- modeller_usage - salilab.org

Modeller API
by James Irving 16 Jan '09

16 Jan '09

Hi, I have written a number of functions in C++ for structural analysis that I was hoping to interface with Modeller via the Modeller API. Specifically, I want to transfer coordinates backwards and forwards between a 'model' object and an external representation of coordinate data without having to write out a PDB file and then re-read it in in either direction, to avoid slow and unnecessary I/O and string conversion. Is this possible? From the structs in mod_types.h it looks as though it should be, but would it suffice to read and write into mod_model.mod_coordinates and mod_model.mod_sequence (my_model.cd.[x,y,z etc.] and my_model.seq.[irestyp, etc.])? If anyone has some code (in any language) or suggestions about the best way to go about this, I would greatly appreciate it. Thanks! James

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Distance Restraints: are they working?
by João Rodrigues 14 Jan '09

14 Jan '09

Hello all! I'm new at Modeller and I'm trying my luck with Distance Restraints to model a small domain of a protein. I was running some tests on my modelling to see if I had those restraints working and, from my preliminary (and rookie) analysis, it seems it's not. Attached are the files I'm using. The MyModel.py script has the MyModel class with my restraints defined. It is then called by the main modeller script (RNF11_1X4J_rest.pdb) (had to use this approach for parallel computation) which runs on modeller 9v5. I've described each restraint like this: rsr.make_distance(at['SG:1'],at['SG:4'],aln,spline_on_site=False,restraint_group=physical.xy_distance,maximal_distance=5) I just want both atoms to be, in a maximal distance of 5A. I made some further tests with that value of maximal_distance at 1.5 and 0.5, just to see if it ran ok, and I found out that the 3 best models (5A, 1.5A, 0.5A) are exactly the same :x (or nearly), with distances in the order of 2-3A, which would violate this restraint I've added in the 1.5A and 0.5A. Is this behaviour normal, or is it something I'm doing that is not the most correct? Thanks in advance for the answers and congrats for the software and for the whole team. João Rodrigues Bijvoet Center for Biomolecular Research Utrecht, Netherlands

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help with using created structure
by Chinwe Ekenna 13 Jan '09

13 Jan '09

Thanks for all the previous and useful replies they helped a lot. i have successfully created protein structures using modeller 9v4 but i am facing a new challenge ..... the structures are to be further used in creating a docking site for identified drug targets..... the challenge i'm facing is that all my structure result as regards the docking site say no site found(using Qsitefinder).... this sir is not possible as they should have docking sites.. what do you advise that i do..... ekenna chinwe

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complete_pdb.py
by Sarath Chandra 08 Jan '09

08 Jan '09

Hi, Now the scripts are working. Log files are being generated successfully. I am trying to use complete_pdb.py to add missing atoms to my pdbfile. Here is the command i am using mod9v5 complete_pdb.py (ChainA.pdb) The following log file is being generated MODELLER 9v5, 2008/10/07, r6498 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2008 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, Windows Vista build 6001 Service Pack 1, EINSTEIN, SMP, x86 Family 6 Model 14 Stepping 12 Date and time of compilation : 2008/10/07 16:19:49 MODELLER executable type : i386-w32 Job starting time (YY/MM/DD HH:MM:SS): 2009/01/08 00:07:19 Total CPU time [seconds] : 0.22 I have been using the following link http://salilab.org/modeller/manual/node403.html Am i missing something. Please help me how to use it. Regards, Sarath On Wed, Jan 7, 2009 at 4:28 PM, Modeller Caretaker < modeller-care(a)salilab.org> wrote: > Sarath Chandra wrote: > > I am Sarath and i am an intern in Max Planck Institute of Biophysical > > Chemistry Gottingen. I am working on Molecular Dynamic simulations of > > Photosystem II a membrane protein which has 17 subunits and all of these > > subunits has all together 200 atoms missing. > > > > I am trying to use complete_pdb.py and i am facing an error "import > > site failed;" > > > > Any suggestions on a the problem and how to use the script > > See #2 at http://salilab.org/modeller/release.html#issues > > The script should still run fine, despite that warning. > > 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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Adding missing atoms
by Sarath Chandra 07 Jan '09

07 Jan '09

Hi, I am Sarath and i am an intern in Max Planck Institute of Biophysical Chemistry Gottingen. I am working on Molecular Dynamic simulations of Photosystem II a membrane protein which has 17 subunits and all of these subunits has all together 200 atoms missing. I am trying to use complete_pdb.py and i am facing an error "import site failed;" Any suggestions on a the problem and how to use the script -- Sarath Chandra Dantu, Ph No: 0044-(0)7504926643

