- modeller_usage - salilab.org

Question about alignment.align()
by Vadim Patsalo 11 Feb '08

11 Feb '08

Hello Modeller Users, I am trying to take a pseudo-symmetric heterodimeric (AB) structure, and build homodimer (AA) and (BB) structures. The chains have ~30-50% identity, nearly the same in length. The way I am doing this is aligning the AA sequence with the AB sequence derived from the PDB with alignment.align(); However, Modeller keeps doing something weird at the ends of the second chain, placing breaks after the first and before the last residue. Chain A is 3 residues shorter than chain B. Example, with underscores inserted instead of the actual sequence: template ___DLH/SVIEN___VNLED/../.. model ___DLH/H-IAN___VDL-H/../.. I would expect to have the model be "-HIA" in the beginning and "DLH-" at the end. This is the alignment that I get from Clustal, and the alignment that makes sense to me. I've tried setting 'overhang=1', using a number of different matrices from '$LIB', to no avail. With other matrices (Gonnet), I get a _horrible_ alignment, like so: VNLED/../.. VDLH/-../.. How could it insert a gap into a HETATM chain? Is there a better way to do this, perhaps aligning only the chains that are changed in the sequence (align A to B), instead of AA with AB? 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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Modeller 9v3 release
by Modeller Caretaker 05 Feb '08

05 Feb '08

The new version of Modeller, 9v3, is now available for download! Please see the download page at http://salilab.org/modeller/ for more information. If you have a license key for Modeller 8 or 9, there is no need to reregister for Modeller 9v3 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 9v3 is primarily a bugfix release relative to the last public release (9v2). Major user-visible changes include: # Mac OS X 10.5 (Leopard) is now supported (with Python 2.5). # PIR alignment file headers are now checked more closely, to avoid potential problems with these headers going unnoticed. # alignment.align() and alignment.consensus() no longer take a max_gap_length parameter, as it is not used in any case. See the Modeller manual for a full change log: http://salilab.org/modeller/9v3/manual/node38.html If you encounter bugs in Modeller 9v3, please see http://salilab.org/modeller/9v3/manual/node10.html for information on how to report them. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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Theory regarding filling of gaps
by Samuel Genheden (a03samge) 01 Feb '08

01 Feb '08

Hello, Modeller users! My question regards the theory behind and how Modeller creates the models. The case is that I have been using the Missing residue-script from the Modeller wiki-page to fill in a gap of 14 missing residues. But how does Modeller build the gap when it does not have any template structure as in my case? Best regards, Samuel

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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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