- modeller_usage - salilab.org

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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Cluster PDBs
by Wang Yanli 29 Sep '08

29 Sep '08

Dear modeller, I had build 500 models, and want cluster the build models. I had try the Cluster_PDBs(http://www.salilab.org/modeller/wiki/Cluster%20PDBs), but I just got the average-structure. I want analysis the clusters of the build models. How to do it? Thanks very much!

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Re: [modeller_usage] Need help in not modeling the propep feature in final model
by Modeller Caretaker 29 Sep '08

29 Sep '08

Saravanan wrote: > I am modeling a protein in which two subunits are linked by a "propep" > which is not present in crystal structurei.e, its cleaved when protein > is active. I want to generate models without the "PROPEP". > > Crystal Structure available looks like this: (chain a and b) > > aaaaaaaaaabbbbbbbbbbb > > Model sequence is like this : (chain a and b and p-propep) > > aaaaaaaaaaapppppppppppppppbbbbbbbbbbb > > Model structure should be like this : (chain a and b AND propep chain p > should not present) > > aaaaaaaaaaabbbbbbbbbbb I don't think I fully understand your question, because the model structure always has the same sequence as the "model sequence", by definition. If you don't want to have the propep sequence in your model, just don't include it in the model sequence in your alignment. If, on the other hand, you want to build a model containing the propep sequence but you don't want to write it into the output PDB file, you can either edit the output PDB file by hand, or you can use selection() to select the non-propep parts and then selection.write() to write out a PDB. 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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W> MODEL atom not classified: GLY:OXT GLY
by Joaquim Rui Rodrigues 24 Sep '08

24 Sep '08

Dear Modellers, I am trying to build some missing loops in a PDB structure with modeller 9v4. For this, I am using the script found in examples/automodel/model-loop-define.py for which I only changed residue_range's, and alnfile, knowns and sequence. The protein is a dimer, and both subunits end with a Gly residue. I am getting this warning at the DOPE potential assessment: >> Model assessment by DOPE potential iatmcls_286W> MODEL atom not classified: GLY:OXT GLY iatmcls_286W> MODEL atom not classified: GLY:OXT GLY A related message in the archives suggests editing modlib/atmcls-melo.lib (http://www.salilab.org/archives/ modeller_usage/2004/msg00169.html). This file seems to be used for loop modelling, but not for DOPE evaluation, as suggested in the log file: openf___224_> Open ${LIB}/atmcls-mf I have also tried to use the dope_loopmodel class, instead of loopmodel. Here, I get the same warnings for both stages (loop modelling and DOPE assessment). How can I avoid such messages? Should I somehow edit atmcls-mf.lib? Many thanks, Rui Rodrigues -- Webmail ESTG de Leiria (http://webmail.estg.ipleiria.pt)

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from ylwang: loop conformation sampling
by Wang Yanli 19 Sep '08

19 Sep '08

Dear modeller, Firt, thanks for Ben Webb's help on my question, I follow your advice and found that error in MASS line. Now, I want to ask questioins about loop conformation. A loop in involved in the ligand binding and also involved in the dimmer interface. In the templet, the loop is short, but for my protein, it is longer than templet by 12 residues. The protein can be monomer or dimmer, but only be funcational in dimmer form. So, I want study: 1: the impact of dimmer on the loop conformation. 2: the impact of ligand on the loop conformation. Can I do loop-refine process times for dimmer and monomer to the study 1 issue 1? And Can I do modeller by "modeling ligands in the binding site" to study the issue 2? Or, is there other ways for my issue. I had read some paper about "ligand-supported homology model", but can't understand it well. It seems a method, but no tool-package availble? Any advices, please! -- PH.D Student Shanghai Key Lab. of Chemical Biology School of Pharmacy East China University of Science and Technology

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how to constrain automodel to remain closer to the template
by Jake Gunn-Glanville 19 Sep '08

19 Sep '08

I have been modeling a protein with a template I am quite confident in, and a loop that I would like to use a separate template for. When I generate 200 models, they all seem to show a great deal of structural diversity. Curious, I developed 20 models of a solved structure against itself, and found a bit of diversity in all of these resulting models as well. Is there a good way to constrain automodel so that it diverses less from the templates when thre are no obvious residue clashes forcing it to make adjustments? -- Jacob Glanville Informatics Associate Rinat Biotherapeutics & Bioinnovation Center; Pfizer Inc. 415 497 3552

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