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POSITION IONS IN MODELS
by Lella Sana 11 Dec '08

11 Dec '08

Greetings Forum users I have a problem with adding Calcium ions in my models. I'm using this TOP script: #Homology modelling by the MODELLER TOP routine 'model'. INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ALNFILE = '23urom-1lmj.ali' # alignment filename SET KNOWNS = '1lmjA' # codes of the templates SET SEQUENCE = '23urom' # code of the target SET ATOM_FILES_DIRECTORY = '/net/rossini/mesana/PROVA_MODELLER/MODELING_CALCIUM/1lmj.atm' # directories for input atom files SET HETATM_IO = ON SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 10 # index of the last model # (determines how many models to calculate) CALL ROUTINE = 'model' # do homology modelling And this is my alignment: >P1;1lmjA structureX:1lmj.pdb: 3 :A:+88 :A:undefined:undefined:-1.00:-1.00 TDIDECRISP--DLCGRGQCVNTPGDFECKCDEGYESGFMMMKNCMDIDECQRDPLLCRGGVCHNTEGSYRCECP PGHQLSPNISACI33* >P1;23urom sequence:phd2: : : : ::: 0.00: 0.00 -DLDECAIPGAHNCSANSSCVNTPGSFSCVCPEGFRLSPGLGCTDVDECAEPGLSHCHALATCVNVVGSYLCVCP AGYRGD--GWHCE33* The models generated by MODELLER contain the ions: ATOM 603 OXT GLU 85 14.608 -30.221 -12.881 1.00 30.85 1SG 604 TER 603 GLU 85 1SG 605 HETATM 604 CAL CAL 86 22.805 -57.972 -18.845 1.00 0.00 1SG 606 HETATM 605 CAL CAL 87 -43.926-115.000-182.203 1.00 0.00 1SG 607 END But the position of these Calcium ions is completely wrong, outside of the molecule and differing from the template. How can I solve this problem? Many thanks in advance for your help,

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import errors
by Mauricio Carrillo Tripp 09 Dec '08

09 Dec '08

I've just installed Modeller 9v5. I ran the examples in the automodel directory. All of them finished fine with the exception of model-parallel. All of them output an "'import site' failed; use -v for traceback" message though. mod9v5 model-parallel.py 'import site' failed; use -v for traceback Traceback (most recent call last): File "model-parallel.py", line 4, in ? from modeller.parallel import * File "/usr/people/trippm/bin/modeller9v5/modlib/modeller/parallel/__init__.py", line 1, in ? from job import job File "/usr/people/trippm/bin/modeller9v5/modlib/modeller/parallel/job.py", line 1, in ? import socket, random, os, select Is this because something is missing in my python libraries? thanks! -- 0 | Mauricio Carrillo Tripp, PhD / | Department of Molecular Biology, TPC6 0 | The Scripps Research Institute \ | 10550 North Torrey Pines Road 0 | La Jolla, California 92037 / | trippm(a)scripps.edu 0 | http://www.scripps.edu/~trippm ** Aut tace aut loquere meliora silentio **

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Multicore Jobs on QB3 Cluster Nodes
by Albion Baucom 08 Dec '08

08 Dec '08

How would I go about passing arguments to sge_qsub_job to get slave node jobs to use multiple cores on the QB3 cluster? I am familiar with using a SGE script to start parallel jobs on QB3 nodes using qsub. What I would like to do is use Modeller to start multiple jobs on nodes using multiple cores. For instance in a qsub script I might pass the following arguments #$ -pe smp 4 #$ -R yes Which uses 4 cores after using the queue to reserve that slave node. I am currently using the following Modeller directive to submit multiple jobs to the cluster j = sge_qsub_job(maxslave=jobparas.maxslave,options =jobparas.optionline,modeller_path=jobparas.modeller_path) where jobparas = jobparameters(maxslave=5, arch='opt64', queue='long.q', name='htpg', modeller_path="/diva1/home/modeller/SVN/bin/ modpy.sh \ /diva1/home/modeller/SVN/bin/ modslave.py") My question, is how do I pass the arguments "-pe smp 4" and "-R yes" for instance? Looking at the Modeller documentation, its not clear how those parameters could be passed as arguments to sge_qsub_job in this instance. Perhaps there is a better way to issue the parallelization options to Modeller? Thanks Albion

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Re: [modeller_usage] parallel modeller
by Mauricio Carrillo Tripp 08 Dec '08

