- modeller_usage - salilab.org

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

4 3

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

4 10

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

2 1

usage of and sequence of commands for salign instead of align2d
by Evelyne Deplazes 21 Oct '16

21 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? Also, if no .pdb file is used then the generated alignment file does not contain information /reference to the structure file. consequently the scritpt model_build.py that I use will complain about not finding the structure information the scripts I have previously used (align2d_old.py) and the ones I tried to use now 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') ************************************************************** ED Evelyne Deplazes Reply all| Today, 11:15 AM modeller_usage(a)salilab.org Sent Items 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') ************************************************************** ************************************************************** #model_build.py from modeller import * from modeller.automodel import * env = environ() a = automodel(env, alnfile='HA1onCtermVP1dc63_Glinker_GSAlinker_pair.ali', knowns='HA1onCtermVP1dc63_Glinker', sequence='HA1onCtermVP1dc63_GSAlinker', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 5 a.make() ************************************************************** ************************************************************** #align2d_old.py 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') **************************************************************

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