- modeller_usage - salilab.org

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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Fwd: model structure of IDP regions
by Priya Dey 25 Nov '20

25 Nov '20

From: "Priya Dey" <pdey(a)chemistry.du.ac.in> To: "modeller usage" <modeller_usage(a)salilab.org> Sent: Tuesday, November 24, 2020 3:37:57 PM Subject: model structure of IDP regions espected sir/ madam i want to model the unmodelled region of an intrinsically disordered protein region. I have tried the basic modelling tutorial with the total sequence of idpr 1mvf and the coordinate of the ordered region of the 1mvf idpr. But the final modelled structure generated have only the coordinate of the ordered one. Please guide me, so that i can find the all region coordinates of the modelled structure of 1mvf. Thanking you Priya dey Research Scholar Department of Chemistry University of Delhi

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MODELLER modelling of a single chain
by Austin Varela 25 Nov '20

25 Nov '20

Hello, I have a PDB file containing a complex composed of 2 proteins interacting. I wish to perform homology modelling of one of these proteins and leave the other one fixed. I have been able to do the modelling of the one protein of interest, however I am not sure how to have MODELLER include the fixed protein in the final PDB outputs as all my current outputs only contain the modelled protein. Is this some option I can modify on running MODELLER? Or would I have to align the new structures to the old one and somehow merge files to reintroduce the other protein. Thanks for the help! Austin -- Austin Varela University of Rochester - Class of 2020 BS Computational Biology & BA Data Science Computational Biology Researcher in the Werren Lab

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multi-chains: modeled separately or jointly?
by Amin Zia 25 Nov '20

25 Nov '20

Hi List, In multi-chain modeling, I am wondering if the alignment and modeling algorithms take into account multiple chains and their spatial locations concurrently or just simply model each chain separately and then combine the results. Related to this, is the dope score assessment a sum of scores for chains in these cases (in which case, it's assumed the statistics are measuring two independent models), or the correlation of chains are considered in the statistical assessment? Thank you in advance Amin Zia, Stanford Immunology

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Mismatch between residues of alignment and pdb
by Sunidhi 30 Oct '20

30 Oct '20

I downloaded the pdb_95.pir files, updated on May 14th 2020, from here <https://salilab.org/modeller/downloads/pdb_95.pir.gz>. I used the tutorial <https://salilab.org/modeller/tutorial/basic.html> to model one chain of a protein. I downloaded the pdb structure from RCSB-PDB. No changes done from my side in either files. Firstly, I was receiving an error " No atoms were read from the specified input PDB file, since the starting residue number and/or chain id in MODEL_SEGMENT (or the alignment file header) was not found; requested starting position: residue number " 1", chain " "; atom file name: 1r42A.pdb". I manually changed the chain id from blank to A and another error popped up stating that initial residue isn't matching, so I changed the initial residue from 1 to 19 and the error got resolved. Now, another error is there and isn't getting resolved anyhow. " After running model_single.py, I am getting the following error - _modeller.ModellerError: read_te_290E> Number of residues in the alignment and pdb files are different: 596 655 For alignment entry: 1 1r42A ". Ideally the pdb_95.pir file should have the same info as pdbs, yet this is popping up. Attaching the alignment section of the stated structure and the PDB is 1r42. Kindly can anyone help me in debugging what the exact issue is. I've been on it since days now. The alignment file has 596 residues while the pdb is supposed to have the same number because it has not been tampered with. Where it is going wrong? How can this be resolved? The alignment section of stated structure - >P1;1r42A structure:1r42A: 19:A: 596: :::-1.00:-1.00 ------------------STIEEQAKTFLDKFNHEAEDLFYQSSLASWNYNTNITEENVQNMNNAGDKWSAFLKE QSTLAQMYPLQEIQNLTVKLQLQALQQNGSSVLSEDKSKRLNTILNTMSTIYSTGKVCNPDNPQECLLLEPGLNE IMANSLDYNERLWAWESWRSEVGKQLRPLYEEYVVLKNEMARANHYEDYGDYWRGDYEVNGVDGYDYSRGQLIED VEHTFEEIKPLYEHLHAYVRAKLMNAYPSYISPIGCLPAHLLGDMWGRFWTNLYSLTVPFGQKPNIDVTDAMVDQ AWDAQRIFKEAEKFFVSVGLPNMTQGFWENSMLTDPGNVQKAVCHPTAWDLGKGDFRILMCTKVTMDDFLTAHHE MGHIQYDMAYAAQPFLLRNGANEGFHEAVGEIMSLSAATPKHLKSIGLLSPDFQEDNETEINFLLKQALTIVGTL PFTYMLEKWRWMVFKGEIPKDQWMKKWWEMKREIVGVVEPVPHDETYCDPASLFHVSNDYSFIRYYTRTLYQFQF QEALCQAAKHEGPLHKCDISNSTEAGQKLFNMLRLGKSEPWTLALENVVGAKNMNVRPLLNYFEPLFTWLKDQNK NSFVGWSTDWSPYA------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- ------------------------------------------------------------------------* Kindly help. Thanks and Warm Regards Sunidhi Center for Computational Biology Indraprastha Institute of Information Technology (IIIT <https://www.iiitd.ac.in/>) New Delhi 110020 India

