modeller_usage

modeller_usage@salilab.org

3151 discussions

Partial structure alignment
by Parker de Waal 21 Nov '16

21 Nov '16

Hello modeller list, Does anyone know if it is possible to perform a 3d alignment between two proteins while only moving the selected atoms? (i.e. leaving the unselected atoms for the alignment unmoved?) Best, Parker

2 1

my email address
by sara20＠mail.ustc.edu.cn 18 Nov '16

18 Nov '16

sara20(a)mail.ustc.edu.cn

1 0

Including Non-Protein Residue to the Model
by Fadhila Balqis N 17 Nov '16

17 Nov '16

Dear All, I wanted to make a model of human flavin-containing monooxydase 3 (FMO3) enzyme from the template FMO of *Saccharomyces pombe*. This enzyme has FAD residue that is important to the project I'm working on. But of all the model output, none came with this FAD residue. I have tried simple usage automodelling provided in the manual and modelling with the guide from basic modelling tutorial (provided here: https://salilab.org/modeller/tutorial/basic.html). Lastly, I also have tried to use the script for including water molecules, HETATM residues, and hydrogen atoms to the model (described in here: https://salilab.org/modeller/manual/node18.html). The FAD residue was not present and I ran out of ideas on how to make this work. The FAD binding site is highly conserved in FMOs across species, so I don't see why it was excluded from the model. In the last try the script gave me this: read_pd_459W> Residue type FAD not recognized. 'automodel' model building will treat this residue as a rigid body. To use real parameters, add the residue type to ${LIB}/restyp.lib, its topology to ${LIB}/top_*.lib, and suitable forcefield parameters to ${LIB}/par.lib. What should I do? Your inputs are so much wanted and appreciated Fadhila Balqis Nurfitria

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ALIGN CODES NOT FOUND
by Fadhila Balqis N 14 Nov '16

14 Nov '16

Dear All, I want to make a model by using this specific template "2GVC" and I try to include HETATM residues to my model. But then this happened: openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL9v17}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL9v17}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 191566 187.076 0.183 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 192094 187.592 0.183 openf___224_> Open ${MODINSTALL9v17}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 240694 235.053 0.230 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 ${MODINSTALL9v17}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041 0.242 openf___224_> Open ${MODINSTALL9v17}/modlib/radii14.lib openf___224_> Open ${MODINSTALL9v17}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL9v17}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL9v17}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL9v17}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL9v17}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL9v17}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 openf___224_> Open align-ligand.ali Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 265487 259.265 0.253 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 266937 260.681 0.255 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 269837 263.513 0.257 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 275637 269.177 0.263 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 287237 280.505 0.274 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 310437 303.161 0.296 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 325013 317.396 0.310 read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 2) = P31513 I used this script: # Comparative modeling with ligand transfer from the template 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'] # Read in HETATM records from template PDBs env.io.hetatm = True a = automodel(env, alnfile = 'align-ligand.ali', # alignment filename knowns = '2gvc', # codes of the templates sequence = 'P31513') # code of the target a.starting_model= 4 # index of the first model a.ending_model = 4 # index of the last model # (determines how many models to calculate) a.make() # do the actual comparative modeling and used this alignment format: >P1;2gvc structureX:2gvc:5: :575: :flavin-containing monooxidase:saccharomyces pombe: : MCLPTIRKIAIIGAGPSGLVTAKALLAEKAFDQVTLFERRGSPGGVWNYTSTLSNKLPVP STNPILTTEPIVGPAALPVYPSPLYRDLQTNTPIELMGYCDQSFKPQTLQFPHRHTIQEY QRIYAQ--PLLPFIKLATDVLDIE-----KKDGSWVVTYKGTKAGSPISKDIFDAVSICNGHYEVPYIPNI-- KGLDEYAKAVPGSVLHSSLFREPELFVGESVLVVGGASSANDLVRHLTPVAKHPIYQSLL GG--------------------------------------------------------- GDIQNES--------------LQQVPEITKFDPTTREIYLKGGKVLSNIDR VIYCTGYLYSVPFPSLAKLKSPETKLIDDGSHVHNVYQHIFYIPDPTLAFVGLALH- VVPFPTSQAQAAFLARVWSGRLKLPSKEEQLKWQDELMFSLSGANNMYHSLDYPKD---ATYINKLH--------- DWCKQATPVLEEE-FP------------SPYWGEKERSIRENMWSIRAK----- FFGI-EPPK-----------------------..* >P1;P31513 sequence:P31513:0:.:0:.:flavin-containing monooxidase 3:homo sapiens: : ----MGKKVAIIGAGVSGLASIRSCLEEGL--EPTCFEKSNDIGGLWKFSDHAEEGR----- -------------------ASIYKSVFSNSSKEMMCFPDFPFPDDFPNF MHNSKIQEYIIAFAKEKNLLKYIQFKTFVSSVNKHPDFATTGQWDVTTER--- DGKKESAVFDAVMVCSGHHVYPNLPKESFPGLN----HFKGKCFHSRDYKEPGVFNGKRVLVVGLGN SGCDIATELSRTAEQVMISSRSGSWVMSRVWDNGYPWDMLLVTRFGTFLKNNLPTAISDW LYVKQMNARFKHENYGLMPLNGVLRKEPVFNDELPASILCGIVSVKPNVKEF-- TETSAIFEDGTIFEGIDCVIFATGYSFAYPFLDESIIKSRNNEIILFKG----VFPPL-- LEKSTIAVIGFVQSLGAAIPTVDLQSRWAAQVIKGTCTLPSMEDMMNDINEKMEKK---RKWFG- KSETIQTDYIVYMDELSSFIGAKPNIPWLFLTDPKLAMEVYFGPCSPYQFRLVGPGQWPGARNAI- LTQWDRSLKPMQTRVVGRLQKPCFFFHWLKLFAIPILLIAVFLVLT..* Please point out my mistakes. Your help is so much appreciated. Thanks in advance Fadhila Balqis Nurfitria

