilab.org> Message-ID: <CFEKJPEBLCOFMLEGBEBCKEJPCGAA.aesteves(a)fcien.edu.uy> Content-Type: text/plain; charset="iso-8859-1" Do anybody knows a web site to run procheck? ___________________________________________________________ Want ideas for reducing your carbon footprint? Visit Yahoo! For Good http://uk.promotions.yahoo.com/forgood/environment.html

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query about alignment type
by Bhavya Jindal 31 Oct '07

31 Oct '07

Hi I am a new modeller user. I built my initial model using a simple blast alignment and other using secondary structure alignment using same template and targets and i got different results. Now i am a bit confused that which type of alignment should be used for modeling. Please somebody help in clarifying my doubt. Regards Bhavya -- Bhavya Jindal Research Scholar School of Biosciences and Bioengineering Indian Institute of Technology Bombay Mumbai Maharashtra 400076

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Asking about energy minimization after initial model
by Chiranjit Chowdhury 30 Oct '07

30 Oct '07

Dear Friends, I got my initial model for my protein using MODELLER 9v1 which was further assessed by DOPE potential in MODELLER to evaluate model fold and with the program PROCHECK and VERIFY3D. In Ramachandran plot my model showed 93.9% core 5.8% allow .0% gener .3% disall region and 3 bad contacts. Verify 3d data showed above 90% of the residues had an averaged 3D-1D score > 0.2. Please suggest whether I shall have to do energy minimization and if energy minimization is necessay also suggest how it is possible and which parameter I shall have to use for energy minimization. Best regards. -- Chiranjit Chowdhury Department of Biotechnology Indian Institute of Technology, Kharagpur West Bengal, India PIN: 721302

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(no subject)
by Chiranjit Chowdhury 30 Oct '07

30 Oct '07

-- Chiranjit Chowdhury Department of Biotechnology Indian Institute of Technology, Kharagpur West Bengal, India PIN: 721302

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validation with procheck
by Adriana Esteves 29 Oct '07

29 Oct '07

Do anybody knows a web site to run procheck? Adriana

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validation
by Adriana Esteves 29 Oct '07

29 Oct '07

I have read the answer you gave to simran jeet about residues in disallowed position, sugesting to build multiple models and pick the best one. Your answer conducts me to the following question. How to build multiple models, with multiple templates or performing several models with the same template and selecting that with the lowest objetive value? In this case, how many models are indicated to run? A second doubt I have is about validation. As the tutorial indictes, one should check the log file from the modeling run for runtime errors (`model-single.log') and restraint violations. I did it but I do not know how to interpretate the restrain violations. Can anyone help me to interpretate them? .I have also run the file `evaluate_model.py' to evaluate my model with the DOPE potential, but I do not know how to access to gnuplot. Finally I'd like to check the model with procheck_NT but something is wrong with the pdb file. Anyone knows other rasonable way to validate the model, preferebly a web site to perform the analysis on line. Thank you very much, Adriana

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plotdope problem
by jacques deruchoud 29 Oct '07

29 Oct '07

hello, I have some problem using plotdope, as I understand the perl script extract not the correct column from the .profile file, so I get only 0 value in the .dat file did anyone experience the same problems ? could anyone run correctly the plotdope script ? thanks for the info jacques dumont __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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help
by simran jeet 24 Oct '07

24 Oct '07

After modeling a protein using modeller some residues remain in the disallowed regions of ramachandran plot. Is that model incorrect ? Is there any way to remove bad contacts and residues in disallowed regions after modeling? I tried to overcome this problem using Deepview by selecting two or more residues and building loop. Though the residues in disallowed regions and bad contacts become zero by this procedure but structure is affected. What should I do please guide me.

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Refine
by Dany Naranjo Feliciano 23 Oct '07

23 Oct '07

Hi, When I use this script some parts of my protein appears streched. Should I put water molecule for better refinment? Why I obtein worse models with refine option? #Modelación por homología con un ligando transferido desde el molde from modeller import * # Carga las clases del Modeller from modeller.automodel import * # Carga la clase automodel log.verbose() # Solicita una salida detallada env = environ() # Crea un nuevo ambiente para construir para construir el modelo # Directorio del fichero pdb/atm de entrada env.io.atom_files_directory = './‘ # Lectura de los heteroátomos en el pdb molde env.io.hetatm = True a = dopehr_loopmodel(env, alnfile = 'hetatm2.ali', # Fichero del alineamiento knowns = '1gmyAok2.pdb', # Código del molde sequence = 'Q8I7B2_sequence') # Código del blanco a.starting_model= 1 # Índice del primer modelo a.ending_model= 50 # Índice del último modelo # (determina el número de modelos a calcular) a.md_level = refine.very_slow # refinar modelo a.loop.starting_model = 1 a.loop.ending_model = 2 a.loop.md_level = refine.very_slow # refinar lazos a.make() # Hacer los modelo Dany Naranjo Feliciano Lic. Bioquímica Grupo Biología Molecular Centro Nacional de Sanidad Agropecuaria (CENSA) Apartado 10. San José de las Lajas. La Habana. CP 32700. Cuba Teléfono 53-47-863014 ext 28 "Participe en Universidad 2008 del 11 al 15 de febrero del 2008. Palacio de Convenciones. La Habana. Cuba. http: //www.universidad2008.cu".

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