- modeller_usage - salilab.org

request a clear method for modelling a dimeric protein
by Othman Houcemeddine 09 Oct '09

09 Oct '09

Dear sir; I am trying to use modeller to predict the structure of a dimeric protein with no obvious symmetry between each of its subunits. My BLAST search shows that the first subunit alpha is homologous to a monomeric protein "C", while the other subunit beta is homologous to another different monomeric protein "D". Basically, I tried to align alpha with "C" and beta with "D" and I decided that the best strategy is to use a typical script from the tutorial"Building a model from multiple templates". I am not quite sure that this procedure is the best way to build my model. Also, I found a problem in writing my alignment file especially the header section and the assignment of each of the subunits to each of the templates. Could any body verify my alignment file and give me a clear method to deal with this situation? Thanks Alignment file.ali: >P1;alpha&beta sequence:alpha&beta:1:A:142:B:::: --xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx/ ------xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx* >P1;C; structureX:C: 1:A:58: : : : : xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx-------------/ -------------------------------------------------------------------------------* >P1;D structureX: D:1:A:78::::: -----------------------------------------------------------------------------/ xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx* script file: # Homology modeling with multiple templates from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = './' a = automodel(env, alnfile = 'Alignment file.ali', # alignment filename knowns = ('C', 'D'), # codes of the templates sequence = 'proteinX') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) a.make() # do the actual homology modeling OTHMAN Houcemeddine Pasteur Institute of Tunis - Tunisia othmanhoucemeddine(a)yahoo.fr

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Helix rotation
by Liam Browne 05 Oct '09

05 Oct '09

I have a question about the most effective way of modelling a protein that is in a different conformation to the structure? I am hoping to make a homology model, then rotate a helix about its center and allow modeller to remake the model (allow energy minimisation etc) to determine the effects on the whole protein. Is there a way to do this? _________________________________________________________________ View your other email accounts from your Hotmail inbox. Add them now. http://clk.atdmt.com/UKM/go/167688463/direct/01/

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zinc coordination
by frank peelman 29 Sep '09

29 Sep '09

dear all, I'm trying to model a zinc binding protein, where the zinc is coordinated by two cysteines, a histidine and a glutamic acid. The bonds are present in the CONECT records of the template. I added upper bound restraints to restrain all distances between the zinc and the four coordinating atoms, and used "rsr.excluded_pairs.append" to exclude the bonds between the zinc and the four coordinating atoms from the nonbonded list. Models were built via the loopmodel routine. In the resulting models, the sulfur atoms are moving away from the zinc, as if the cysteine sulfurs are protonated. What is the best way to prevent this? Is there an easy way to define the cysteines as unprotoneated? best wishes, frank

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How to deal with a part of protein sequence that have no alignment with the template
by xiazhendong1986 29 Sep '09

29 Sep '09

alignment: _aln.pos 10 20 30 40 50 60 1kv9A -------------------------------------------------------------------- 1yiqA -------------------------------------------------------------------- 1kb0A -------------------------------------------------------------------- sldha MRRPYLLATAAGLALACSPLIAHAQFAPAGAGGEPSSSVPGPGNASEPTENSPKSQSYFAGPSPYAPQ _consrvd _aln.p 70 80 90 100 110 120 130 1kv9A ------------AGVDEAAIRATEQ------AGGEWLSHGRTYAEQRFSPLKQIDASNVRSLGLAWYM 1yiqA --------ADIPANVDGARIIAADK------EPGNWMSTGRTYDEQRYSPLKQISDQNVGQLGLAWSY 1kb0A -TGPAAQAAAAVQRVDGDFIRANAA------RTPDWPTIGVDYAETRYSRLDQINAANVKDLGLAWSY sldha APGVNAANLPDIESIDPSQVPAMAPQQSANPARGDWVAYGRDDHQTRYSPLSEITPENASKLKVAFVY _consrvd * * * * * * * * * * * As we can see from above, the templates have no sequence from amino 1 to 70 to align with the target protein "sldha", and the modelling result is that the structure of sequence 1-70 is a just a long chain with no fold. So how can I get the structure of sequence 1-70? Best wishs. James