2 1

PDB problem
by deepak kumar 02 Nov '16

02 Nov '16

Hi, Thanks for your previous kind reply. I came across a problem which is quite strange to me: When running modeller to model a sequence on a template pdb 4QTA (obtained from BLAST, pdbaa database), I figured out that the sequence of the pdb from blast output is different from the original pdb sequence, Please see below the error I get from modeller because of this issue: Alignment sequence: MAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKIL LRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDL KPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNR PIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHK RIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS PDB sequence matching range provided in alignment: GPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENII GINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNT TCDLKICDFGLARVADTRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPS QEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEP IAEAPFKFDMELDDLPKEKLKELIFEETARFQPGY Traceback (most recent call last): File "modified-comp-align.py", line 11, in <module> a.auto_align() # get an automatic alignment File "/data/deepak-protein-modeling/modlib/modeller/automodel/automodel.py", line 146, in auto_align self.sequence, matrix_file, overhang, write_fit) File "/data/deepak-protein-modeling/modlib/modeller/scripts/align_strs_seq.py", line 8, in align_strs_seq aln = alignment(env, file=segfile, align_codes=knowns) File "/data/deepak-protein-modeling/modlib/modeller/alignment.py", line 20, in __init__ self.append(**vars) File "/data/deepak-protein-modeling/modlib/modeller/alignment.py", line 79, in append allow_alternates) _modeller.SequenceMismatchError: get_ran_648E> Alignment sequence does not match that in PDB file: 1 ./4QTA.pdb (You didn't specify the starting and ending residue numbers and chain IDs in the alignment, so Modeller tried to guess these from the PDB file.) Suggestion: put in the residue numbers and chain IDs (see the manual) and run again for more detailed diagnostics. You could also try running with allow_alternates=True to accept alternate one-letter code matches (e.g. B to N, Z to Q). when checking the alignment file, I see that the alignment (obtained from BLAST result) and modified to PIR format is fine: >P1;NP_002736.3.35214 sequence:NP_002736.3.35214:1 : :360 : :::-1.00:-1.00 MAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS* >P1;4QTA structure:4QTA: :A : :A :::-1.00:-1.00 MAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS* The problem is arising because the original PDB file 4QTA has different chain A sequence than the chain A sequence obtained from BLAST. May I please ask your comments and solution to how this problem can be solved? , and please let me know why is this problem occurring? Thanks much, Deepak On Sun, Oct 30, 2016 at 4:18 AM, Modeller Caretaker < modeller-care(a)salilab.org> wrote: > On 10/28/16 9:33 AM, deepak kumar wrote: > >> However, does not >> mentioning the "start" and "end" residue of the PDB file influence the >> quality of the structure? or influence the model any way? >> > > No. > > Am I right, if I say, that modeller by default takes the residues of >> chain "B", finds the corresponding residues in chain B and correctly >> models the sequence as per the alignment. >> > > That's correct. > > > Ben Webb, Modeller Caretaker > -- > modeller-care(a)salilab.org https://salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage >

