- modeller_usage - salilab.org

Re: [modeller_usage] Modeller on SGE
by Modeller Caretaker 18 Oct '11

18 Oct '11

On 10/18/11 6:02 AM, Matías wrote: > HI, I´m trying to run modeller in multiple cores on a Cluster with > SGE. Do you have an example script to do this? No, since it is highly dependent on your SGE setup. And it depends what you mean by "run modeller". There are two classes in Modeller for running on SGE systems: sge_qsub_job and sge_pe_job. The first uses 'qsub' from within the Modeller run to start an SGE job to do the computation (typically you run Modeller on your head node or some other machine which can 'qsub' to your cluster). The second is designed to be used in a Modeller job which is running on your cluster in a PE; it will allow Modeller to use all the nodes in that PE. A basic usage of the first for comparative modeling would be something like (see also examples/automodel/model-parallel.py): from modeller import * from modeller.automodel import * from modeller.parallel import * j = sge_qsub_job(maxslave=10) env = environ() a = automodel(env, alnfile=...) a.starting_model = 1 a.ending_model = 100 a.use_parallel_job(j) a.make() This will automatically 'qsub' an SGE array job containing 10 tasks when you call a.make(), so that the modeling is split between 10 processors. See also http://salilab.org/modeller/9.10/manual/node438.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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Request for papers.
by Sehrish Batool 18 Oct '11

18 Oct '11

Sir I request you to send me full length papers of the following, 1. N. Eswar, M. A. Marti-Renom, B. Webb, M. S. Madhusudhan, D. Eramian, M. Shen, U. Pieper, A. Sali. Comparative Protein Structure Modeling With MODELLER. Current Protocols in Bioinformatics, John Wiley & Sons, Inc., Supplement 15, 5.6.1-5.6.30, 2006. 2. M.A. Marti-Renom, A. Stuart, A. Fiser, R. Sánchez, F. Melo, A. Sali. Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 29, 291-325, 2000. 3. A. Sali & T.L. Blundell. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815, 1993. 4. A. Fiser, R.K. Do, & A. Sali. Modeling of loops in protein structures, Protein Science 9. 1753-1773, 2000 Thank you

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Re: [modeller_usage] Restraining Secondary Structure
by bharat lal 17 Oct '11

17 Oct '11

Hi, I am modelling a sequence in which I am restraining some portions of the sequence to be helix as I have copied that sequence from a known structure. But I want to ask whether the same restrained sequence would also be same in real or not. What is the basis of restraining the structure to be helix or sheets ?? --------- Bharat

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Changing the directory.
by Sehrish Batool 17 Oct '11

17 Oct '11

I am using Modeller9.10 and I am unable to define directry in Command Prompt using 'Dir' keyword. Please tell me how can I define it and where Did I made mistake. The command that I used is : Dir = C:\Program Files\Modeller9.10\examples\automodel

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Correct the small scripting error
by Ashish Runthala 17 Oct '11

17 Oct '11

Dear MODELLERS, I tried writing a script to automatically take 3 templates from the current folder and do iterative modeling for the same target sequence. i.e., I want to run Modeller with three templates (2 fixed (1SHWA, 1SHXA) + 1 variable, taken as different individual template files from the current folder iteratively). def align(fileName): #fileName iteratively contains name of all pdb files log.verbose() env = environ() env.io.atom_files_directory = ['.', '../atom_files'] pdbfile=fileName + 'A' aln = alignment(env) for (code,code,atomfile, chain) in (('1SHWA','1SHXA','1SHX','A'),(pdbfile,pdbfile,fileName,'A')): mdl = model(env, file=atomfile, model_segment=('FIRST:'+chain, 'LAST:'+chain)) aln.append_model(mdl, atom_files=atomfile, align_codes=code) There is some mistake in last four lines as only two templates are coming in the alignment file and not the third one. So correct my mistake in this piece of code. Thanks, Ashish -- Ashish Runthala, Lecturer, Structural Biology Cell, Cabin: 3222-U Biological Sciences Group, Faculty Division III, Birla Institute of Technology & Science, Pilani Rajasthan, INDIA - 333 031 Website: https://sites.google.com/site/ashishrunthala/ Phone: +91-1596-245073-273 (O) +91-7597971146 (M) Fax: +91-1596-244183 E-mail: ashishr(a)bits-pilani.ac.in ashish.runthala(a)gmail.com

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energy
by Jin-Rui Xu 16 Oct '11

16 Oct '11

Hi there, What is the indication of modeller mod energy? The higher the better? Thanks!