08 Dec '08

I ran into the same problem. I searched the wiki but couldn't find a solution. From the description provided in the thread is not obvious how to proceed. Is there a working script that could be used as a starting point to run parallel jobs in a cluster using PBS? I managed to submit jobs using independent modeller.py scripts differing in the start and end model parameter only: in file modeller01.py start=1 end=1 in file modeller02.py start=2 end=2 each one of these run in a different node (jobs submitted with qsub), but the two resulting models 1s58.B99990001.pdb and 1s58.B99990002.pdb are exactly the same, which brings me to my second question: Is there a way to specify the initial random seed used by each modeller script? Thanks! Starr Hazard wrote: > The references to parallelization seem to point rather strongly to the SGE scheduler... Not at all - the 'job' class is simply a bag of 'slave' objects. There is no requirement that you use any particular resource management system. For example, local_slave starts up a slave on the local machine (ideal if you have a multi-core machine). ssh_slave starts up a slave on a machine accessible by ssh, ideal if you have a cluster set up to allow passwordless ssh (or rsh) to individual nodes. The only slave classes which use SGE are sge_pe_slave and sge_qsub_slave. I wrote those because we happen to have an SGE cluster. But there's no reason why you couldn't write your own slaves to use PBS mechanisms. Can any of the commands eg sge_qsub_job(options, maxslave, seq=(), modeller_path=None, host=None) work with PBS scheduler? Well, obviously not sge_qsub_job, as the name would suggest, since that is a convenience class for SGE. Just use the regular job base class. If you then have a traditional ssh-to-any-node setup, all you then need to do is loop over the nodes in your machine file and make an ssh_slave for each one. Alternatively, it would be pretty simple to write a class that used the PBS TM mechanism via something like mpiexec. I suggest you put the result into the Modeller wiki, so that other PBS users can use or modify it. -- 0 | Mauricio Carrillo Tripp, PhD / | Department of Molecular Biology, TPC6 0 | The Scripps Research Institute \ | 10550 North Torrey Pines Road 0 | La Jolla, California 92037 / | trippm(a)scripps.edu 0 | http://www.scripps.edu/~trippm ** Aut tace aut loquere meliora silentio **

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Re: [modeller_usage] R: R: question for a (putative?) disulfide bridge
by Modeller Caretaker 02 Dec '08

02 Dec '08

Anna Marabotti wrote: > I'm attaching here the pdb file of the model in which I would like to > create the disulfide bridge, and the > scripts I used to do it. My knowledge of Python language is very very > poor and so I'm doing a trial&error > procedure, but at present I obtain only errors... If I understand > well, I should only provide the PDB file to Modeller, > since I don't see any request of > alignment. The sequence then should be read from the PDB file, right? Correct. > The PDB file I have attached is the one that I obtained using > mutate_model: residue 55 was previously a Gly, > and now is a Cys in both subunits.So, the number of the residue > should be correct. Well, your first problem is that there is no residue "55" in your input PDB. There is, however, a residue "55:A". The chain ID must be specified if it is present in the PDB. > I tried to model a disulfide bridge between Cys55 of the subunit A > and Cys180 of the subunit B, and I tried: > > 1) model-patch_1.py (see attachment): here the error message: ... > KeyError: 'No such residue: 55:' OK, here it's because you didn't specify the chain IDs. > 2) model-patch_2.py (see attachment): here the error message: ... > KeyError: 'No such residue: 180:B' See http://salilab.org/modeller/9v5/manual/node403.html. By default, complete_pdb (and Modeller in general) renumbers residues starting from 1, and chains starting from A. This deals with PDBs containing duplicated residue numbers, and in the general case of comparative modeling, where there are gaps and multiple templates, the residue numbers in the target cannot be deduced from those in the templates anyway. So in your model, there is no residue 180:B; your residues are labeled 1:A through 359:A and 360:B through 718:B. So in your case you have two options: 1. Modify your script to a) not call special_patches and b) write out the resultant PDB file, e.g. # Read the sequence: code = '1R3ACYS55CYS55' mdl = complete_pdb(env, code) mdl.write(file='test.pdb') By inspecting test.pdb you can then figure out what the residue numbers should be for your disulfide bridge in the model. You can then use your original model-patch_2.py script with these corrected residue numbers. 2. Specify transfer_res_num=True when you call complete_pdb, to have Modeller use the original PDB file residue numbering. By the way, since all your script is doing is calculating the energy (not optimizing the model) you won't see the disulfide bridge pulling those two Cys residues together, although you may see some restraint violations in the log file if they're quite far apart. 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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