2 1

energy of interface between selections
by David De Sancho 02 Nov '16

02 Nov '16

Hi I’m handling a problem where it is important to evaluate energies of interfacial residues (e.g. interface residues between two helices in a protein). In order to carry out this energy evaluation with Modeller, I start by producing a model for the protein. Then I generate two selections (e.g. one for each helix). Would it be possible to calculate the energy for residues in the interface between both selections? Thanks, David

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how to make PIR file
by Nikhil Maroli 29 Oct '16

29 Oct '16

Dear all, I'm a new user of the modeller.I have a protein fast sequence and template protein PDB as well as fasta. I couldn't understand how I should make PIR file for the input? I have to make it manually by copying fasta sequence and editing required fields or is there any other method available ? -- Regards, Nikhil Maroli

2 1

Unable to run parallel job
by Del Genio, Charo 26 Oct '16

26 Oct '16

Dear all, I'm trying to run a parallel job with modeller. The script is from modeller import * from modeller.automodel import * from modeller import soap_protein_od j = job() for i in range(16) j.append(local_slave()) log.verbose() env.io.atom_files_directory = ['.', '../atom_files'] a = dopehr_loopmodel(env, alnfile='OurAlignment.ali', knows='2p1mB', sequence='Rece', assess_methods=(assess.DOPEHR, soap_protein_od.Scorer(), assess.GA341), loop_assess_methods=assess.DOPEHR) a.starting_model = 1 a.ending_model = 16 a.loop.starting_model = 1 a.loop.ending_model = 10 a.use_parallel_job(j) a.make() However, it doesn't seem to work properly. In particular, it creates 16 slave output files containing exclusively 'import site' failed and then it hangs there, doing nothing at all, until I kill it with CTRL-C. What am I doing wrong? For sake of completeness, I'm running modeller 9.17, the distribution is Gentoo Linux, and single-CPU runs of modeller work fine without problems (so far). Thanks!

