- modeller_usage - salilab.org

optimization protocol and HETATM flexibility
by sdimicco 20 Nov '12

20 Nov '12

Dear Modellers, I am tring to set up my script to build a multimeric model with loop refinement. The script looks like: log.verbose() class dope_loopmodel(dope_loopmodel): def special_patches(self, aln): # Rename both chains and renumber the residues in each self.rename_segments(segment_ids=['A', 'B'], renumber_residues=[1, 1]) env = environ() env.io.hetatm = True a = dope_loopmodel(env, alnfile='TvLDH-1bdm.ali', knowns='1bdm', sequence='TvLDH', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 2 # Very thorough VTFM optimization: a.library_schedule = autosched.slow a.max_var_iterations = 300 # Thorough MD optimization: a.md_level = refine.very_slow # Repeat the whole cycle 2 times and do not stop unless obj.func. > 1E6 a.repeat_optimization = 2 a.max_molpdf = 1e6 a.loop.starting_model = 1 # First loop model a.loop.ending_model = 1 # Last loop model a.loop.md_level = refine.fast # Loop model refinement level a.make() automodel.final_malign3d = True It seems that the script works but I would like to check if all optimization steps have been done. How could I check it? Please, if you note errors in the script, give me suggestions Moreover, I built a model with an HETATM residue. If I want to treat it as flexible residue: how could I do that? Thank you in advance. Bests Simone

2 1

Modeller Help
by mario rossi 19 Nov '12

19 Nov '12

Hello everyone I'am Simone an italian student, ineed to learn to use modeller to do homology modelingbut i have some trouble. I downloaded and installed both modeller and python on my pc (windows 7). To learn what to do I tried to follow the basic tutorial but I find serious problems in giving the input. I can not even load the sequence as the file (.ali) is not recognized by python and if the command is entered manually, I get syntax error?? Can you help me to understand where is the mistake?

2 1

multimeric model and loop refinement
by sdimicco 16 Nov '12

16 Nov '12

Dear Member, I am trying to built a multimeric model. I would like to if I have to use restraints symmetry to model it. Moreover, i would like to built a model with all hydrogens and to refine loop automatically. How can I do that? I am trying to use allh model and loop model in the same script, but without success. Thank you in advance Simone

2 1

Re: [modeller_usage] Introduction of Zinc restraints
by flavio seixas 06 Nov '12

06 Nov '12

Hi Mehdi I never used the restrains you listed before. I can not say if it is right or not. You may try to modeller and see the results by overlaying model and template (SSM superpose) in a graphic software like Coot. My suggestion was more simple. I suggest you modify your alignment file. You may have a lot of identical residues in the alignment of zinc finger region. Try to modeller them as rigid bodies, replacing then in your sequence by dots "." This will copy the restrains of your template to your model. Another suggestion is to do as Ben advised. Regards, Flavio --- On Tue, 11/6/12, Mehdi Talebzadeh Farooji <mahditzf(a)yahoo.com> wrote: From: Mehdi Talebzadeh Farooji <mahditzf(a)yahoo.com> Subject: Re: [modeller_usage] Introduction of Zinc restraints To: "flavio seixas" <oivalf_nix(a)yahoo.com> Date: Tuesday, November 6, 2012, 2:29 AM Hi Flavio Thank you for your reply. I have to sets of restraints, the distance between SG of Cysteins and Zn 2.3 A, ND1 of his and Zn 2.0 A. I intruduced these restraints in MyModel.py class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints for ids in (('SG:204:B', 'ZN:238:B'), ('SG:207:B', 'ZN:238:B'), ('SG:225:B', 'ZN:238:B'), ('ND1:228:B', 'ZN:238:B')): atoms = [self.atoms[i] for i in ids] rsr.add(forms.upper_bound(group=physical.upper_distance, feature=features.distance(*atoms), mean=2.3, stdev=0.03) I am not sure if I am doing right thing. Regards, Mehdi From: flavio seixas <oivalf_nix(a)yahoo.com> To: mahditzf(a)yahoo.com Sent: Sunday, November 4, 2012 9:07:58 PM Subject: Re: [modeller_usage] Introduction of Zinc restraints Hi. try to build identical residues of zinc finger as well zinc atom as rigid bodies "." and modeler only the different residues. Regards flavio ------------------------------ Em sex, 2 de nov de 2012 18:41 GMT Mehdi Talebzadeh Farooji escreveu: >Dear Users, > >I am trying to build a model of a Zinc finger protein, I am having problem with zinc coordination. Since the Zinc coordination residues of the model (CCCH) are slightly different from that of the template (CCCD), in the built model, the distances between atoms of the coordination residues and zinc do not match the standard zinc coordination. I was wondering if I could introduce the Zinc coordination restraints of the model in calculation. Any idea or help would be appreciated. > >Mehdi

