modeller_usage

modeller_usage@salilab.org

2 participants
3148 discussions

Fibrillar collagen structure model 3hr2 Inbox
by Amadeus Cavalcanti Salvador de Alcântara 27 Jan '21

27 Jan '21

Dear Modeller Users, I am trying to use Modeller to model a comparative protein structure for the type I collagen. I came to this trying to reproduce a model from this paper: doi 10.1021/nl103943u ( *Nano Lett.* 2011, 11, 2, 757–766 ) It also used Modeller to create such a model. I contacted the 1st author for instructions on how he created the model, but unfortunately he said not to remember anymore (it has been 10 years since). I also want to mention that before posting this, I read the Modeller manual and several questions and answers posted in the mail listing. They helped me get to this point. In the following I will describe in some details what I have done, with what files and how: All necessary files for reproduction are attached in this email (I tried to attach all files - pdb, target fasta, outputs, etc. - , but it exceeded the limit of 100 KB). *1 - Target:* P02452 (CO1A1_HUMAN) and P08123 (CO1A2_HUMAN) from https://www.uniprot.org/uniprot/P02452 and https://www.uniprot.org/ uniprot/P08123 The Targets are in the Fasta format. I converted them to .ali files in the PIR format, as suggested by Ben Webb in https://salilab.org/archives/modeller_usage/2010/msg00072.html . (see FASTAtoPIR.py in the attached files). I manually edited the protein code and field2 of the .ali files (based on what I read in the manual - *File formats B.1 Alignment file (PIR)*) That is how it looks like now: * COL1A1.ali* ___________________________________________________________________ >P1;COL1A1 sequence:COL1A1: : : : :::-1.00:-1.00 MFSFVDLRLLLLLAATALLTHGQEEGQVEGQDEDIPPITCVQNGLRYHDRDVWKPEPCRICVCDNGKVLCDDVIC ...* ___________________________________________________________________ *2 - Template:* 3hr2.pdb from https://www.rcsb.org/structure/3HR2 It is very important to me to get a model as close to this structure as possible, since it comprises the collagen fibrillar structure. *3 - Alignment: *I decided to align each chain and sequence individually, as many answers in the mail listing suggested. First of all I tried to align the COL1A1.ali with the chain A of the 3hr2. pdb structure. I aligned the sequences using salign (align2d was taking too long). The 3hr2.pdb contains 2 non standard amino acids: HYP hydroxyproline LYZ Hydroxylysine I added - env.io.hetatm = True - in order to read them. *1A_salign.py* ___________________________________________________________________ env = environ() aln = alignment(env) env.io.hetatm = True mdl = model(env, file='3hr2', model_segment=('FIRST:A','LAST:A')) aln.append_model(mdl, align_codes='3hr2A', atom_files='3hr2.pdb') aln.append(file='COL1A1.ali', align_codes='COL1A1') aln.salign() aln.write(file='COL1A1-3hr2A.ali', alignment_format='PIR') aln.write(file='COL1A1-3hr2A.pap', alignment_format='PAP') ___________________________________________________________________ I added to restyp.lib: HETATM | HYP | O | | HYP | hydroxyproline HETATM | LYZ | K | | LYS | lysine, +1 I have HYP topology and parameters, but since I don't have them for LYZ I chose to treat LYZ as LYS (Lysine). I do not know if I can do it. Is it better to do so or to simply let Modeller continue with the following warning? *read_pd_459W> Residue type LYZ not recognized. 'automodel' model building will treat this residue as a rigid body.* *4 - Automodel: *I created 10 models and chose the one with lowest DOPE score (all scored 1.0 in the GA341 score), in my case, COL1A1.B99990010.pdb. I included HYP topology and parameters information to the *top_heav*.lib and *par*.lib files from the Modeller Library. Furthermore I added the HB1 (new type in HYP top) atom type information to *solv*.lib, *radii*.lib and *radii14*.lib. The HYP information was taken from *top_all36_prot_modify_res*.str and *par_all36_prot_modify_res*.str in the CHARMm FF. *2A_model-single.py* ___________________________________________________________________ from modeller.automodel import * env = environ() env.io.hetatm = True env.libs.topology.read('${LIB}/top_heav.lib') env.libs.parameters.read('$(LIB)/par.lib') # from manual a = automodel(env, alnfile='COL1A1-3hr2A.ali', knowns='3hr2A', sequence='COL1A1', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 10 a.make() ___________________________________________________________________ *5 - Final model: *I also ran the 3A_evaluate_model and 4A_plot_profiles python scripts and after that opened the 3hr2 A chain and the final model in VMD. The model looks good, however, it is not as close to the 3hr2 structured as I wished. As a mechanical engineer I am no used to those models nor to homology modeling and have been learning all here by reading the manual, instructions and mail listing. Did I make many/any mistakes? Where and what? Can the model become better (more close to the 3hr2 template structure)? If yes, how? How to know if a model is "good enough"? Can I proceed like that and create the models for the chains B and C and complete the collagen structure? I am afraid to lose the fibrillar collagen structure (which in this case is similar to a crystalline periodic structure) from 3hr2.pdb if the model is not very similar to the the 3hr2 structure. Thank you in advance for reading up to here. I am looking forward to reading your observations, suggestions and corrections. They are all very welcome. Amadeus

2 1

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

20 Jan '21

3 2

Objective function scores
by Tiglath Moradkhan 12 Jan '21

12 Jan '21

Hi I have a question about objective function scores. Why is it that lower objective function scores are indicative of better models. I've searched online for how objective function scores are computed but the explanation is too technical and I would be very grateful if you could provide a much simpler explanation of the objective function score. Thanks Tiglath

2 1

Import site failed
by Li,Haoxi 06 Jan '21

06 Jan '21

Dear Modeller Users, Hope you had a great holiday! I was implementing mod9.25 on Linux system (Ubuntu 16.04.6), but encountered this output: Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] 'import site' failed; use -v for traceback The jobs were still completed. Would this error matter? If so, how can I fix it? Thank you in advance! Best wishes, Haoxi

2 1

Getting a ligand to work in homology models
by Casey Becker 04 Jan '21

04 Jan '21

Hello, I'm currently trying to model a hemoglobin monomer that has a heme group as a ligand. If I run Modeller through the chimera interface, the ligand carries over to the models. However, if I run through IDLE, which I prefer to do because I'm using parallel jobs, the ligand does not carry over. Any help appreciated.

2 1

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.

2 1

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

2 2

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?

2 1

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

2 1

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

2 1

← Newer
1
...
6
7
8
9
10
11
12
...
315
Older →

Jump to page:

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

2003

2002

2001

2000

1999

1998

1997

modeller_usage