December 2020 - modeller_usage

Query regarding the modelling of a particular set of residues in a protein
by Sruthi Sudhakar 20 Jan '21

20 Jan '21

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Structural alignment of multiple chains
by Tal Weizmann 21 Dec '20

21 Dec '20

Hello, I would like to run structural alignment using all chains of the same protein with salign (different PDB files). Can I do that with modeller? Thanks, Tal No.1 Modern University in the Midlands Guardian University Guide 2021 1st for Overseas Student Experiences based on student trips abroad from HESA 2018/19 UK data Top 30 in the World for International Students QS World University Rankings 2021 University of the Year for Student Experience 2019 The Times and Sunday Times Good University Guide 2019 NOTICE This message and any files transmitted with it is intended for the addressee only and may contain information that is confidential or privileged. Unauthorised use is strictly prohibited. If you are not the addressee, you should not read, copy, disclose or otherwise use this message, except for the purpose of delivery to the addressee. Any views or opinions expressed within this e-mail are those of the author and do not necessarily represent those of Coventry University.

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modeling two chains while preserving their structural orientation wrt each other
by shivu shiv 04 Dec '20

04 Dec '20

Dear All, I am working on modeling a protein with two chains (heterodimer). I have used two separate pdb files for each chain and oriented the two template structures appropriately before the modeling. Modeller is able to model both the chains, however not preserving the orientation of both the chains. I am seeking suggestions for how to specify restraints to preserve the orientation of both the chains with respect to each other. Please provide your suggestions. Thanks and Regards shivu

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Trouble with SOAP Score
by Brenda de Souza Ferrari 04 Dec '20

04 Dec '20

Dear users, I am having trouble to use the SOAP score. I already read the manual and tried to find tutorials online but none addressed the issues I am having. I downloaded the SOAP-Protein potential file from the SOAP website and placed at C:\ProgramFiles\Modeller9.25\lib\x86_64-w64, uncommented the SOAP-related lines in model-single.py but when i try to run the script i receive an error: hdf5err____E> unable to open file Here's a description of what I get back from the code: MODELLER 9.25, 2020/09/03, r11894 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2020 Andrej Sali All Rights Reserved Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong, M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, WinNT 10.0 build 18363, BRENDA, SMP, unknown Date and time of compilation : 2020/09/03 08:23:39 MODELLER executable type : x86_64-w64 Job starting time (YY/MM/DD HH:MM:SS): 2020/12/04 14:09:46 check_ali___> Checking the sequence-structure alignment. Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms: ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------- END OF TABLE read_to_681_> topology.submodel read from topology file: 3 The following 1 residues contain 6-membered rings with poor geometries after transfer from templates. Rebuilding rings from internal coordinates: <Residue 38 (type TYR)> mdtrsr__446W> A potential that relies on one protein is used, yet you have at least one known structure available. MDT, not library, potential is used. 0 atoms in HETATM/BLK residues constrained to protein atoms within 2.30 angstroms and protein CA atoms within 10.00 angstroms 0 atoms in residues without defined topology constrained to be rigid bodies condens_443_> Restraints marked for deletion were removed. Total number of restraints before, now: 6900 6307 >> Model assessment by DOPE potential iatmcls_286W> MODEL atom not classified: ARG:OXT ARG >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 81 Number of all, selected real atoms : 681 681 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 6307 6307 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 109400 Dynamic pairs routine : 1, NATM x NATM double loop Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 LENNARD_JONES_SWITCH : 6.500 7.500 COULOMB_JONES_SWITCH : 6.500 7.500 RESIDUE_SPAN_RANGE : 1 9999 NLOGN_USE : 15 CONTACT_SHELL : 15.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T F F F T SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : -5509.1812 << end of ENERGY. DOPE score : -5509.181152 >> Model assessment by SOAP-Protein-OD score HDF5-DIAG: Error detected in HDF5 (1.10.5) thread 0: #000: C:\Users\ben\Desktop\hdf5-1.10.5\src\H5F.c line 509 in H5Fopen(): unable to open file major: File accessibilty minor: Unable to open file #001: C:\Users\ben\Desktop\hdf5-1.10.5\src\H5Fint.c line 1498 in H5F_open(): unable to open file: time = Fri Dec 04 14:09:54 2020 , name = 'C:\Program Files\Modeller9.25/modlib\/soap_protein_od.hdf5', tent_flags = 0 major: File accessibilty minor: Unable to open file #002: C:\Users\ben\Desktop\hdf5-1.10.5\src\H5FD.c line 734 in H5FD_open(): open failed major: Virtual File Layer minor: Unable to initialize object #003: C:\Users\ben\Desktop\hdf5-1.10.5\src\H5FDsec2.c line 346 in H5FD_sec2_open(): unable to open file: name = 'C:\Program Files\Modeller9.25/modlib\/soap_protein_od.hdf5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0 major: File accessibilty minor: Unable to open file hdf5err____E> unable to open file Traceback (most recent call last): File "c:/Users/Brenda/Documents/Doutorado/Modelagem_ProFurina/1KN6_model1/model-single.py", line 13, in <module> a.make() File "C:\Program Files\Modeller9.25\modlib\modeller\automodel\automodel.py", line 150, in make self.multiple_models(atmsel) File "C:\Program Files\Modeller9.25\modlib\modeller\automodel\automodel.py", line 255, in multiple_models self.outputs.append(self.single_model(atmsel, num)) File "C:\Program Files\Modeller9.25\modlib\modeller\automodel\automodel.py", line 352, in single_model self.model_analysis(atmsel, filename, out, num) File "C:\Program Files\Modeller9.25\modlib\modeller\automodel\automodel.py", line 391, in model_analysis assess_keys = self.assess(atmsel, self.assess_methods, out) File "C:\Program Files\Modeller9.25\modlib\modeller\automodel\automodel.py", line 515, in assess (key,value) = method(atmsel) File "C:\Program Files\Modeller9.25\modlib\modeller\terms.py", line 60, in __call__ return (self.name, atmsel.assess(self)) File "C:\Program Files\Modeller9.25\modlib\modeller\selection.py", line 726, in assess molpdf, terms = assessor._assess(self, output=output, **vars) File "C:\Program Files\Modeller9.25\modlib\modeller\terms.py", line 56, in _assess return atmsel.energy(edat=self._get_energy_data_cached(), File "C:\Program Files\Modeller9.25\modlib\modeller\terms.py", line 68, in _get_energy_data_cached self._edat = self._get_energy_data_all() File "C:\Program Files\Modeller9.25\modlib\modeller\terms.py", line 73, in _get_energy_data_all edat.energy_terms.append(self) File "C:\Program Files\Modeller9.25\modlib\modeller\util\modlist.py", line 154, in append self.insert(len(self), obj) File "C:\Program Files\Modeller9.25\modlib\modeller\util\modlist.py", line 166, in insert self._insfunc(indx, obj) File "C:\Program Files\Modeller9.25\modlib\modeller\terms.py", line 38, in _insfunc obj._add_term(self.__edat(), indx) File "C:\Program Files\Modeller9.25\modlib\modeller\soap_protein_od.py", line 20, in _add_term _modeller.mod_soap_od_create(edat, indx, self._group.get_type(), _modeller.ModellerError: hdf5err____E> unable to open file Could someone help me with this problem?

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