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Question about Search for templates command...
by Sergio Garay 19 Sep '09

19 Sep '09

Hi I'm following the modeller tutorial to make a search for templates but with no success. May be I'm doing something wrong. Below I detail what I did: 1) download the supplemental files: - All PDB sequences: pdball.pir.gz <http://www.salilab.org/modeller/downloads/pdball.pir.gz> - Clustered at 95% identity: pdb_95.cod.gz <http://www.salilab.org/modeller/downloads/pdb_95.cod.gz>(PDB codes of cluster representatives) pdb_95.grp.gz <http://www.salilab.org/modeller/downloads/pdb_95.grp.gz>(PDB codes in each cluster) pdb_95.pir.gz <http://www.salilab.org/modeller/downloads/pdb_95.pir.gz>(sequences of cluster representatives) 2) I unpack them into the directory where Modeller should find them: /usr/lib/modeller9v7/modlib. In this point, I have a doubt: in the tutorial said that I should replace the files: CHAINS_3.* with the downloaded before. But I did not find them, at least in that directory. Anyway I renamed the files accordingly the tutorial as: pdball.pir to CHAINS_all.seq pdb_95.cod to CHAINS_3.0_40_xn.cod With these modifications I run seqsearch.top and apparently it worked, but after many (3-4) hours I stopped it. it never writes any line in the log file. seqsearch.top file used as input. SET SEARCH_RANDOMIZATIONS = 100 SET FILE = 'TvLDH.ali' READ_SEQUENCE_DB SEQUENCE_SEARCH ALIGN_CODES = 'TvLDH', DATA_FILE = ON Any help will be appreciated. Sergio -- Dr. Sergio Garay Facultad de Bioquimica y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221

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Adding a salt bridge
by Umang Shah 19 Sep '09

19 Sep '09

Hi, How do I add a salt bridge between 2 residues in my model? Thank you, Regards, Umang

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Evaluation of membrane proteins models
by BESSADOK Anis 19 Sep '09

19 Sep '09

Hi, I am using modeller to model MEMBRANE proteins. I want to evaluate my models but I don't know if DOPE score can be used to do this. Thank you Anis Bessadok PhD student

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Sehrish Batool invites you to connect
by Sehrish Batool via Yahoo! 13 Sep '09

13 Sep '09

Join Sehrish Batool on Yahoo! Messenger. (your message goes here) Stay in the loop with all your friends. Get started : http://invite.msg.yahoo.com/invite?op=accept&intl=us&sig=rshen8fDEoJ3jbxm7O… * Stay connected at home, at work, or on the go * Have fun with games, emoticons, and more * Join a community of over 100 million people from around the world Join Your Friends : http://invite.msg.yahoo.com/invite?op=accept&intl=us&sig=rshen8fDEoJ3jbxm7O… -- this email was sent to you by an automated system - please do not reply directly

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Loop Modeling using only part of a PDB file
by Robert Selwyne 08 Sep '09

08 Sep '09

Dear Modeller Users Residues from PHE 1223 to LEU 1245 are missing from PDB:2RFN. I want to use ONLY the residues from 382 to 406 in my template sequence PDB:3LCK for loop modelling. Remaining part of the residues in the target shouldnot be disturbed. (2RFN) Target : PHE 1223 to LEU 1245 (24 residues) (3LCK) Template : ASP 382 to TRP 406 (24 residues) Could you please tell me how to model this? Regards Robert

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Model evaluation
by vidhya ganesh 08 Sep '09

08 Sep '09

Hello, I have questions on "Model evaluation" step in "Basic modeling". As far as i know, if it is a best model,the dope score profile shows region of low energy.But, the plot in my model with template looks as if some residue position have relatively high energy and in some showing of low energy.How can i judge whether it is a good model or bad? See the Web's breaking stories, chosen by people like you. Check out Yahoo! Buzz. http://in.buzz.yahoo.com/

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