- modeller_usage - salilab.org

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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[Fwd: to model only specific region]
by Nicee 18 May '10

18 May '10

------------------------------- Original Message ------------------------------- Subject: to model only specific region From: "Nicee" <nicee.srivastava(a)imtech.res.in> Date: Tue, May 18, 2010 3:32 pm To: modeller_usage(a)salilab.org -------------------------------------------------------------------------------- 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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Re: [modeller_usage] How to create a Pentameric Channel?
by Michael Accardi 17 May '10

17 May '10

Hello Mr. Webb, On May 16th I had asked how to form a pentamer, but I have settled for tackling the dimer situation first. As you suggested, I have included the chain break (/) character in my alignment. I have also tried using both automodel and the mymodel subclass inputs I obtained from http://salilab.org/modeller/9v8/manual/node28.html. Unfortunately, my resulting dimer does not look good. The automodel commands (#3; see below) produce a better model but with that said, one subunit appears to be normal where as the second subunit appears to have no structure whatsoever. Additionally, the subunit that appears to be 'normal' does not look as it would if I were to perform a single subunit model generation as some loops are slightly shifted. The alignment I have been using is as follows: >P1;1I9B structureX:1I9B.pdb: 1 :A:+205 :A:MOL_ID 1; MOLECULE ACETYLCHOLINE BINDING PROTEIN; CHAIN A, B, C, D, E; SYNONYM ACHBP; ENGINEERED YES; MUTATION YES:MOL_ID 1; ORGANISM_SCIENTIFIC LYMNAEA STAGNALIS; ORGANISM_COMMON GREAT POND SNAIL; ORGANISM_TAXID 6523; EXPRESSION_SYSTEM PICHIA PASTORIS; EXPRESSION_SYSTEM_TAXID 4922; EXPRESSION_SYSTEM_STRAIN GS 115; EXPRESSION_SYSTEM_VECTOR_TYPE PLASMID; EXPRESSION_SYSTEM_PLASMID PPIC9: 2.70:-1.00 ------F-----------DRA---DILYNIRQTSRP-D-----VIPTQR------DRPVAVSVSLKFINILEVNEITNEVDVVFWQQTTWSDRTLAWNS-----SHSPDQVSVPIS---SLWVPDLAAYNAI-SKPEVLTP--QLARVVSDGEVLYMPSIRQRFSCDVS-GVDTESGATCRIKIGSWTHHSREISVDPTTENSDDSEYFSQYSRFEILDVTQKKNSVTYS---CCPEAYEDVEVSLNFRKK-G-* >P1;HcoUnc49B.B99990038 sequence:HcoUnc49B.B99990038:1:A:508:B:::0.00: 0.00 MRISDLFLFATTATFYHVSRAQEDDIIVDTSQLSTVLDRLTNKTIYDKRLRPRYGDKPVDVGITIHVSSISAVSEVDMDFTLDFYMRQTWQDPRLAFGTLDLGIAKQITSLTVGVDYLDRLWKPDTFFPNEKKSFFHLATTHNSFLRIDSDGTVYTSQRLTVTATCPMKLQLFPMDSQRCKLEIESYGYTMADIDYFWGRQRSDPRQSAVVFGNFMLPQFKQTCYHVNYTQATTSSGSYRRLYFEILLVRNMGF/MRISDLFLFATTATFYHVSRAQEDDIIVDTSQLSTVLDRLTNKTIYDKRLRPRYGDKPVDVGITIHVSSISAVSEVDMDFTLDFYMRQTWQDPRLAFGTLDLGIAKQITSLTVGVDYLDRLWKPDTFFPNEKKSFFHLATTHNSFLRIDSDGTVYTSQRLTVTATCPMKLQLFPMDSQRCKLEIESYGYTMADIDYFWGRQRSDPRQSAVVFGNFMLPQFKQTCYHVNYTQATTSSGSYRRLYFEILLVRNMGF* HcoUnc49B.B99990038 - denotes a pdb file I created when I formed just a single subunit model. I subsequently ran the above alignment file (named: HcoUnc49B_two.ali) in one of the following three commands: 1) Cut and paste The input command from node 28 (link above) and changed the following three lines: alnfile = 'HcoUnc49B_two.ali' , # alignment filename knowns = '1i9b', # codes of the templates sequence = 'HcoUnc49B.B99990038') # code of the target 2) Cut and paste the same input as #1 (with corrections) but instead wrote automodel where node28 insisted the user use 'MyModel' (i.e. # Be sure to use 'MyModel' rather than 'automodel' here!) 3) The following input which was in a file I created called 'model.py': from modeller import * from modeller.automodel import * env = environ() a = automodel(env, alnfile='HcoUnc49B_two.ali', knowns='1I9B', sequence='HcoUnc49B.B99990038') assess_methods=(assess.DOPE, assess.GA341) a.starting_model = 1 a.ending_model = 5 a.make() Do you see any roadblocks in my commands, that may be preventing me from producing two nice looking (possibly interacting) subunits? Ideally what I would like to create is a dimer that looks like two of my HcoUnc49B.B99990038.pdb files positioned beside each other so that one loop (i.e. amino acids 187-190 in the above sequence) on the primary subunit is adjacent to another loop (i.e. amino acids 84-86) on the corresponding subunit. I apologize for the length of the email. Any advice is greatly appreciated. Thank you in advance, All the best, Mike

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How to create a Pentameric Channel?
by Michael Accardi 17 May '10

17 May '10

To whom this may concern, I am new to MODELLER 9v7 and, as such, am having difficulty creating a pentameric channel. I am using the acetylcholine binding protein (PDB ID 1I9B) as a template for my protein sequence. However, I appear to only ever produce a single subunit. I have searched for command inputs to produce a pentameric channel as the acetylcholine binding protein itself is a pentameric channel. Unfortunately I have had no luck. I have very basic computer language skills. If anyone has any advice or useful tutorials I could review in order to produce a pentamer, it would be greatly appreciated! Thanks in advance, Mike

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