modeller_usage February 2011

modeller_usage@salilab.org

16 participants
31 discussions

Re: [modeller_usage] Retrieving full sequence from PDB file
by Romain.Studer＠unil.ch 10 Feb '11

10 Feb '11

Hello, You can try the PDB module of the Biopython, it does it very well. http://biopython.org/DIST/docs/cookbook/biopdb_faq.pdf How do I extract polypeptides from a Structure object? Use PolypeptideBuilder. You can use the resulting Polypeptide object to get the sequence as a Seq object or to get a list of C atoms as well. Polypeptides can be built using a C-N or a C -C distance criterion. Example: # Using C-N ppb=PPBuilder() for pp in ppb.build_peptides(structure): print pp.get_sequence() # Using CA-CA ppb=CaPPBuilder() for pp in ppb.build_peptides(structure): print pp.get_sequence() Note that in the above case only model 0 of the structure is considered by PolypeptideBuilder. However, it is possible to use PolypeptideBuilder to build Polypeptide objects from Model and Chain objects as well. How do I get the sequence of a structure? The first thing to do is to extract all polypeptides from the structure (see previous entry). The sequence of each polypeptide can then easily be obtained from the Polypeptide objects. The sequence is represented as a Biopython Seq object, and its alphabet is defined by a ProteinAlphabet object. Example: > > > seq=polypeptide.get_sequence() > > > print seq Seq(SNVVE..., <class Bio.Alphabet.ProteinAlphabet>) Best regards, Romain ----- Original Message ----- Expéditeur: sneha bairy <bairysneha(a)gmail.com> à: modeller_usage(a)salilab.org Sujet: [modeller_usage] Retrieving full sequence from PDB file Date: Mon, 7 Feb 2011 11:23:10 -0600 > Hello, > For the project I am working on, I need all the sequence > residues from the pdb file irrespective of whether the > residues have atom information or not. I saw that there is > a way to write out the residues with atom information from > the pdb file. But is there a way to write out all the > sequence residues mentioned at the top of the pdb file? > > Thanks, > Sneha > > > _______________________________________________ > modeller_usage mailing list > modeller_usage(a)salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > ----- Romain Studer Dept of Structural and Molecular Biology Darwin Building University College London Gower Street, WC1E 6BT London Tel +44(0)20 7679 3890 Fax +44(0)20 7679 7193

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assess multiple chain modelling
by Dimitri Gilis 10 Feb '11

10 Feb '11

Hello, I have successfully modelled a population of tetramers. But I would like to assess them. I found that the DOPE and the GA341 scores are not suitable to assess multiple chain proteins. So, which scoring scheme can I use ? Thanks in advance. Dimitri ---------------------------------------------------------------------------------------- Dimitri Gilis Genomic and Structural Bioinformatics 3BIO - Service de Biosystèmes, Biomodélisation et Bioprocédés (Biosystems, Biomodelling and Bioprocess Department) Université Libre de Bruxelles Av. F. Roosevelt, 50 CP 165/61 1050 Brussels Belgium Tel: +32 2 650 36 15 Fax: +32 2 650 35 75 e-mail: dgilis(a)ulb.ac.be

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Retrieving full sequence from PDB file
by sneha bairy 07 Feb '11

07 Feb '11

Hello, For the project I am working on, I need all the sequence residues from the pdb file irrespective of whether the residues have atom information or not. I saw that there is a way to write out the residues with atom information from the pdb file. But is there a way to write out all the sequence residues mentioned at the top of the pdb file? Thanks, Sneha

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How to make Modeller run Iteratively
by Ashish Runthala 07 Feb '11

07 Feb '11

Dear Modellers, I am facing a small problem. Just like command line arguments are there in scripts, is it possible to make MODELLER run iteratively, based on my defined set of parameters integrated with MODELLER. If so, how. I want to use Modeller in this way. 1. I want to call salign_iterative/align2d.py with varying proteins and dynamically considered constraints. 2. Run align2d.py ( If salign is called, with my own set of defined parameters). 3. Run model_mult.py (Dynamically changing PDB template names with chainID with every run) 4. Iterate the loop 1-3 until some set of conditions are satisfied. How to make MODELLER functions change the considered parameters declared during the function call. Thanks Ashish

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how to include a pepetide during homology modelling?
by albert 07 Feb '11

07 Feb '11

Hi: I just find that Modeller could build model containing a small molecular within it. And I am wondering how to building model including a peptide from template? THX

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symmetry restrain
by flavio seixas 07 Feb '11

