May 2010 - modeller_usage

Loop Refinement - Clustering necessary?
by Jan H. Löhr 22 Jun '10

22 Jun '10

Dear Modeller users, according to posts in this mailing list as well as the background information to ModLoop, the best loop-model is chosen by lowest pseudo-energy score (http://modbase.compbio.ucsf.edu/modloop/ - Fiser's and Sali's papers cited at the bottom of the page). However, the tutorial of Modeller indicates that "it is important to note that a most accurate approach to loop refinement requires the modeling of hundreds of independent conformations and their clustering to select the most representative structures of the loop" http://www.salilab.org/modeller/tutorial/advanced.html) I have been comparing different loop-models generated by loop.model for a selected region of a pdb-file and I am tempted to simply choose the best DOPE-HR-scoring model. Yet the clustering idea does makes sense. So far, the greatest cluster of models often contains (one of) the best scoring model(s), but not in every case. My question is therefore: Should the best model be chosen, or should the best model of the greatest cluster be chosen? I wonder about your opinions regarding this issue. In case anyone is voting for the clustering method: What method is easily suitable for clustering - unfortunately, the loop.model-class does not seem to have an integrated clustering option, does it? Regards Jan Jan H. Löhr Univ. Hamburg, Germany

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side-chains like in template
by sdh 01 Jun '10

01 Jun '10

Hello, I want to create a model based on two templates. How can I constraint few selected positions, so they would preserve (if possible) side-chain conformation of one of the templates? Thanks for hints, sdh

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Modelling a really large structure with a lot of chains
by Claudio M. Soares 28 May '10

28 May '10

Dear Modellers, I am trying to model a really large structure with a lot of chains (180 to be more exact - this is a complete virus capside) and I am encountering problems with the PDB format used in the automodel class. I manage to convince it to read a PDB file with 4 false chains (corresponding each to 45 "real" chains). However, the script finds out 180 chains internally (so much for fooling it...), writes them to the *.INI file with bogus chain IDs (and bogus residue and atom numbers) that it cannot read again when trying to produce the models. How to solve this? Can I change the automodel class to read mmCIF instead of PDB? Thanks in advance, Cláudio M. Soares -- -------------------------------------------------------- Claudio M. Soares Instituto de Tecnologia Química e Biológica Universidade Nova de Lisboa Av. da República – EAN, 2780-157 Oeiras PORTUGAL Phone:(351)214469610/214469100 Fax :(351)214411277 email:claudio@itqb.unl.pt http://www.itqb.unl.pt/~claudio Skype: claudio.m.soares

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Modeling magnesium ion: Segmentation fault
by Renuka Robert 28 May '10

28 May '10

I want to model ONLY magnesium ion (from protein B) on an already crystallized structure (protein A). So the sequence of my target and template is exactly the same. My alignment file is ---------------------------------------------------------------------------------------------------------------------------- >P1;proteinA structureX:proteinA: 37 :B:+266 :B:::-1.00:-1.00 -QYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGEGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIGGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLH* >P1;proteinB structureX:proteinB: 401 :A:+1 :A:::-1.00:-1.00 $--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------* >P1;target sequence:target: : : : ::: 0.00: 0.00 $QYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGEGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIGGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLH* when i run this script from modeller import * from modeller.automodel import * log.verbose() env = environ() env.io.atom_files_directory = ['.', '../atom_files'] env.io.hetatm = True a = automodel(env, alnfile = 'alignment.ali', knowns=('proteinA','proteinB'), sequence='target') a.starting_model= 1 a.ending_model = 1 a.make() I am getting segmentation fault. Could you please help me? Regards Renu

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weight restraints
by Armin Meier 27 May '10

27 May '10

Hi, I have a pir file with more than one template. Each template has its distance restraints in the rsr-file. How can I weight the distance restraints for each template individually, i.e. all CA_CA-distance restraints for template t1 are weighted by a factor w_t1, for template t2 w_t2 and so on, so that templates with higher weight have more influence on the final structure. Rewriting the distance restraints and adding a weight as parameter maybe is a solution, i.e. starting with cuser_form.c from examples/c-extensions, multiplying *val = RT * 0.5 * delta * delta / stdev2; by an additionally passed weight would do it? Is the weight relative or absolute? Best regards Armin Meier

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Re: [modeller_usage] weight restraints
by Modeller Caretaker 27 May '10

27 May '10

On 5/27/10 12:17 PM, meier(a)lmb.uni-muenchen.de wrote: > Ok, suppose I have a single restraint for every template and a method > to combine them in an apropriate way. It is possible to weight a set > of restraints, e.g. CA-CA distances for all templates by writing > e.g.: env.schedule_scale=physical.values(default=1.0, ca_distance=2) Sure. You just have to put your restraints in the relevant group (e.g. in this case, physical.ca_distance) and the weight will apply to all the restraints in that group. > So what I basically wanted to know is how this (up-)weighting > (ca_distance=2) is implemented in Modeller. There's nothing complicated about it. The restraint function is simply multiplied by the weight. 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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Re: [modeller_usage] How to set starting residue number in modeling
by Modeller Caretaker 27 May '10

27 May '10

On 5/27/10 9:17 AM, Keehyoung Joo wrote: > Today, I tried it by using rename_segments method. > But, I did not make model that I want. > The following is my script to model. > I add MyModel class and function rename_segments. > I want to build model that have chain id ='A' and starting residue number=5. To use rename_segments in combination with automodel, use the special_patches() method, as detailed at http://salilab.org/archives/modeller_usage/2009/msg00245.html A minimal script which should do what you want is: from modeller import * from modeller.automodel import * class MyModel(automodel): def special_patches(self, aln): self.rename_segments(segment_ids='A', renumber_residues=5) log.verbose() env = environ() a = MyModel(env, alnfile='alignment.ali', knowns='5fd1', sequence='1fdx') a.make() 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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How to set starting residue number in modeling
by Keehyoung Joo 26 May '10

26 May '10

Dear modeller users, I use MODELLER 9v7. In automodel script, I want to build protein model starting specific residue number instead of 1. How to set starting residue number in modeling. Thanks, Keehyoung Joo

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occupancy <1 in my models
by Anna Marabotti 25 May '10

25 May '10

Hi crew, I obtained a model of a protein using Modeller 9v7. Looking at the resulting PDB file, I saw that several atoms (in some cases the entire sidechain, in other cases only one or two atoms) show an occupancy <1 (typically 0,5, but also 0.3 in some cases). In the template, the corresponding residues show two or sometimes three alternative conformations of their sidechains, with occupancy <1, so I imagine that Modeller chose one of the conformations and transferred directly the information about occupancy in the PDB file it creates. My question is: what is the criterium that Modeller follows to choose one alternative conformation? It simply chooses the first one, or are there other criteria? And what about the fact that a single atom has an occupancy <1 without any other alternative conformations? Could this be able to perturb the protein behavior? Many thanks and best regards Anna ____________________________________________________ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma, 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Email: anna.marabotti(a)isa.cnr.it Skype account: annam1972 Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm "If you think you are too small to make a difference, try sleeping with a mosquito"

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to model only specific region
by Nicee 18 May '10

18 May '10

Hello all, I have a pdb file(pdb1.pdb) which is having some missing residues like from 89 to 96 and 137 to 141,etc. I wish to model only this missing region such that rest of the structure remains the same as in the initial pdb(pdb1.pdb). I have searched a template(pdb2.pdb) having 64% identity with sequence(seq1)of pdb1. Is it possible to model the missing residues using pdb2 as template but the remaining portion of pdb1 remains the same. Kindly help.Eagerly witing for response. Thanking you. With regards, Nicee.

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