1 0

Introduction of Zinc restraints
by Mehdi Talebzadeh Farooji 06 Nov '12

06 Nov '12

Dear Users, I am trying to build a model of a Zinc finger protein, I am having problem with zinc coordination. Since the Zinc coordination residues of the model (CCCH) are slightly different from that of the template (CCCD), in the built model, the distances between atoms of the coordination residues and zinc do not match the standard zinc coordination. I was wondering if I could introduce the Zinc coordination restraints of the model in calculation. Any idea or help would be appreciated. Mehdi

2 1

Force B-hairpin loop when modelling
by Rienk Doetjes 26 Oct '12

26 Oct '12

Hi all! I am working with a structure that, according to all available information I have, contains a beta hairpin loop. Whenever I use modeller to produce a homology model, this beta-hairpin will not be formed. Is there a way I can force modeller to actually generate this feature I want? Forcing the standard secondary structure does not seem to work. Thanks, Rienk

2 1

Protein-complex
by Mehdi Talebzadeh Farooji 22 Oct '12

22 Oct '12

Dear Modeller users, I have a template complex (A1:B1); I would like to create a model of A2:B1 complex, A1 and A2 are similar about 50% and the structure of the A2 is known. I want to use the known structure (not the template structure of A1 subunit from complex) for modelling and refinement. I was wondering if it I could do it with modeller and how? Thanks in advance, Mehdi

2 1

Make model containing alpha-helix in addition to template
by Iain Aspley 10 Oct '12

10 Oct '12

Hello Modellers, I am having difficulty getting modeller to produce a model for my sequence containing a region which has no template which I wish to be an alpha-helix, the rest of the sequence should be modelled according to the template. I used the following script from modeller.automodel import* from modeller import* # Set up environment log.verbose() env=environ() env.libs.topology.read('${LIB}/top_heav.lib') env.libs.parameters.read('${LIB}/par.lib') env.io.atom_files_directory='./:../3BO9.pdb' a=automodel(env, alnfile='target2.ali', knowns='3BO9', sequence='query') a.restraints.add(secondary_structure.alpha(a.residue_range('129:A', '154:A'))) a.starting_model=1 a.ending_model=5 a.make() and I receive the following error messages 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 Traceback (most recent call last): File "target2.py", line 14, in ? a.restraints.add(secondary_structure.alpha(a.residue_range('129:A', '154:A'))) File "/usr/lib/modeller9.10/modlib/modeller/coordinates.py", line 304, in residue_range start = self.residues[start]._num File "/usr/lib/modeller9.10/modlib/modeller/coordinates.py", line 234, in __getitem__ (self.offset, self.length, self.suffix)) File "/usr/lib/modeller9.10/modlib/modeller/util/modutil.py", line 23, in handle_seq_indx int_indx = lookup_func(*args) File "/usr/lib/modeller9.10/modlib/modeller/coordinates.py", line 298, in _indxres raise KeyError("No such residue: %s" % indx) KeyError: 'No such residue: 129:A' I have checked the pdb file and the residues do indeed exist! The log file reads as follows MODELLER 9.10, 2011/09/28, r8346 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2011 Andrej Sali All Rights Reserved Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, 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, Linux bio-haw-pc10 2.6.32-43-generic x86_64 Date and time of compilation : 2011/09/28 18:39:17 MODELLER executable type : x86_64-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2012/10/10 11:28:47 openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL9v10}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL9v10}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234076 3158.277 3.084 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234604 3158.793 3.085 openf___224_> Open ${MODINSTALL9v10}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3283204 3206.254 3.131 rdrdih__263_> Number of dihedral angle types : 9 Maximal number of dihedral angle optima: 3 Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5 openf___224_> Open ${MODINSTALL9v10}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3292444 3215.277 3.140 openf___224_> Open ${MODINSTALL9v10}/modlib/radii14.lib openf___224_> Open ${MODINSTALL9v10}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL9v10}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL9v10}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL9v10}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL9v10}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL9v10}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 openf___224_> Open ${LIB}/top_heav.lib read_to_681_> topology.submodel read from topology file: 3 openf___224_> Open ${MODINSTALL9v10}/modlib/models.lib openf___224_> Open ${LIB}/par.lib Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 4241404 4141.996 4.045 openf___224_> Open ${LIB}/par.lib read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 io_data____W> Setting io.atom_files_directory to a colon-delimited string is deprecated, as it is not robust on Windows systems. Set it to a list of directories instead. For example: env.io.atom_files_directory = ['./', '../3BO9.pdb'] automodel__W> Topology and/or parameter libraries already in memory. These will be used instead of the automodel defaults. If this is not what you want, clear them before creating the automodel object with env.libs.topology.clear() and env.libs.parameters.clear() Can anybody help me please? Thanks in advance Iain Aspley

2 1

No atoms were read from the specified input PDB file
by yael steuerman 10 Oct '12

