- modeller_usage - salilab.org

PIR format
by Urszula Uciechowska 22 Nov '07

22 Nov '07

Dear Modeller users, I am new in this program. I would like to build a model using multiple template. Could someone tell me how can I get alignment in the PIR format? which programs can I use? Thank you in advance for any help Best Regards, Urszula Uciechowska MSc.PhD Student Medicinal Chemistry Group University of Halle-Wittenberg Best Regards, Urszula Uciechowska MSc.PhD Student Medicinal Chemistry Group University of Halle-Wittenberg

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comparing models
by simonagi＠chemres.hu 21 Nov '07

21 Nov '07

Dear users, do you have experience in comparing models prepared by Swiss Model and Modeller9v2 ? Thanks, Agnes

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alignment_question
by Urszula Uciechowska 21 Nov '07

21 Nov '07

Dear Modeller users, I am new in using this program. I would like to build a model using multiple template. Could someone tell me how can I get alignment in the PIR format? which programs can I use? Thank you in advance for any help Best Regards, Urszula Uciechowska MSc.PhD Student Medicinal Chemistry Group University of Halle-Wittenberg

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by Canadian Doctor Willa Gillespie 20 Nov '07

20 Nov '07

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HOH
by Adriana Esteves 15 Nov '07

15 Nov '07

Using the scritp model-ligand.py I introduced a ligand in my model, but the waters were no added. Did I omitted anything in the alignment? Can I copy the waters coordinates from de template file to the modelled one and .... I don't know what to do then, but I something can be done!! This is the script and this the alignment # Homology modeling with ligand transfer from the template 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 = './:../atom_files' # Read in HETATM records from template PDBs env.io.hetatm = True a = automodel(env, alnfile = 'align-ligand.ali', # alignment filename knowns = '1O8v', # codes of the templates sequence = 'EgFABP2') # code of the target a.starting_model= 4 # index of the first model a.ending_model = 4 # index of the last model # (determines how many models to calculate) a.make() # do the actual homology modeling C; >P1;1O8v structureX:1O8v:1 :A :134 : :EgFABP1 :Echinococcus granulosus: : MEAFLGTWKMEKSEGFDKIMERLGVDFVTRKMGNLVKPNLIVTDLGGGKYKMRSESTFKT TE.S-FKLGEKFKEVTPDSREVASLITVENGVMKHEQDDKTKVTYIERVVEGNELKATVKV DEVVCVRTYSKVA.* >P1;EgFABP2 sequence:EgFABP2:1 : :134 : :EgFABP2:Echinococcus granulosus: : MEPFIGTWKMEKSEGFDKIMERLGVDYFTRKMGNMMKPNLIISDLGDGRYNMRSESKFKT SE-FSFKLGEQFKEVTPDSREVMSMLTVEDGVLKQEQVGKDKTTYIDRVVDGNELRATVKA DELVCVRTYSKRM.* Dra. A. Esteves Secc. Bioquímica Faculty of Sciences Iguá 4225-Montevideo URUGUAY tel.(5982)525 2095 fax (5982)525 8617

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Modeller creating strange structures
by Russell Green 12 Nov '07

12 Nov '07

Dear Modeller community, I have a good structure template to model the missing segment of a protein chain; however, the portion I'm tyring to model should contain a sharp bend. I'm actually using one part of the template for one side of the chain and the other part of the template for the other side of the chain after the bend. When I align the template (wich overlaps with the structure containing the missing portion) the two template pieces look reasonable aside from missing the loop that constitues the bend. After running automodel the template structure is not even retained; instead, it just builds large loops in no particular orientation. Is it possible that the problem is that automodel's constraints make it unable to model the bend correctly? If so, would using the model() class without certain constraints allow me to model this bend? Thanks in advance, Russell Green

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ligand 2
by aesteves＠fcien.edu.uy 12 Nov '07

12 Nov '07

I think I have found the problem but I don´t know how to solve it. The residue in question is an HETATM; I mean that where the sequence indicates a SER the pdb file has an HETATM (CSO). How can I solve it? Thank you ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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Fwd: validation and log file
by aesteves＠fcien.edu.uy 12 Nov '07

12 Nov '07

I still worried about validation. I know I have to read the model-default.log file to look for: objetive function and chose the one with the lowest(I did it; the DOPE pseudo-energy value and de value of GA341, and finally the restraint violations, but I did not find the third value and I dont know how to read violations. Can anybody help me to read the log file and find the information I need to validate my model? Thank you very much. Adriana ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. ----- Fin del mensaje reenviado ----- ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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Writing out chain ID in the PDB
by Vadim Patsalo 12 Nov '07

12 Nov '07

Hello Modeller Users, I am building models in the way described in the basic tutorial. I noticed that the completed model PDB is missing the chain ID column. The template I am modelling from has only one chain, A. Here's an example: Template: ATOM 1 N SER A 2 -6.487 9.533 21.436 1.00 2.23 1SG 2 ATOM 2 CA SER A 2 -5.822 10.328 20.343 1.00 2.86 1SG 3 ATOM 3 CB SER A 2 -6.345 11.788 20.283 1.00 2.67 1SG 4 and model: ATOM 1 N SER 1 -0.662 11.979 19.810 1.00 65.26 1SG 2 ATOM 2 CA SER 1 0.191 12.970 19.122 1.00 65.26 1SG 3 ATOM 3 CB SER 1 -0.325 14.388 19.420 1.00 65.26 1SG 4 Is there a way to force Modeller to print the chain ID? I convert the resulting PDB to charmm format, and some unpleasantness follows because of the missing chain info. Thanks for your help! Vadim -- five.sentenc.es is a personal policy that all email responses regardless of recipient or subject will be five sentences or less. It's that simple.

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ligand
by aesteves＠fcien.edu.uy 10 Nov '07

10 Nov '07

----- Mensaje reenviado de aesteves(a)fcien.edu.uy ----- Fecha: Sat, 10 Nov 2007 11:50:45 -0200 De: aesteves(a)fcien.edu.uy Responder-A: aesteves(a)fcien.edu.uy Asunto: ligand Para: modeller-care(a)salilab.org Hi friends of modeller list: Now, I want to model my protein with a ligand but the program says me that one of the alignment residue does not match with pdb residues. In this site there is a gap in the pdb sequence introduced during alignment since the target has an insertion. The same alignmet file was used to build the model without any problem!! What I have to do? Thank you again, and forgive me for too much questions, but I want to learn how to use Modeller!! Sincerely, Adriana ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. ----- Fin del mensaje reenviado ----- ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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