- modeller_usage - salilab.org

ALIGN_CODES(i) error, Again
by Zumot, Elia Nabil 19 Mar '12

19 Mar '12

Hello Modeller people, I realize this error has been posted repeatedly and I have tried to check for all possible solutions mentioned but I still can't do it right. My alignment filename is 2nwx_ASCT.ali and my pdb filename is 2nwx_A.pdb so the names and letter cases match exactly. The error I'm getting is: ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 2) = ASCT The script and alignment files are below. Thank you in advance for the help Elia Zumot The script I use with modeller version 9.10 on Linux is: from modeller import * from modeller.automodel import * env = environ() def do_align(): a = automodel(env, alnfile='2nwx_ASCT.ali', knowns='2nwx_A', sequence='ASCT', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 5 a.make() do_align() and my alignment file (2nwx_ASCT.ali) is: >P1;2nwx_A structure:2nwx_A.pdb:4:A:416:A:::: EYPVLQKILIGLILGAIVGLILGHYGYAHAVHTYVKPFGDLFVRLLKMLVMPIVFASLVVGAASISPAR- LGRVGVKIVVYYLLTSAFAVTLGIIMARLFNPGAGIHLAVGG---------QQFQPHQAPPLVHILLDIV PTNPFGALANG----------------------------------------------------QVLPTIF FAIILGIAITYLMNSENEKVRKSAETLLDAINGLAEAMYKIVNGVMQYAPIGVFALIAYVMAEQG--VHV VGELAKVTAAVYVGLTLQILLVYFVLLKIY-GIDPISFIKHAKDAMLTAFVTRSSSGTLPVTMRVAKE-M GISEGIYSFTLPLGATINMDGTALYQGVCTFFIANALGSHLTVGQQLTIVLTAVLASIGTAGVPGAGAIM LAMVLHSVGLPLTDPNVAAAYAMILGIDAILDMGRTMVNVTGDLTGTAIVAKTE* >P2;ASCT sequence:ASCT:4::::::: RNAFVLLTVTAVIVGTILGFTLRPYRMSYREVKYFSFPGELLMRMLQMLVLPLIISSLVTGMAAL-DSKA SGKMGMRAVVYYMTTTIIAVVIGIIIVIIIHPGKGTKENMH-------REGKIVRVTAADAFLDLIRNMF PPNLVEASFKQFKTNYEKRSFKVPIQANETLVGAVINNVSEAMETLTRITEELVPVPGSVNGVNALGLVV FSMAFGFVIGNMK--------EQGQALREFFDSLNEAIMRLVAVIMWYAPVGILFLIAGKIVEMEDMGVI GGQLAMYTVTVIVGLLIHAVIVLPLLYFLVTRKNPWVFIGGLLQALITALGTSSSSATLPITFKGLEENN GVDKRVTRFVLPVGATINMDGTALYEALAAIFIAQVNNFELNFGQIITISITATAASIGAAGIPQAGLVT MVIVLTSVGLPTDD------ITLIIAVDWFLDRLRTTTNVLGDSLGAGILHHLN* Elia Zomot, PhD Computational and Systems Biology Department School of Medicine, University of Pittsburgh 3089 BST3, 3501 Fifth Ave, Pittsburgh, PA 15213 Voice: 412 624 8699 - Fax: 412 648 3163 enz1(a)pitt.edu

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Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 30
by Alexander Predeus 16 Mar '12

16 Mar '12

Dear Ashish, thank you for your suggestions! I have some follow-up questions though. 1. Did you mean some simplified replica exchange with MODELLER or a real replica-exchange simulation? Because simple temperature replica exchange is most probably not feasible for a system of this size - number of replicas necessary to achieve the same exchange rates grows as ~ sqrt (N) and will be too high in this case. 2. As for increased temperature MD for loops - you imply that I keep the structure restrained and only let loops relax? I was under the impression MODELLER's refinement does something of this sort in CG model, which should be a lot faster than AA MD anyway. 3. About the normalized DOPE - again, I was under the impression that it only matters when you are comparing different proteins. My task is only to compare different models of the same protein. Thank you in advance! -- Alex Predeus, MSU

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Re: [modeller_usage] Loop Modeling in a Protein-DNA Complex
by Modeller Caretaker 16 Mar '12