10 Oct '12

Hello, I'm using thos PIR file: >P1;2ks9 structureX:2ks9:1 :A :364 : :::: MDNVLPVDSDLSPNISTNTSEPNQFVQPAWQIVLWAAAYTVIVVTSVVGNVVVMWIILAHKRMRTVTNYFLVNLAFAEAS MAAFNTVVNFTYAVHN-EWYYGLFYCKFHNFFPIAAVFASIYSMTAVAFDRYMAIIHPLQPR--LSATATKVVICVIWVL ALLLAFPQGYYSTTETM-PSRVVCMIEWPEHP---------NKIYEKVYHICVTVLIYFLPLLVIGYAYTVVGITLWASE IPGDSSDRYHEQVSAKRKVVKMMIVVVCTFAICWLPFHIFFLLPYINPDLYLKK---FIQQVYLAIMWLAMSSTMYNPII YCCLNDRFRLGFKHAFRCCPFISAGDYEGLEMKSTRYLQTQGSVYKVSR* >P1;FPR1 sequence:FPR1:1 : :350 : :::: METNSSL------PTNISGGTPAVSAGYLFLDIITYLVFAVTFVLGVLGNGLVIWVAGFRMT-HTVTTISYLNLAVADFC F-TSTLPFFMVRKAMGGHWPFGWFLCKFVFTIVDINLFGSVFLIALIALDRCVCVLHPVWTQNHRTVSLAKKVIIGPWVM ALLLTLPVIIRVTTVPGKTGTVACTFNFSPWTNDPKERINVAVAMLTVRGIIRFIIGFSAPMSIVAVSYGLIATKIHKQG ------------LIKSSRPLRVLSFVAAAFFLCWSPYQVVALIATVRIRELLQGMYKEIGIAVDVTSALAFFNSCLNPML YVFMGQDFRERLIHALPASLERALTEDSTQTSDTATNSTLPSAEVELQA* ***The file 2ks9.pdb is exactly as I downloaded it from RCSB.. then I'm running the script: from modeller import * from modeller.automodel import * env = environ() a = automodel(env, alnfile='alnPrev.pir', knowns='2ks9', sequence='FPR1', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 1 a.make() I can't seem to understand why do I get the following error: rdpdb___303E> 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 " A"; atom file name: 2ks9.pdb read_te_288W> Protein not accepted: 1 2ks9 It seems like it can't find residue number 1 but I think I can see it.. And when I'm changing the PIR file in the structure line from 1 to first I get the following error: read_te_291E> Sequence difference between alignment and pdb : x (mismatch at alignment position 1) Alignment MDNVLPVDSDLSPNISTNTSEPNQFVQPAWQIVLWAAAYTVIVVTSVVGNVVVMWI PDB DNVLPVDSDLSPNISTNTSEPNQFVQPAWQIVLWAAAYTVIVVTSVVGNVVVMWII Match ** * * ** * Alignment residue type 11 (M, MET) does not match pdb residue type 3 (D, ASP), for align code 2ks9 (atom file 2ks9), pdb residue number "2", chain "A" Please check your alignment file header to be sure you correctly specified the starting and ending residue numbers and chains. The alignment sequence must match that from the atom file exactly. Another possibility is that some residues in the atom file are missing, perhaps because they could not be resolved experimentally. (Note that Modeller reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.) In this case, simply replace the section of your alignment corresponding to these missing residues with gaps. read_te_288W> Protein not accepted: 1 2ks9 What am I missing? The beggining of the ATOM part in the PDB file: MODEL 1 ATOM 1 N ASP A 2 -17.531 -22.009 -19.661 1.00 97.08 N ATOM 2 CA ASP A 2 -17.664 -21.563 -18.309 1.00 97.08 C ATOM 3 C ASP A 2 -17.647 -20.070 -18.302 1.00 97.08 C ATOM 4 O ASP A 2 -18.309 -19.432 -17.485 1.00 97.08 O ATOM 5 CB ASP A 2 -16.522 -22.041 -17.395 1.00 97.08 C ATOM 6 CG ASP A 2 -15.222 -21.430 -17.892 1.00 97.08 C ATOM 7 OD1 ASP A 2 -15.049 -21.341 -19.136 1.00 97.08 O ATOM 8 OD2 ASP A 2 -14.389 -21.037 -17.033 1.00 97.08 O ATOM 9 H ASP A 2 -16.684 -22.502 -19.945 1.00 0.00 H ATOM 10 HA ASP A 2 -18.637 -21.921 -17.898 1.00 0.00 H ATOM 11 HB2 ASP A 2 -16.714 -21.822 -16.319 1.00 0.00 H ATOM 12 HB3 ASP A 2 -16.471 -23.152 -17.318 1.00 0.00 H ATOM 13 N ASN A 3 -16.889 -19.477 -19.238 1.00123.41 N Thanks, Yael.

2 1

Regarding the Modelling Utility
by Ashish Runthala 01 Oct '12

01 Oct '12

Dear Modellers, Is there a way that i can switch on the Steepest_Descent or Conjugated_Gradient (i.e. SD or CG) in the modelling script? More specifically, is there any option like env.io.sd=true or env.io.cg=true. So for the sampling or building up the desired set of models, it uses the considered option only. Best, Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

2 1