07 Feb '11

Hi, I'm trying to built a protein with 4 identical chains using the symmetry restrain to CA atoms as section "2.2.11 Building multi-chain models with symmetry" from modeller 9v7 manual. This is my input: # Homology modeling with multiple templates from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class log.verbose() # request verbose output # Override the special_restraints and user_after_single_model methods: class MyModel(automodel): def special_restraints(self, aln): # Constrain the A, B, C and D chains to be identical (but only restrain # the C-alpha atoms, to reduce the number of interatomic distances # that need to be calculated): s1 = selection(self.chains['A']).only_atom_types('CA') s2 = selection(self.chains['B']).only_atom_types('CA') s3 = selection(self.chains['C']).only_atom_types('CA') s4 = selection(self.chains['D']).only_atom_types('CA') self.restraints.symmetry.append(symmetry(s1, s2, s3, s4, 1.0)) def user_after_single_model(self): # Report on symmetry violations greater than 1A after building # each model: self.restraints.symmetry.report(1.0) 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='xynB1-multiple.ali', knowns=('3C2U', '1YIF', '2EXH'), sequence = 'xynB', assess_methods=(assess.DOPE, assess.GA341)) # code of the target a.starting_model= 1 a.ending_model = 2 a.make() The problem is that the program stops and the following error message appears at the shell: File "model-multiple.py", line 37, in ? a.make() File "/usr/lib/modeller9v7/modlib/modeller/automodel/automodel.py", line 98, in make self.homcsr(exit_stage) File "/usr/lib/modeller9v7/modlib/modeller/automodel/automodel.py", line 435, in homcsr self.mkhomcsr(selection(self), aln) File "/usr/lib/modeller9v7/modlib/modeller/automodel/automodel.py", line 523, in mkhomcsr self.special_restraints(aln) File "model-multiple.py", line 19, in special_restraints self.restraints.symmetry.append(symmetry(s1, s2, s3, s4, 1.0)) TypeError: __init__() takes exactly 4 arguments (6 given) This is line 19: self.restraints.symmetry.append(symmetry(s1, s2, s3, s4, 1.0)) Someone could tell me what i am doing wrong? I can not find clues at the google. Thanks for any help. Flavio

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GETF, IUPAC_M and IATMCLS errors
by Seth Tanner 07 Feb '11

07 Feb '11

I could not find what the following three error messages mean in the log file. I would be grateful if you could explain what the causes are and suggest several possible solutions. Thanks. Message 1) getf_______W> RTF restraint not found in the atoms list: residue type, indices: 17 384 atom names : C +N atom indices : 3127 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 17 384 atom names : C CA +N O atom indices : 3127 3123 0 3128 Message 2) iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_484W> Dihedral still outside +-90: -90.3341 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_484W> Dihedral still outside +-90: -90.7680 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. Message 3) << end of ENERGY. DOPE-HR score : -13843.593750 >> Model assessment by DOPE potential iatmcls_286W> MODEL atom not classified: THR:OXT THR iatmcls_286W> MODEL atom not classified: THR:OXT THR iatmcls_286W> MODEL atom not classified: THR:OXT THR iatmcls_286W> MODEL atom not classified: THR:OXT THR

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HETATM reading
by Seth Tanner 07 Feb '11

07 Feb '11

I have a HETATM entry at the end of one of my protein chains. I have included the "env.io.hetatm = True" statement in my code. I have also included "." residues in my alignment file for each HETATM residue and formed a separate chain out of them using the "/" separator. I did this in both the template sequence and in the sequence to be modelled. However, I still get the following error: -- read_te_290E> Number of residues in the alignment and pdb files are different: 1566 1560 For alignment entry: 1 1GWP.pdb x (mismatch at alignment position 1561) Alignment KLFHIRTGNMDTYYWHRYT.. PDB KLFHIRTGNMDTYYWHRYT Match ******************** -- It appears that Modeller cannot read the HETATM entries in the PDB file. I wonder if anyone has a suggestion. Thanks.

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Syntax of Restraints Commands
by Seth Tanner 04 Feb '11

04 Feb '11

Dear Modeller Community, I would like to ask how the unexpleained parameters affect the restraining process in restraints.make() and restraints.make_distance() commands The manual is very good but I cannot see that this is fully explained. Also, as a person who is using MODELLER homology modelling the first time, I would like to ask what types of restraints I should use at the beginning. I thought of using sterics first, and then try distance restraints. For the distance restraints I thought of generating two 'same' selections including CA atom of the first, middle and the last residues within each secondary structure. Then one can use both of these two selections to generate a ( n x n ) distance matrix to train the homology model. How do you think that this sounds? Any other ideas for distance restraints? FOR REFERENCE: p.92 make(atmsel, restraint type, spline on site, residue span range=(0, 99999), residue span sign=True, restraint sel atoms=1, basis pdf weight=’LOCAL’, basis relative weight=0.05, intersegment=True, dih lib only=False, spline dx=0.5, spline min points=5, spline range=4.0, mnch lib=1, accessibility type=8, surftyp=1, distngh=6.0, aln=None, edat=None, io=None) p.95 make distance(atmsel1, atmsel2, aln, spline on site, restraint group, maximal distance, residue span range=(0, 99999), residue span sign=True, distance rsr model=1, basis pdf weight=’LOCAL’, basis relative weight=0.05, spline dx=0.5, spline min points=5, spline range=4.0, accessibility type=8, restraint stdev=(0.1, 1.0), restraint stdev2=(0.0, 0.0, 0.0), surftyp=1, distngh=6.0, edat=None, io=None, exclude distance=0.0)

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amino acids in the favoured region
by sankari thirumal 04 Feb '11

04 Feb '11

Hi all, I would like to know what is the percentage of amino acids that has to lie in the favoured region (only favoured region) in ramachandran plot after modeling the protein. thanks Sankari ThirumalMolecular Biology and Microbiology Reputation is something that you crave when you do not have it; When you have it, you tend to detest it.

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modeller_usage February 2011