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Consctruct a model with different templates' height
by Miguel Lacerda 28 Oct '20

28 Oct '20

Hi, Is it possible to build a model setting different heights for the templates, say , according to template similarity or other parameters? Regards, Enviado do Correio<https://go.microsoft.com/fwlink/?LinkId=550986> para Windows 10

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Modelling missing N-terminal residues
by Aathithya Diaz 23 Oct '20

23 Oct '20

Dear team, How to model the missing N-terminal residues (Residue number: 1-16) from the protein structure? My PDB structure consists of residues beginning from residues number 17. We tried modeling the structure using advanced modelling. When the missing residues were given in the loop refine step, there occurred an error stating, "The region cannot be found on the template" Is there any way you could help us in modelling the missing residues from the N-terminal? Thanks in advance Aathithya D SASTRA University Thanjavur

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Building missing atoms using MODELLER
by Zeineb Si Chaib 16 Oct '20

16 Oct '20

Dear Modeller users, I have a PDB file with missing atoms and residues. I would like to build the missing atoms only without touching the rest. I tried to build an alignment file where the sequence of the template is the same as the target and without putting any gaps (since I don't want to build any missing loops/residues). My alignment file looks like this: >P1;4xfa_atom_temp structureX:4xfa_atom: 5 :A:+186 :A:::-1.00:-1.00 ELLKPRTLADLIRILHELFAGDEVNVEEVQAVLEAYESNPAEWALYAKFDQYRYTRNLVDQGNGKFNLMILCWGE GHGSSIHDHTDSHCFLKLLQGNLKETLFDWPDKKSNEMIKKSERTLRENQCAYINDSIGLHRVENVSHTEPAVSL HLFSPPFDTCHAFDQRTGHKNKVTMTFHSKFGIRTP* >P1;4xfa_atom structureX:4xfa_atom: 5 :A:+186 :A:::-1.00:-1.00 ELLKPRTLADLIRILHELFAGDEVNVEEVQAVLEAYESNPAEWALYAKFDQYRYTRNLVDQGNGKFNLMILCWGE GHGSSIHDHTDSHCFLKLLQGNLKETLFDWPDKKSNEMIKKSERTLRENQCAYINDSIGLHRVENVSHTEPAVSL HLFSPPFDTCHAFDQRTGHKNKVTMTFHSKFGIRTP* Next, I am using the automodel class to build the missing atoms. I am using the following script: *from* modeller *import* * *# Load standard Modeller classes* *from* modeller.automodel *import* * *# Load the automodel class* 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 = automodel(env, alnfile = 'alignment.ali', *# alignment filename* knowns = '4xfa_atom_temp', *# codes of the templates* sequence = '4xfa_atom') *# code of the target* a.starting_model= 1 *# index of the first model* a.ending_model = 1 *# index of the last model* a.make() It seems that Modeller built the missing atoms (4) but I am ending up with a new model that has fewer atoms than the original one (1512 vs 1558) although they both have the same number of residues. Any idea where could be the problem? Is my approach correct? I would appreciate your help with this. Best, Zina

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Sequence difference between alignment and pdb:
by Arnau PC 05 Oct '20

05 Oct '20

Hello, I have been using Modeller a few times for simple approaches but, currently, I have to face a more complex problem. I have the crystal structure of my template (740 residues, PDB: 4J0M) and I want to model three putative homolog sequences coming from a different organism. In that sense, the putative protein sequences are 1100 residues long, so I can only model the region that it locally matches with my template. For this reason, I have to use a local alignment (Smith-Waterman algorithm) between the target and the template and you may imagine which kind of problems I have to face when trying to run Modeller with this alignment: as it is a local alignment, there are multiple positions in the pdb file that have been skipped in the alignment so I have to remove those atoms from the pdb file one by one. Additionally, there are missing positions in the crystal template so I have to remake the alignment (deleting from the template fasta file these residues) each time I find missing atoms in the pdb, plus removing the atoms in the pdb file that do not match with the local alignment. I am pretty sure there is a more intelligent and practical solution to this problem since I have to do this for more than 700 residues and it can take hours for only one model. Since I am a new Modeller user and I have only used it for simple purposes, any help you can provide it would be very appreciated. Thank you very much for your attention and sorry for the inconvenience.

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