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Regarding align2d & CS-BLAST alignments PLEASE ANSWER ME QUICKER ..I AM STUCK UP IN A FEW CASES
by Ashish Runthala 03 Oct '11

03 Oct '11

Dear Modellers and Sir Ben Webb, I am finding a critical difference in the pairwise alignment computed by MODELLER and the corresponding alignment cognitive to the CS-BLAST undertaken alignment. These are the differences. Will someone help me understanding why there is the case of shifted alignments in the the alignment case mentioned below for the following alignments of templates 2Q7BA and 3PP9A for the CASP8 target T0400? I have written TARGE in the MODELLER Alignment file for target sequence for better one-to-one alignment residue correlation. On top of it the CS-BLAST residue order is not available in the template PDB files. So i am confused..Where CS-BLAST has got the altered sequences from, when i precisely called the PDB for it. 2Q7BA ALIGNMENT MODELLER ALIGNMENT 2Q7BA>FQGMEIKEYENNPYHLAQLVDLINYCQNIEAKLDIKMAEQDDIFQIENYYQNRKGQFWIALEN-EKVVGSIALLRIDDKTAVLKKFFTYPKYRGNPVRLGRKLFERFMLFARASKFTRIVLDTPEKEKRSHFFYENQGFKQITRDELDVDYIFPDRDSRIYVKLL--* TARGE>M-AINIIEY-NRSY-KEELIEFILSIQKNEFNIKIDRDDQPDLENIEHNYLNSGGQFWLAINNHQNIVGTIGLIRLDNNMSALKKMFVDKGYR-N-LKIGKKLLDKVIMTCKEQNIDGIYLGTIDKFISAQYFYSNNGFREIKRGDLPSSFPKLDVDNRFYYRNLKD* CS-BLAST ALIGNMENT Query: 1 MAINIIEYNRSYKEELIEFILSIQKNEFNIKIDRDDQPDLENIEHNYLNSGGQFWLAINN 60 M I E N + +L++ I Q E + I +Q D+ IE+ Y N GQFW Sbjct: 20 MEIKEYENNPYHLAQLVDLINYCQNIEAKLDIKMAEQDDIFQIENYYQNRKGQFW-IALE 78 Query: 61 HQNIVGTIGLIRLDNNMSALKKMFVDKGYRN--LKIGKKLLDKVIMTCKEQNIDGIYLGT 118 ++ +VG+I L+R+D+ + LKK F YR +++G+KL ++ ++ + I L T Sbjct: 79 NEKVVGSIALLRIDDKTAVLKKFFTYPKYRGNPVRLGRKLFERFMLFARASKFTRIVLDT 138 Query: 119 IDKFISAQYFYSNNGFREIKRGDLPSSFPKLDVDNRFYYRNLK 161 +K + +FY N GF++I R +L + D D+R Y + L Sbjct: 139 PEKEKRSHFFYENQGFKQITRDELDVDYIFPDRDSRIYVKLLD 181 3PP9A ALIGNMENT MODELLER ALIGNMENT 3PP9A>SLLIRELETNDLDNFPEIDDSFIVNARLMLSLSKVNRRIEYTVEDVPSYEKSYLELVYNEYINKPNQIIYIALLHNQIIGFIVLKKNWNNYAYIEDITVDKKYRTLGVGKRLIAQAKQWAKEGNMPGIMLETQNNNVAACKFYEKCGFVIGGFDFLVYKGLNMTSDEVAIYWYLHF* TARGE>------M---AI-NIIEYNRSY-KEELIEFILS-I-QKNEFNIK-IDRDDQPDLENIEHNYLNSGGQFWLAINNHQNIVGTIGLIRLDNNMSALKKMFVDKGYRNLKIGKKLLDKVIMTCKEQNIDGIYLGTIDKFISAQYFYSNNGFREIKRGDLPSSFPKLDVDNRFYYRNLKD* CS-BLAST ALIGNMENT Query: 1 MAINIIEYNRSYKEELIE----------FILSIQKNEFNIKIDRDDQPDLEN-------- 42 M++ I E + + E +LS+ K I+ +D P E Sbjct: 4 MSLLIRELETNDLDNFPEIDDSFIVNARLMLSLSKVNRRIEYTVEDVPSYEKSYLQNDNE 63 Query: 43 --IEHNYLNSGGQFWLAINNHQNIVGTIGLIRLDNNMSALKKMFVDKGYRNLKIGKKLLD 100 + + Y+N Q H I+G I L + NN + ++ + VDK YR L +GK+L+ Sbjct: 64 ELVYNEYINKPNQIIYIALLHNQIIGFIVLKKNWNNYAYIEDITVDKKYRTLGVGKRLIA 123 Query: 101 KVIMTCKEQNIDGIYLGTIDKFISAQYFYSNNGFRE 136 + KE N+ GI L T + ++A FY GF Sbjct: 124 QAKQWAKEGNMPGIMLETQNNNVAACKFYEKCGFVI 159 Thanks Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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Modeller 9.10 release
by Modeller Caretaker 29 Sep '11

