November 2007 - modeller_usage

Alignment editors?
by Esben Jannik Bjerrum 19 Feb '08

19 Feb '08

Hi, This is not entirely modeller specific, but related. Do anyone know of an alignment editor which accepts, but doesn't delete the PIR comment lines? So far I have just hand edited the PIR file from a fasta file, but now I'm trying to model a multimeric and multidomain protein which makes it very complicated and cumbersome. Best Regards Esben ____________________________________________________________________________________ Get easy, one-click access to your favorites. Make Yahoo! your homepage. http://www.yahoo.com/r/hs

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pir format
by Urszula Uciechowska 27 Nov '07

27 Nov '07

Dear Modeller users, I am trying to use this script for my aligment. But my target sequence is in Fasta format file, can I use it also or should i convert it? Maybe someone could write me how can i get sucha a file from fasa format. thank you in advance from modeller import * env = environ() aln = alignment(env) mdl = model(env, file='file', model_segment=('FIRST:A','LAST:A')) aln.append_model(mdl, align_codes='file', atom_files='file.pdb') aln.append(file='Sirt1.ali', align_codes='Sirt1') aln.align2d() aln.write(file='file.ali', alignment_format='PIR') aln.write(file='file.pap', alignment_format='PAP') Best Regards, Urszula Uciechowska MSc.PhD Student Medicinal Chemistry Group University of Halle-Wittenberg

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loop refinement
by Laura Lopez 22 Nov '07

22 Nov '07

Hello! I'm trying to obtain refined models of a loop region from a existing pdb file (a model I built before with modeller). I only want to refine a loop, and I've followed the steps in http://www.salilab.org/modeller/manual/node34.html. But it always appears me this error message: File "<string>", line 1, in ? File "/Library/modeller-9v2/modlib/modeller/top_interpreter/__init__.py", line 36, in run self._runlines(self.lines) File "/Library/modeller-9v2/modlib/modeller/top_interpreter/__init__.py", line 153, in _runlines subrout) File "/Library/modeller-9v2/modlib/modeller/top_interpreter/__init__.py", line 384, in _run_top_cmd eval('self.topcmds.' + lowcmd + '()') File "<string>", line 0, in ? File "/Library/modeller-9v2/modlib/modeller/top_interpreter/commands.py", line 230, in optimize optimization_method=ometh) File "/Library/modeller-9v2/modlib/modeller/top_interpreter/topcmds.py", line 412, in optimize outs = _modeller.mod_top_optimize(mdl, edat, libs, *args) ValueError: read_op_662E> Invalid choice LONG for variable OUTPUT: can choose one or more from the following: NO_REPORT REPORT I've tried to change some settings in the .top file but always appear this error.What can I do? Another question: if in the model I've built and from which I've to refine a loop, I had to make a disulfide bridge in this loop, in the loop refinement I also have to make the disulfide restraint? Thank you!! Laura

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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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