- modeller_usage - salilab.org

Building a tetramer
by Nicky Thrupp 11 Nov '08

11 Nov '08

Hi, I am building a protein with four chains (based on a tetrameric template). I was wondering about the algorithms that Modeller uses - does it build all four chains simultaneously, or does it build them one at a time? I am worried about steric clashes if the chains are built indiviudally and then put together afterwards. Thanks in advance for any help. Nicky

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Help
by nagaraju ngaraju 11 Nov '08

11 Nov '08

Dear sir/madam I want to do project in homology modelling using modeller but I am unable to crete .pir file Can you suggest me in this regard Thanks In adavance I.Nagaraju Sugen Life Sciences Tirupati 9949860196 Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/

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Re: [modeller_usage] Heme
by Bo Yang 04 Nov '08

04 Nov '08

Hi, Rubben: I use dot (.) . Heme is shown as BLK in the model. Using Chimera and VMD, the whole molecule of heme is there, but not Fe. If I select "Fe" from "element", no selection returns. The "Fe" is in the pdb file as shown below: HETATM 3620 FE BLK 455 -54.160 -1.094 -33.073 1.00999.99 1SG3621 HETATM 3621 CHA BLK 455 -55.567 -1.736 -30.032 1.00999.99 1SG3622 HETATM 3622 CHB BLK 455 -53.632 -4.396 -33.562 1.00999.99 1SG3623 HETATM 3623 CHC BLK 455 -53.011 -0.451 -36.189 1.00999.99 1SG3624 HETATM 3624 CHD BLK 455 -54.469 2.229 -32.529 1.00999.99 1SG3625 HETATM 3625 NA BLK 455 -54.569 -2.714 -32.020 1.00999.99 1SG3626 HETATM 3626 C1A BLK 455 -55.107 -2.789 -30.763 1.00999.99 1SG3627 HETATM 3627 C2A BLK 455 -55.133 -4.176 -30.354 1.00999.99 1SG3628 HETATM 3628 C3A BLK 455 -54.608 -4.886 -31.328 1.00999.99 1SG3629 HETATM 3629 C4A BLK 455 -54.246 -3.991 -32.395 1.00999.99 1SG3630 HETATM 3630 CMA BLK 455 -54.416 -6.422 -31.313 1.00999.99 1SG3631 HETATM 3631 CAA BLK 455 -55.621 -4.804 -29.030 1.00999.99 1SG3632 HETATM 3632 CBA BLK 455 -56.992 -4.376 -28.593 1.00999.99 1SG3633 HETATM 3633 CGA BLK 455 -57.255 -5.010 -27.253 1.00999.99 1SG3634 HETATM 3634 O1A BLK 455 -56.915 -4.439 -26.202 1.00999.99 1SG3635 HETATM 3635 O2A BLK 455 -57.828 -6.104 -27.233 1.00999.99 1SG3636 HETATM 3636 NB BLK 455 -53.437 -2.204 -34.573 1.00999.99 1SG3637 HETATM 3637 C1B BLK 455 -53.311 -3.583 -34.605 1.00999.99 1SG3638 HETATM 3638 C2B BLK 455 -52.782 -3.991 -35.882 1.00999.99 1SG3639 HETATM 3639 C3B BLK 455 -52.616 -2.872 -36.580 1.00999.99 1SG3640 HETATM 3640 C4B BLK 455 -53.040 -1.749 -35.784 1.00999.99 1SG3641 HETATM 3641 CMB BLK 455 -52.468 -5.428 -36.363 1.00999.99 1SG3642 HETATM 3642 CAB BLK 455 -52.091 -2.736 -38.019 1.00999.99 1SG3643 HETATM 3643 CBB BLK 455 -51.725 -3.825 -38.678 1.00999.99 1SG3644 HETATM 3644 NC BLK 455 -53.752 0.535 -34.116 1.00999.99 1SG3645 HETATM 3645 C1C BLK 455 -53.394 0.607 -35.442 1.00999.99 1SG3646 HETATM 3646 C2C BLK 455 -53.466 1.977 -35.904 1.00999.99 1SG3647 HETATM 3647 C3C BLK 455 -53.869 2.676 -34.858 1.00999.99 1SG3648 HETATM 3648 C4C BLK 455 -54.062 1.807 -33.747 1.00999.99 1SG3649 HETATM 3649 CMC BLK 455 -53.156 2.502 -37.344 1.00999.99 1SG3650 HETATM 3650 CAC BLK 455 -54.149 4.182 -34.765 1.00999.99 1SG3651 HETATM 3651 CBC BLK 455 -53.972 4.970 -35.805 1.00999.99 1SG3652 HETATM 3652 ND BLK 455 -54.923 0.052 -31.560 1.00999.99 1SG3653 HETATM 3653 C1D BLK 455 -54.874 1.432 -31.525 1.00999.99 1SG3654 HETATM 3654 C2D BLK 455 -55.330 1.916 -30.258 1.00999.99 1SG3655 HETATM 3655 C3D BLK 455 -55.681 0.681 -29.488 1.00999.99 1SG3656 HETATM 3656 C4D BLK 455 -55.392 -0.425 -30.350 1.00999.99 1SG3657 HETATM 3657 CMD BLK 455 -55.447 3.379 -29.780 1.00999.99 1SG3658 HETATM 3658 CAD BLK 455 -56.248 0.648 -28.080 1.00999.99 1SG3659 HETATM 3659 CBD BLK 455 -57.738 0.802 -28.197 1.00999.99 1SG3660 HETATM 3660 CGD BLK 455 -58.352 0.774 -26.836 1.00999.99 1SG3661 HETATM 3661 O1D BLK 455 -59.545 1.081 -26.729 1.00999.99 1SG3662 HETATM 3662 O2D BLK 455 -57.669 0.458 -25.858 1.00999.99 1SG3663 Thank you for your advice. Bo --- On Tue, 11/4/08, Rubben Torella <rubben.torella(a)gmail.com> wrote: From: Rubben Torella <rubben.torella(a)gmail.com> Subject: Heme To: n62star(a)yahoo.com Date: Tuesday, November 4, 2008, 1:01 AM Hi,Bo! What do you use in the alignment for heme? dot (.) or (*)? Because if you use (.), heme is considered as a block, while (*) consider heme as a co-factor. But you see heme and you can't see iron, or you can't see anything? I'm sorry if I don't understand your question. Rubben Torella