29 Sep '11

The new version of Modeller, 9.10, is now available for download! Please see the download page at http://salilab.org/modeller/ for more information. If you have a license key for Modeller 8 or 9, there is no need to reregister for Modeller 9.10 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 9.10 is primarily a bugfix release relative to the last public release (9.9). Major user-visible changes include: # Add Python 3 support. # Add support for Mac OS X 10.7 (Lion). # Modeller on 64-bit Macs is now built with Intel Fortran, resulting in a roughly 2x speedup compared to 9.9. # Add Unicode support; all filenames should be UTF-8 encoded. See the Modeller manual for a full change log: http://salilab.org/modeller/9.10/manual/node38.html If you encounter bugs in Modeller 9.10, please see http://salilab.org/modeller/9.10/manual/node10.html for information on how to report them. Note: you are receiving this email either because you subscribed to the modeller_usage mailing list, or you provided this address when you requested a Modeller license and you ticked the "notify me of new releases" box. In the latter case, if you no longer wish to receive announcements of new Modeller releases, simply reply to this email and let us know. 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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Restricting parts of the protein to alpha helix
by Kalavera＠gmx.net 06 Sep '11

06 Sep '11

Dear modeller users, my current project involves the refinement of an tertrameric protein, which is already an homology model generated with modeller. Now, I tried to refine the existing model, because its N-terminus should be alpha helical. My strategy involved creating an alpha-helix and generating a new chimeric protein with this. Maybe my strategy is bad or do carry some failure. Searching your archives, I found no fitting topic. I hope this community might be able to help me with my issues. There must be a slightly more elegant way to receive an helical n-terminus. My strategy in detail:(all files/examples/scripts are shown below). In a first step I created an alpha-helix (22 AA) matching the N-terminal AA sequence of my template pdb. The helix was created based on an script tutorial I found here : http://salilab.org/modeller/wiki/Make%20alpha%20helix In a second step I created a pir file, which seems to cause the problems. I followed the Pir-format on the modeller webpage, but the python script exits pointig at problems in the pir file. At least a simple pythonscript should create my chimera. I figured out, that there is a problem in the pir file. I don't know, how to create four helices or assign the already created to all four monomers. Thanks for all your help, Kalavera Information: My Pir file in principle:(Original residues are masked) >P1;My-PDB structureX:My-PDB:1:A:82:D:::0.00:0.00 AAAAAAAAAAAAAAAAAAAAAMMMMMMMMMMMMMMMMMMMMMMMMMM MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM/ AAAAAAAAAAAAAAAAAAAAAMMMMMMMMMMMMMMMMMMMMMMMMMM MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM/ AAAAAAAAAAAAAAAAAAAAAMMMMMMMMMMMMMMMMMMMMMMMMMM MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM/ AAAAAAAAAAAAAAAAAAAAAMMMMMMMMMMMMMMMMMMMMMMMMMM MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM/* >P1;alpha-helix structureX:alpha-helix:1: :22: :::0.00:0.00 ----------------------------------------------- -----------------------------------/ ----------------------------------------------- -----------------------------------/ ----------------------------------------------- -----------------------------------/ XAAAAAAAAAAAAAAAAAAAAA------------------------- -----------------------------------/* >P1;chimera sequence:chimera:::::::0.00:0.00 AAAAAAAAAAAAAAAAAAAAAMMMMMMMMMMMMMMMMMMMMMMMMMM MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM/ AAAAAAAAAAAAAAAAAAAAAMMMMMMMMMMMMMMMMMMMMMMMMMM MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM/ AAAAAAAAAAAAAAAAAAAAAMMMMMMMMMMMMMMMMMMMMMMMMMM MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM/ XAAAAAAAAAAAAAAAAAAAAMMMMMMMMMMMMMMMMMMMMMMMMMM MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM/* my *.py script: from modeller.automodel import * from modeller import * log.verbose() env = environ(rand_seed=-42) env.io.atom_files_directory = '.' #env.io.hetatm = env.io.hydrogen = True a = automodel(env, alnfile = 'my_pir_file.pir', knowns = ('My-PDB','alpha-helix'), sequence = 'chimera') a.repeat_optimization = 1 a.starting_model= 1 a.ending_model = 1 a.final_malign3d = True a.make() a.energy(output='VERY_LONG') Parts of My-PDB: ATOM 1 N MET 1 9.237 -14.594 13.390 1.00133.02 1SG 2 ATOM 2 CA MET 1 10.424 -14.242 12.577 1.00133.02 1SG 3 ATOM 3 CB MET 1 9.978 -13.883 11.150 1.00133.02 1SG 4 ATOM 4 CG MET 1 11.111 -13.752 10.133 1.00133.02 1SG 5 ATOM 5 SD MET 1 10.531 -13.360 8.454 1.00133.02 1SG 6 ATOM 6 CE MET 1 9.496 -14.845 8.300 1.00133.02 1SG 7 ATOM 7 C MET 1 11.086 -13.059 13.198 1.00133.02 1SG 8 ATOM 8 O MET 1 10.511 -12.420 14.078 1.00133.02 1SG 9 ATOM 9 N LEU 2 12.328 -12.738 12.784 1.00173.80 1SG 10 ATOM 10 CA LEU 2 12.915 -11.582 13.388 1.00173.80 1SG 11 ATOM 11 CB LEU 2 14.364 -11.293 12.962 1.00173.80 1SG 12 ATOM 12 CG LEU 2 15.370 -12.347 13.459 1.00173.80 1SG 13 ATOM 13 CD1 LEU 2 15.119 -13.714 12.806 1.00173.80 1SG 1 ..... ATOM 634 CH2 TRP 82 -2.392 -10.968 17.703 1.00228.90 1SG 635 ATOM 635 C TRP 82 -1.256 -4.168 15.227 1.00228.90 1SG 636 ATOM 636 O TRP 82 -1.869 -3.238 14.636 1.00228.90 1SG 637 ATOM 637 OXT TRP 82 -0.880 -4.112 16.427 1.00228.90 1SG 638 TER 637 TRP 82 1SG 639 ATOM 638 N MET 83 -9.978 -14.264 9.752 1.00140.79 2SG 640 ATOM 639 CA MET 83 -11.395 -14.650 9.550 1.00140.79 2SG 641 ATOM 640 CB MET 83 -11.772 -14.541 8.059 1.00140.79 2SG 642 ATOM 641 CG MET 83 -11.766 -13.103 7.529 1.00140.79 2SG 643 ..... -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de

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MODELLER thinks HSEs are ATOM instead of HETATM
by Yingjie Lin 02 Sep '11

02 Sep '11

Hi Modellers, I ran into a problem with PDB file 1j9n, which contains HSE residues. Each HSE line starts with "HETATM". However, when I read them into MODELLER, MODELLER thinks HSEs are ATOMs. env = environ() env.io.hydrogen = False env.io.hetatm = True mdl = model(env) mdl.read(file = '1j9n.pdb') for chain in mdl.chains: for residue in chain.residues: if residue.name=='HSE': print residue.name, residue.hetatm ... <Residue 16:C (type HSE)> False ... Does anyone know what is happening here? Where can I find MODELLER's lists/libraries of HETATM/ATOM residue types? Thank you. Yingjie - Yingjie

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