December 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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Re: [modeller_usage] December 74% OFF
by Doctor Harriett Lacey 29 Dec '07

29 Dec '07

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multiple target sequences
by Han Choe 20 Dec '07

20 Dec '07

Dear Modellers, If you have accession numbers of multiple, say hundreds, target sequences, what could be an easy way to model the target protein structures from a template structure? Cheers, Han

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model-loop
by Urszula Uciechowska 19 Dec '07

19 Dec '07

Hi, Thanks Marcin,this part works now after putting the brackets but now after starting the script model-loop.py I am getting: 'import site' failed; use -v for traceback Traceback (most recent call last): File "model-loop.py", line 15, in ? a.starting_model= 1 # index of the first model TypeError: 'tuple' object has only read-only attributes (assign to .starting_model) in my input file I have: 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 How should I define the starting model? What is exactly the "index of the first model"? Thank you in advance for any help Best Regards, Urszula MSc.PhD Student Medicinal Chemistry Group University of Halle-Wittenberg

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Dope output?
by Dany Naranjo Feliciano 18 Dec '07

18 Dec '07

Hi: How could I see with gnuplot my target and template graphics in the same window, as appear in the tutorial. Dany Naranjo Feliciano Lic. Bioquímica Grupo Biología Molecular Centro Nacional de Sanidad Agropecuaria (CENSA) Apartado 10. San José de las Lajas. La Habana. CP 32700. Cuba Teléfono 53-47-863014 ext 28 "40 ANIVERSARIO DEL CENSA " (diciembre/2007-enero/2009) " El futuro de Cuba tiene que ser un futuro de hombres de ciencia, de hombres de pensamiento." Fidel. --------------------- "Participe en Universidad 2008 del 11 al 15 de febrero del 2008. Palacio de Convenciones. La Habana. Cuba." http://www.universidad2008.cu --------------------- "Evento Sanidad Vegetal, del 22 al 26 de Septiembre del 2008. Palacio de las Convenciones. La Habana. Cuba."

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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

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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/

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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

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