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Modelling an oligomer
by Lucas Bleicher 17 Oct '08

17 Oct '08

I want to model a heterotrimer consisting of proteins A, B and C, where the structure of the A:B complex is already known, and C should be modelled. There is a known structure of another structure made of proteins D, E and F, where D and E are homologous to A:B (and can be easily spatially superposed) and F is homologous to C. Do I have to work with restraints or is there a way to set a PIR file using the A:B and D:E:F complexes as "knowns" so that Modeller can assume that it must build an A:B:C complex so that A:B would be in the equivalent positions to D:E (but should of course be nearly identical to the A:B x-ray structure more than the D:E structure, since A:B is the real thing) and C must be modelled using F as template and be in the position it would occupy in the D:E:F structure? To add insult to injury, although C and F are homologous, there is a better template, G, for it in terms of identity and alignment size. So the ideal solution to the problem would be: A trimer consisting of A:B:C where A and B are knowns, C is modelled against G, and the A:B is positioned against D:E and the C model against G is positioned against F in the known D:E:F structure. I hope my message is not too confusing... Lucas P.S.: I already tried to separately model only the protein C against G and then using SSM to superpose the C model against F and the A:B complex against D:E, but that would produce some serious clashes, so I really need to build the whole thing on modeller. Novos endereços, o Yahoo! que você conhece. Crie um email novo com a sua cara @ymail.com ou @rocketmail.com. http://br.new.mail.yahoo.com/addresses

