- modeller_usage - salilab.org

Asking about energy minimization after initial model]
by Chiranjit Chowdhury 06 Nov '07

06 Nov '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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Transfer_xyz question
by Ali Algarrous 06 Nov '07

06 Nov '07

Hello, If i have the following alignment >P1;1ji4 structureX:1ji4:FIRST:A:LAST:A:::: MKTFEILKHLQADAIVLFMKVHNFHWNVKGTDFFNVHKATEEI---------Y EEFADMFDDLAERIVQLGHHPLVTLSEAIKLTRV-----KEETKTSFHSKDIF KEILEDYKYLEKEFKELSNTAEKEGDKVTVTYADDQLAKLQKSIWMLQAHL-- -----A* >P1;madeup sequence:madeup::::::: -------------------------------------------MSFIEKMIGS LNDKREWKAMEARAKAL---PKEYHHAYKAIQKYMWTSGG--PTDWQDTKRIF GGILDLFEEGAAEGKKVTDLTGE--D--VAAFCDELMKDTKTWMDKYRTKLND SIGRD-* and i want to transfer the coordinates from my template to my sequence without building the loops. How should I change my code so it would do that for me?? This is the code that i have been using. from modeller import * env = environ() env.libs.topology.read(file='$(LIB)/top_heav.lib') env.libs.parameters.read(file='$(LIB)/par.lib') aln = alignment(env, file='alignment.ali',align_codes=('1ji4', 'madeup')) mdl = model(env) mdl.generate_topology(aln['madeup']) # Assign the average of the equivalent template coordinates to MODEL: mdl.transfer_xyz(aln) # Get the remaining undefined coordinates from internal coordinates: mdl.build(initialize_xyz=False, build_method='INTERNAL_COORDINATES') # Write the final MODEL coordinates to a PDB file: mdl.write(file='madeup.pdb') Regards, Ali Algarrous

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Re: [modeller_usage] DOPE applied to multichains
by Modeller Caretaker 02 Nov '07

02 Nov '07

DimitryASuplatov wrote: > Thanks for the answer. Could you paste me the link (to web or article, > the latter would be even better) to DOPE specification and evaluation > because I did not find it. the DOPE publication is #172 at http://salilab.org/publications/ which is Protein Science 15, 2507 - 2524, 2006. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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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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