modeller_usage

modeller_usage@salilab.org

3151 discussions

model-loop
by Urszula Uciechowska 18 Dec '07

18 Dec '07

Dear Modeller users, I am trying to use the model-loop.py script: Homology modeling by the automodel class from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = './:../atom_files' a = loopmodel(env, alnfile = 'Sirt1-multi.ali', # alignment filename knowns = '1j8fAA','1j8fBB','1j8fCC','1q1aA','1yc5A','2od7A' # codes of the templates sequence = 'Sirt1' ) # 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.md_level = None # No refinement of model a.loop.starting_model = 1 # First loop model a.loop.ending_model = 4 # Last loop model a.loop.md_level = refine.fast # Loop model refinement level a.make() # do homology modeling but i am getting the error 'import site' failed; use -v for traceback File "model-loop.py", line 14 sequence = 'Sirt1' ) # code of the target ^ SyntaxError: invalid syntax Could someone tell me how to figure out this error? thank you in advance Best Regards, Urszula Uciechowska MSc.PhD Student Medicinal Chemistry Group University of Halle-Wittenberg

2 1

Modelling long alpha-chains
by DimitryASuplatov 07 Dec '07

07 Dec '07

Hello, I`am trying to model a 170 aa long peptide chain. It is a part of big enzyme complex. It is a straight long alpha-chain, of course with some small turns but not exeeding 20 degrees. I have found 3 pieces in pdb that together form by target. I made an alignment with almost no gaps and sumbitted it to modeller. For output I have a globular structure, because modeller made many >20 big turns. Do you have any suggestions how to do my job. Thank you. Dimitry.

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post translational modification
by suji george 05 Dec '07

05 Dec '07

Hi, Can Modeller be used to study the effect of post translational modification on the structure of protein. For instance if a lysine in a protein is modified to carboxymethyllysine. In such situation, can the modified template be used for modeling. The model so obtained by the alignment of modified protein as template and native protein reflect the effect of modification on the structure. Is it necessary to consider the modified amonoacid (carboxymethyllysine)as unnatural amino acid and modify the charmm topology and parameter files. Kindly help Suji george Dept of Life Sciences University Of Mumbai India -- Over 2 Million Holiday Gift Ideas - Take a Look! mail.com shopping at http://mail.shopping.com/?linkin_id=8033174

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Modeller
by Nataly Amorim 04 Dec '07

04 Dec '07

Caros, Gostaria de saber porque quando uso algum aplicativo do Modeller9v2 recebo a seguinte mensagem: 'import site' failed; use -v for traceback. O que devo fazer para que isso não aconteça mais? Grata, Nataly Abra sua conta no Yahoo! Mail, o único sem limite de espaço para armazenamento! http://br.mail.yahoo.com/

2 1

mutate model
by suji george 03 Dec '07

03 Dec '07

Hi, I want to study the effect of mutation on the back bone structure of a protein. I am currently using the mutate_model script, which mutates the residue and minimizes the conformation of side chain keeping the rest of the protein intact (Correct me if I am wrong). Is it the right way to study the effect of mutation on the the entire protein, is there any other option in modeller to study the effect of mutation on the protein structure. Anticipating a reply soon Suji George Dept of Life Sciences university of Mumbai India. -- Over 2 Million Holiday Gift Ideas - Take a Look! mail.com shopping at http://mail.shopping.com/?linkin_id=8033174

1 0

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

2 1

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

2 1

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

1 0

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

1 0

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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modeller_usage