- modeller_usage - salilab.org

ask for your kindful help
by 典范 25 Feb '06

25 Feb '06

Hello everyone: Could you please tell me how to prepare the alignment(*.ali) file for modelling a protein-protein complex with known structures? thank you! Best regards, amber ly lidianfan(a)163.com 2006-02-26

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"Structure not read in" error
by Omid Khalouei 24 Feb '06

24 Feb '06

Hello, I am just starting to use Modeller. Even though I have a major in computer science, have used many bioinformatics tools, and am familiar with Python, I haven't been able to figure out how to run this program. To be honest I don't find it that user-friendly! Basically I'm not sure in which folder I have to put my alignment and PDB coordinate files. This is the alignment file that I have created but am not sure if it meets the specifications (they both refer to HIV-1 protease, residues 1 to 99 of chain A); P1;1A8GA structureX:1A8GA:1:A 99:A:.:.:.:. PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYD QILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF* P1;1ZPA sequence:1ZPA:1:A 99:A:.:.:.:. PQITLWKRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYD QILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF* The error message that I'm getting is "Structure not read in: 1" and it's raised from the Modeller8v1\modlib\modeller\util\top.py file. I would appreciate your help on this. Omid K.

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query
by abhilasha kirti 24 Feb '06

24 Feb '06

Sir we have just now started working with modeller.we would like to have step wise guide for preparing input file and running modeller,as in the manial also it is not mentioned so clearly. Please do the needful,we will be ever greaful to u. Thanking u Abhilasha __________________________________________________________ Yahoo! India Matrimony: Find your partner now. Go to http://yahoo.shaadi.com

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pls help me to identify.
by smitha vishwas 24 Feb '06

24 Feb '06

hi all, I have modelled a protein using modeller & opted for 5 structures. but of those how do i identify the better one. pls help. Regards smitha --------------------------------- Jiyo cricket on Yahoo! India cricket Yahoo! Messenger Mobile Stay in touch with your buddies all the time.

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modeller ga341 score
by jo hanna 23 Feb '06

23 Feb '06

Hi After having built my models, i have decided to assess them using the ga341 score. the script i am using is: # Example for: model.assess_ga341() env = environ() # Read a model previously generated by Modeller's automodel class mdl = model(env, file='.59.pdb') # Set template-model sequence identity. (Not needed in this case, since # this is written by Modeller into the .pdb file.) mdl.seq_id = 30.174 score = mdl.assess_ga341() the ouput of this script for two different models is: model1 % sequence identity : 30.174000 Sequence length : 531 Compactness : 0.270804 Native energy (pair) : -225.273799 Native energy (surface) : -13.946407 Native energy (combined) : -6.357012 Z score (pair) : -9.813731 Z score (surface) : -7.147611 Z score (combined) : -11.464915 GA341 score : 1.000000 model2 % sequence identity : 30.174000 Sequence length : 531 Compactness : 0.256617 Native energy (pair) : -268.422282 Native energy (surface) : -16.727187 Native energy (combined) : -7.618686 Z score (pair) : -9.969647 Z score (surface) : -7.755271 Z score (combined) : -12.156111 GA341 score : 1.000000 how do i interpret these outputs? should both scores be 1? Jo

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as1 matrix
by Schulze, Diana 22 Feb '06

22 Feb '06

Hi. To build an alignment in MODELLER the standard is the as1 matrix. Does somebody know why this matrix is used as standard and whats the difference to pam or blosum? Thanks Dina

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Help needed concerning the alignment file
by doppelt olivia 21 Feb '06

21 Feb '06

Hello, I've been trying to use Modeller on an alignement file obtained from a clustalw use. I have the pdb file in the same repertory. I used a script, that i found in the examples files of Modeller. When I try to use Modeller, the following error is made : rdpir___648E> Alignment sequence not found in PDB file: 1 ./1tu7.pdb Here is my scipt : #! /usr/bin/env python from modeller.automodel import * import sys env = environ() ali = sys.argv[1] pdb = sys.argv[2] nb = int(sys.argv[3]) env.io.atom_files_directory = pdb a = automodel(env, alnfile=ali, knowns='1tu7', sequence='13gs') a.starting_model = 1 a.ending_model = nb a.make() Here is my alignment file 13gs-1tu7.ali: >P1;1tu7 structureX:1tu7: ::: ::: 0.00: 0.00 MS-YKLTYFSIRGLAEPIRLFLVDQDIKFIDDRIAKDDFS--SIKSQFQFGQLPCLYDGD QQIVQSGAILRHLARKYNLNGENEMETTYIDMFCEGVRDLHVKYTRMIYMAYETEKDPYI KSILPGELAKFEKLLATRGNGRNLILGDKISYADYALFEELDVHQILDPHCLDKFPLLKV FHQRMKDRPKLKEYCEKRDAAKVPVNGNGKQ* >P1;13gs sequence:13gs: : : : ::: 0.00: 0.00 MPPYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKASCLYGQLPKFQDGD LTLYQSNTILRHLGRTLGLYGKDQQEAALVDMVNDGVEDLRCKYISLIYTNYEAGKDDYV K-ALPGQLKPFETLLSQNQGGKTFIVGDQISFADYNLLDLLLIHEVLAPGCLDAFPLLSA YVGRLSARPKLKAFLASPEYVNLPINGNGKQ* the pdb file 1tu7.pdb is in the same directory. I changed a lot of things in the script or in the alignment file, it doesn't change anything. Any help would be good, Thanks in advance, Olivia Doppelt ___________________________________________________________________________ Nouveau : téléphonez moins cher avec Yahoo! Messenger ! Découvez les tarifs exceptionnels pour appeler la France et l'international. Téléchargez sur http://fr.messenger.yahoo.com

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alingment score using salign
by jo hanna 21 Feb '06

21 Feb '06

Hi If i have a set of alignments that I have generated is it possible to calculate just the score using salign in modeller? Thanks Jo

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what is the correct alignment
by rudra 21 Feb '06

21 Feb '06

hi, i'm new to homology modeling, i was trying to solve a structure by homology modeling, i want to know what is the correct alignment among these two: case 1: template abbadfaclkzcdtcfdgswchc target aabadaacckzcct----ccghc secondary structure CCCCCCCHHHHHHHHHHHHHHHH CLUSTALW * *** ** *** * ** case 2: template abbadfaclkzcdtcfdgswchc target aabadaacckzcctccghc---- secondary structure CCCCCCCHHHHHHHHHHHHHHHH CLUSTALW * *** ** *** ** regards, rudra

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Request for correcting errors
by Aparna Apurba Roy 20 Feb '06

20 Feb '06

Respected Sir/Madam, I am Miss Aparna Roy student of Rishi Biotech Institute, Thane. I am facing some problem in running the Modeller 6v2 software. Attachment ( Atm, Ali, Top files) Thanking you. Yours faithfully, Aparna Roy.

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