2 2

sequence of salign/align2d
by Evelyne Deplazes 24 Oct '16

24 Oct '16

Hi I want to make a homology model using the .pdb structure of a template and a target sequence (that is very similar to the template) I have previosly used align2d (see script align2d_old.py below) to prepare homology models. but the current sequences are very long (a pentamer with 573 aa per chain) and align2d was taking a very long time (hours). so I wanted to use salign. based on what I read in tutorials and forums I am however rather confused about the sequence of scritpts/commands to use Essentially, I have three questions: - what is the sequence of scripts / commands to use? do I first use salign to prepare an alignment and then align2d (or salign that emulates align2d). - what is the purpose of first using salign and then align2d ? - in the previous scripts of align2d the .pdb file was used as an input. in the new scripts that I used the .pdb file does not seem to be used. so how is the known structure of the template taken in to consideration for the alignment? the scripts I have previously used and the ones I now use are below. name of template: Glinker (known sequence and structure (pdb)) name of target: GSAlinker (known sequence ) thanks Evelyne ************************************************************* # profile-profile alignment using salign # based on salign_profile_profile.py # on https://salilab.org/modeller/9v7/manual/node288.html from modeller import * log.level(1, 0, 1, 1, 1) env = environ() aln = alignment(env, file='HA1onCtermVP1dc63_Glinker_GSAlinker.fasta', alignment_format='FASTA') aln.salign(rr_file='${LIB}/blosum62.sim.mat', gap_penalties_1d=(-500, 0), output='', align_block=2, # no. of seqs. in first MSA align_what='PROFILE', alignment_type='PAIRWISE', comparison_type='PSSM', # or 'MAT' (Caution: Method NOT benchmarked # for 'MAT') similarity_flag=True, # The score matrix is not rescaled substitution=True, # The BLOSUM62 substitution values are # multiplied to the corr. coef. #write_weights=True, #output_weights_file='test.mtx', # optional, to write weight matrix smooth_prof_weight=10.0) # For mixing data with priors #write out aligned profiles (MSA) aln.write(file='HA1onCtermVP1dc63_Glinker_GSAlinker.ali', alignment_format='PIR') # Make a pairwise alignment of two sequences aln = alignment(env, file='HA1onCtermVP1dc63_Glinker_GSAlinker.ali', alignment_format='PIR', align_codes=('HA1onCtermVP1dc63_Glinker', 'HA1onCtermVP1dc63_GSAlinker')) aln.write(file='HA1onCtermVP1dc63_Glinker_GSAlinker_pair.ali', alignment_format='PIR') aln.write(file='HA1onCtermVP1dc63_Glinker_GSAlinker_pair.pap', alignment_format='PAP') ************************************************************** ************************************************************** # based on example on salign_align2d.py # on https://salilab.org/modeller/9v7/manual/node288.html # align2d/align using salign # parameters to be input by the user # 1. gap_penalties_1d # 2. gap_penalties_2d # 3. input alignment file from modeller import * log.verbose() env = environ() env.io.atom_files_directory = ['../atom_files'] aln = alignment(env, file='HA1onCtermVP1dc63_Glinker_GSAlinker_pair.ali', align_codes='all') aln.salign(rr_file='$(LIB)/as1.sim.mat', # Substitution matrix used output='', max_gap_length=20, gap_function=True, # If False then align2d not done feature_weights=(1., 0., 0., 0., 0., 0.), gap_penalties_1d=(-450, -50), gap_penalties_2d=(3.5, 3.5, 3.5, 0.2, 4.0, 6.5, 2.0, 0.0, 0.0), # d.p. score matrix #write_weights=True, output_weights_file='salign.mtx' similarity_flag=True) # Ensuring that the dynamic programming # matrix is not scaled to a difference matrix aln.write(file='HA1onCtermVP1dc63_Glinker_GSAlinker_align2d.ali', alignment_format='PIR' , alignment_features=' INDICES CONSERVATION ACCURACY HELIX BETA') aln.write(file='HA1onCtermVP1dc63_Glinker_GSAlinker_align2d.pap', alignment_format='PAP' , alignment_features=' INDICES CONSERVATION ACCURACY HELIX BETA') ************************************************************** ************************************************************** from modeller import * log.verbose() # create evironment and new alignment env = environ() aln = alignment(env) # create a model for the template HA1onCtermVP1dc63_Glinker mdl = model(env, file='HA1onCtermVP1dc63_Glinker', model_segment=('FIRST:A','LAST:E')) aln.append_model(mdl, align_codes='HA1onCtermVP1dc63_Glinker', atom_files='HA1onCtermVP1dc63_Glinker.pdb') # create a model for the target HA1onCtermVP1dc63_GSAlinker aln.append(file='HA1onCtermVP1dc63_GSAlinker.ali', align_codes='HA1onCtermVP1dc63_GSAlinker') aln.align2d() aln.write(file='HA1onCtermVP1dc63_Glinker_HA1onCtermVP1dc63_GSAlinker.ali', alignment_format='PIR') aln.write(file='HA1onCtermVP1dc63_Glinker_HA1onCtermVP1dc63_GSAlinker.pap', alignment_format='PAP') **************************************************************

2 1

Modeller query
by deepak kumar 24 Oct '16

24 Oct '16

Dear All, I am using modeller for the first time. Before mentioning the problems I am facing, please allow me to mention my goals to be performed by modeller. I already have a BLAST generated fasta alignment file. I need to convert the fasta alignment to PIR format, and generate the comparative model. May I please request you to let me know how this goal can be achieved. Moreover, after installing the modeller tarball package for ubuntu x86_64, when running the script to convert the fasta alignment to PIR I get this error. /media/deepak/modeller/bin/modpy.sh python modeller.py Traceback (most recent call last): File "modeller.py", line 2, in <module> from modeller import * File "/media/deepak/Nourhan/deepak_research2016/NM_005343_NM_002880_RAS_RAF/modeller.py", line 3, in <module> env = environ() NameError: name 'environ' is not defined *modeller.py*: import sys, os from modeller import * env = environ() a = alignment(env, file='NM_005343-native-protein.fasta', alignment_format='FASTA') a.write(file='NM_005343-native-protein.pir', alignment_format='PIR') Thank you so much for your time and consideration. Sincerely, Deepak _____________ Researcher, Carnegie Mellon University, Computational Biology Department

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modeller_usage