16 Mar '12

On 3/16/12 12:36 PM, Alexander Predeus wrote: > Thank you very much for your prompt response! > > I have a small follow-up question. I was under the impression that > refinement is essentially and MD simulation, and thus if I start two > scripts, requesting to generate a 100 models in each, I would end up > with 200 different models. > > I was surprised to see that the scripts actually generate precisely the > same series of models, and with same energies etc. > > Why is that? Is there a way to run several parallel simulations and get > independent sampling, or does it have to go consecutively? Modeller results are reproducible, so yes, given the same input conditions (including scripts, Modeller version, and operating system) you'll get the same outputs. If you want to get different results, set a different random seed for each of your runs using the rand_seed argument to environ(): http://salilab.org/modeller/9.10/manual/node111.html Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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Re: [modeller_usage] Loop Modeling in a Protein-DNA Complex
by Alexander Predeus 16 Mar '12

16 Mar '12

Thank you very much for your prompt response! I have a small follow-up question. I was under the impression that refinement is essentially and MD simulation, and thus if I start two scripts, requesting to generate a 100 models in each, I would end up with 200 different models. I was surprised to see that the scripts actually generate precisely the same series of models, and with same energies etc. Why is that? Is there a way to run several parallel simulations and get independent sampling, or does it have to go consecutively? Thank you again! -- Alex Predeus MSU

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Loop Modeling in a Protein-DNA Complex
by Alexander Predeus 15 Mar '12

15 Mar '12

Hello all, I'm trying to fill the gaps in a protein-DNA complex of a moderate size (~ 15k heavy atoms). There are two protein chains with 13 missing pieces overall, most are 2 to 8 AA, but two are fairly long (~ 15 AA). I'm modeling ONLY the missing parts for I don't want the X-ray structure perturbed, and I included DNA molecule as a ligand (with HETATM identifier and "." in alignment). >From reading this mailing list, I've realized that it's better to generate a lot of models using a faster routine (e.g. refine.very_fast) and then take the best one, rather than do longer refinement and generate less models. The question I wanted to ask, is what is the best assess method I can use, considering the nature of my task? I'm using DOPE right now, but in the manual I've also seen mentioning of DOPE-HR. Would it slow down the loop refinement process a lot (or at all)? Thank you for any suggestions. -- Alex Predeus Michigan State University

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Regarding .tree
by Ashish Runthala 12 Mar '12

12 Mar '12

Dear Modellers, How is the evolutionary tree .tree file constructed for multiple templates through salign_multiple_struc. What algorithm is used? Is it ML, MP, NJ, or anything else. Regards, Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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(no subject)
by pawan raghav 11 Mar '12

11 Mar '12

http://demos.mclanka.com/aquanew/BIT/admin/BIT-debug-backup/BIT-debug/PEAR/…

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Re: [modeller_usage] Modeller9.10 on Centos 6.2
by Irene Newhouse 07 Mar '12