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Modeller 9v5 release
by Modeller Caretaker 16 Oct '08

16 Oct '08

The new version of Modeller, 9v5, 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 9v5 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 9v5 is primarily a bugfix release relative to the last public release (9v4). Major user-visible changes include: # New normalized DOPE assessment method, which returns a Z-score, and is thus comparable between different proteins. # PDB atom files are now also looked for in PDB-style subdirectories (the first two characters after the digit); e.g. 1abc is searched for in the 'ab' subdirectory, pdb4xyz.ent in the 'xy' subdirectory. # Libraries updated to correctly read and write remediated RNA and DNA, some other HETATMs (e.g. ions) and to use the new hydrogen names, in PDB v3. # Modeller now outputs new-style PDBs, with the element in columns 77 and 78, rather than older-style PDB which has a sequence number in this position. See the Modeller manual for a full change log: http://salilab.org/modeller/9v5/manual/node38.html If you encounter bugs in Modeller 9v5, please see http://salilab.org/modeller/9v5/manual/node10.html for information on how to report them. Note: you are receiving this email either because you subscribed to the modeller_usage mailing list, or you provided this address when you requested a Modeller license. In the latter case, if you no longer wish to receive announcements of new Modeller releases, simply reply to this email and let us know. 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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Using of a template with the coordinates of the Calpha atoms only.
by Jean-Paul Becker 16 Oct '08

16 Oct '08

Dear Modeller users, I constructed a model of a protein using a template which contains only the Calpha trace. Due to a question of a reviewer of the article i submitted for publication, i am seeking for precisions on how the Calpha trace is rebuilt to atomic resolution and then made into the model. I guess these steps are performed by the functions: model.generate_topology() and/or Restraints.make(), but i do not understand how modeller generates all the essential restraints to build the model when almost all the atoms of the template are missing except the Calpha. Does these restraints come from a library ? In this case, how is this library built ? I did not mange to find many details concerning this point in the manual, so i would really appreciate if anyone could give me some explanations. Many thanks in advance for your time and knowledge. JPB -- Jean-Paul BECKER Structure et Fonction des Membranes Biologiques (SFMB) Centre de Biologie Structurale et de Bioinformatique (CBSB) Faculté des Sciences Université Libre de Bruxelles Campus de la Plaine CP 206/2 Boulevard du Triomphe 1050 BRUXELLES BELGIQUE

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Is there anything wrong with my configuration file?My models look so strange
by wayj86 wayj86 09 Oct '08

09 Oct '08

Hi all, Two days ago I wanted to model an antibody with specifying the CDR regions.Here is my configuation file: # Homology modeling by the automodel class from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class # Redefine the special_patches routine to include the additional disulfides # (this routine is empty by default): class mymodel(loopmodel): def special_patches(self, aln): # A disulfide between residues 22 and 96: self.patch(residue_type='DISU', residues=(self.residues['22'], self.residues['95'])) self.patch(residue_type='DISU', residues=(self.residues['158'], self.residues['228'])) def select_loop_atoms(self): return selection(self.residue_range('26','33'),self.residue_range('51','57'),self.residue_range('96','110'),self.residue_range('162','172'),self.residue_range('190','192'),self.residue_range('229','237')) 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' a = mymodel(env, alnfile = '3.ali', # alignment filename knowns = ('HL','y','121','113'), # codes of the templates sequence = '6b4', loop_assess_methods=assess.DOPE) # code of the target a.starting_model= 1 # index of the first model a.ending_model = 8 # index of the last model # (determines how many models to calculate) a.loop.starting_model=1 a.loop.ending_model=2 a.make() # do the actual homology modeling I don't know what is wrong with it but the models it built were so strange,I can see some breakpoints in the structures. However,if I delete the sentences for loops specifying,the breakpoints would disappear. # Homology modeling by the automodel class from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class # Redefine the special_patches routine to include the additional disulfides # (this routine is empty by default): class mymodel(loopmodel): def special_patches(self, aln): # A disulfide between residues 22 and 96: self.patch(residue_type='DISU', residues=(self.residues['22'], self.residues['95'])) self.patch(residue_type='DISU', residues=(self.residues['158'], self.residues['228'])) 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' a = mymodel(env, alnfile = '3.ali', # alignment filename knowns = ('HL','y','121','113'), # codes of the templates sequence = '6b4') a.starting_model= 1 # index of the first model a.ending_model = 8 # index of the last model # (determines how many models to calculate) a.make() # do the actual homology modeling So could you please tell me how can I specify the CDR loops correctly?Thank you very much for any help. Best wishes, Stanley -- The future is now!