07 Mar '12

Thanks so much for the quick response. I've tried the suggestions & get similar results to before: [newhoir@hals cpt6short]$ python cps6.py 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 hals 2.6.32-220.4.1.el6.x86_64 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): 2012/03/07 06:52:00 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 ${MODINSTALL9v10}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 openf______E> Cannot open file cp6s.ali: No such file or directory Traceback (most recent call last): File "cps6.py", line 42, in <module> a.make() # do the actual homology modeling File "/usr/lib64/python2.6/site-packages/modeller/automodel/automodel.py", line 96, in make self.homcsr(exit_stage) File "/usr/lib64/python2.6/site-packages/modeller/automodel/automodel.py", line 408, in homcsr aln = self.read_alignment() File "/usr/lib64/python2.6/site-packages/modeller/automodel/automodel.py", line 398, in read_alignment aln.append(file=self.alnfile, align_codes=self.knowns+[self.sequence]) File "/usr/lib64/python2.6/site-packages/modeller/alignment.py", line 78, in append allow_alternates) IOError: openf______E> Cannot open file cp6s.ali: No such file or directory Yes, the ali file is there: [newhoir@hals cpt6short]$ ls *ali My .py file is: cps6.alifrom modeller import * from modeller.automodel import * # build 20 copies of a dimer from a single template log.verbose() # request verbose output # Override the 'special_restraints' and 'user_after_single_model' methods: class MyModel(automodel): def special_restraints(self, aln): # Constrain the A and B chains to be identical (but only restrain # the C-alpha atoms, to reduce the number of interatomic distances # that need to be calculated): s1 = selection(self.chains['A']).only_atom_types('CA') s2 = selection(self.chains['B']).only_atom_types('CA') self.restraints.symmetry.append(symmetry(s1, s2, 1.0)) def user_after_single_model(self): # Report on symmetry violations greater than 1A after building # each model: self.restraints.symmetry.report(1.0) env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = ['.', '/home/newhoir/rub-atfiles/'] #read HETATMS in template env.io.hetatm = True # Be sure to use 'MyModel' rather than 'automodel' here! a = MyModel(env, alnfile = 'cp6s.ali' , # alignment filename knowns = ('2x06'), # codes of the templates sequence = 'cps6', # code of the target assess_methods=assess.GA341) # request model assessment a.starting_model= 1 # index of the first model a.ending_model = 20 # index of the last model # (determines how many models to calculate) a.library_schedule = autosched.slow # thorough VTFM opt a.max_var_iterations = 300 a.md_level = refine.very_slow a.make() # do the actual homology modeling It makes no difference if I insert a first line #!/usr/bin/python or not. Thanks again! Irene ----- Original Message ----- From: Modeller Caretaker <modeller-care(a)salilab.org> Date: Tuesday, March 6, 2012 12:03 pm Subject: Re: [modeller_usage] Modeller9.10 on Centos 6.2 To: Irene Newhouse <irenenew(a)hawaii.edu> Cc: modeller_usage(a)salilab.org > On 3/6/12 1:31 PM, Irene Newhouse wrote: > > I've installed Modeller9.10 on my Centos 62. linux station. I > had an > > earlier version working under Centos 5.x. Now I find that if I > set an > > alias I call mod9v10 to point to modeller9.10_x86_64-intel8 in > > analogy to the alias I successfully set to its analog previously > > There's no need to do that - there's already a script called > mod9.10 > which does basically that, which ships as part of Modeller. But > we > generally recommend to use Python instead if you can. > > > Furthermore, I get an error indicating that my > > .ali file can't be found& I've triple-checked to make > sure I've > > entered the name correctly. > > Are you sure it's complaining about the .ali file and not > something > else? Or maybe you're running in the wrong directory. > > > There is no modpy.sh in the directory to which the web pages point. > > If you installed the RPM, there is no modpy.sh because it isn't > necessary. You can just run your regular system Python, e.g. > "python > foo.py". > > > it cannot find the equivalent of foo.py unless I give the full > path to foo.py > > If you're trying to run "foo.py" in the current directory by > just typing > "foo.py", that typically won't work on a Unix system since the > current > directory isn't usually in your path. Try "./foo.py" instead. > > > When I specify the full path, I get error > > messages such as "from: command not found"& > a crash, indicative of > > a massive failure to access python. > > This sounds like you have tried to run the Python script as a > shell > script. Either prefix it with "python", as above, or add > "#!/usr/bin/python" to the first line of your Python script to > tell the > system to use Python to run it. > > Ben Webb, Modeller Caretaker > -- > modeller- > care(a)salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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Modeller9.10 on Centos 6.2
by Irene Newhouse 06 Mar '12

06 Mar '12

I've installed Modeller9.10 on my Centos 62. linux station. I had an earlier version working under Centos 5.x. Now I find that if I set an alias I call mod9v10 to point to modeller9.10_x86_64-intel8 in analogy to the alias I successfully set to its analog previously, I get the messages about not finding libraries described on the modeller web pages. Furthermore, I get an error indicating that my .ali file can't be found & I've triple-checked to make sure I've entered the name correctly. There is no modpy.sh in the directory to which the web pages point. Instead, there is a file modpy.sh.in. Regardless of whether I use the copy of this script in its installed location, or whether I copy it to my cwd, it cannot find the equivalent of foo.py unless I give the full path to foo.py. When I specify the full path, I get error messages such as "from: command not found" & a crash, indicative of a massive failure to access python. If I try to use the script mod9.10, whether in its original location or a copy in cwd, it fails to find the ali file, whether or not I enter its full path. The inputs I am using are all derived from successful modeller runs, albeit an earlier version running under an earlier Centos, so I did not expect these results. But what really makes me want to tear my hair out is this: a previous modeller manual included a short python code to extract a sequence from a PDB file. I've called it pdb2ali.py. If I type the command: mod9v10 pdb2ali.py, I get the error messages about failing to find platform dep/indep files, but I have output! There is no problem finding the input pdb file in cwd. Please help me debug this! Thanks in advance! Irene

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Regarding BLOSUM MATRICES & MODELLER ALIGNMENT
by Ashish Runthala 04 Mar '12

04 Mar '12

Dear Modellers, I found some interesting results today.Though some of these were much discussed by Sadowsky in some articles since 2007, But still check these out. Target1 molpdf DOPE Z-Score GDT-TS GDT-HA TM-Score RMSD 2P31 Modeling Scores BLOSUM50 924.97821 -19218.93945 -1.37493 89.634 76.22 0.917 0.844 BLOSUM62 924.97821 -19218.93945 -1.37493 89.634 76.22 0.917 0.844 2I3Y Modeling Scores BLOSUM50 1027.70447 -18048.86914 -0.89869 79.268 57.165 0.873 1.568 BLOSUM62 1027.70447 -18048.86914 -0.89869 79.268 57.165 0.873 1.568 2OBI Modeling Scores BLOSUM50 1019.33649 -18713.56836 -1.16924 85.671 68.293 0.914 1.325 BLOSUM62 993.73724 -14176.32422 0.67751 39.482 15.244 0.586 .3.727 Target2 2RIR molpdf DOPE Z-Score GDT-TS GDT-HA TM-Score RMSD BLOSUM50 1528.87537 -34527.82422 -1.28434Complete89.568 68.255 0.973 1.037 Domain1 96.507 83.824 0.972 0.77 Domain2 99.823 89.184 0.985 0.553 BLOSUM62 1528.87537 -34527.82422 -1.28434Complete89.568 68.255 0.973 1.037 Domain1 96.507 83.824 0.972 0.77 Domain2 99.823 89.184 0.985 0.553 2CUK molpdf DOPE Z-Score GDT-TS GDT-HA TM-Score RMSD BLOSUM50 1942.12292 -25812.05664 0.82958 Complete17.356 5.665 0.382 4.106 Domain1 25.735 13.419 0.361 2.613 Domain2 30.674 13.121 0.411 2.93 BLOSUM62 2036.98694 -26931.20703 0.55814 Complete16.277 5.036 0.348 4.12 Domain1 15.625 6.066 0.256 2.82 Domain2 34.752 15.426 0.456 2.747 Target3 molpdf DOPE Z-Score GDT-TS GDT-HA TM-Score RMSD 2Q7B BLOSUM50 1212.10278 -16748.72461 -0.8108 81.414 61.184 0.879 1.283 BLOSUM62 1175.47266 -17014.03516 -0.92678 87.336 66.118 0.925 1.227 2OH1 BLOSUM50 1450.15808 -12735.95215 0.94347 28.947 13.487 0.426 2.797 BLOSUM62 1007.18695 -15380.72852 -0.21275 56.743 33.388 0.73 2.367 1S60 BLOSUM50 836.13391 -13656.52148 0.54102 55.428 35.526 0.674 1.961 BLOSUM62 1039.06799 -13509.62109 0.60524 57.237 37.500 0.698 2.002 So You might have realized there is a huge differences in the alignments. Sometime same and different for quite others. Even the accuracies, molpdf and other scores are different, when it comes to the models created on basis of only this factor keeping all others constant. Even the accuracy of MODELLER single template models also gets inferior sometimes. So I infer that it seems 1. MODELLER pairwise algorithm is not purely biased on local fold alignment, though it uses Smith Waterman based align2d.py module. 2. All algorithmic alignments are almost similar with minimal differences for easy targets. However, when the PDB profile is employed for Pairwise alignments through any BLOSUM matrix, the case may differ much when the employed template shares a negligible sequence identity to the target. 3. Will these results be still different when BLOSUM80 is used for these targets the same way? I hope a good explanatory reply from Sir Ben Webb. Thanks Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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