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radii.lib
by Joaquim Rui Rodrigues 09 Oct '08

09 Oct '08

Dear Modellers, I am trying to model a non-standard residue, with non-standard lib files, by following the examples in the wiki page "Using non-standard parameter files". This works fine for toplib and parlib. However, I also need to read my extended versions of radii.lib and radii14.lib. Here is the relevant part of my script: env = environ(restyp_lib_file='/Users/jrui/modeller/LIBS/restyp.lib') class MyModel(automodel): .............. a = MyModel(env, ....) a.toplib = '/Users/jrui/modeller/LIBS/top_heav.lib' a.parlib = '/Users/jrui/modeller/LIBS/par.lib' I tried the obvious a.radlib = '/Users/jrui/modeller/LIBS/radii.lib' but I get: runcmd_____W>: creation of new member 'radlib' in <Model containing 0 chains, 0 residues, and 0 atoms>: possible typo! I searched for toplib and parlib in the manual but could not anything about these keywords. How can I tell modeller to read my radii files? Many thanks, Rui Rodrigues -- Webmail ESTG de Leiria (http://webmail.estg.ipleiria.pt)

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PCA problem
by Julien Pele 06 Oct '08

06 Oct '08

Dear all, My question deals with the command which performs Principal Component Analysis (PCA). I use an input matrix of pairwise distances calculated from percentage residue identity of a multiple protein sequence alignment. I executed the following script : ################# env = environ() aln = alignment(env, file='alignment.pir') aln.id_table(matrix_file='id.mat') env.principal_components(matrix_file='id.mat', file='alignment_mod.princ') ################# The file 'alignment_mod.princ' contains projected coordinates of the first two principal components. I compared these results with other programs which hold PCA and go by the same input matrix. For instance, ade4, a package of the R software. I executed the following commands under R : ################# require (ade4) x <- read.table("id.mat", sep="") y <- dudi.pca(x, scan = F, nf = 2) write.table(y$li, file = "alignment_ade4.princ") ################# The file 'alignment_ade4.princ' also contains projected coordinates of the first two principal components. However, the coordinates acquired with these two softwares are not the same. I would like to know if the PCA command of Modeller uses internal procedures which could explain this disagreement ? How does the treatment of input matrix work with Modeller ? Any help on this will be greatly appreciated. Best regards, Julien

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clockwise pentamer to anticlockwise model
by plmallip＠mail.uh.edu 29 Sep '08

29 Sep '08

Dear colleagues, I want to model a pentamer. I have two templates. One of the templates is arranged anti-clockwise in the order ABCDE. The other template runs clockwise (AEDCB) and has identical chains. Thus if I overlap the two templates, subunit B overlaps with subunit E and so on. I want to do modelling in 2 steps. a. I want to get an initial anticlockwise model (ABCDE) from clockwise template (identical chains AEDCB). b. The model obtained from step 1 will be overlapped with the anticlockwise template to build some missing residues. I tried to get through step a by 1. Changing the alignment file 2. by changing chain identification number in the template 3. by changing the order of subunits arranged in the template Each time, I end up with the same clockwise model. Thanks in advance for any kind of suggestion in this regard. Prema, Graduate student, UOH.

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