July 2010 - modeller_usage

Parallel task using sge_pe_job()
by Charles Xue 28 Jul '10

28 Jul '10

Hello, I am attempting to run MODELLER in parallel on a cluster with multiple nodes. The script I used is below: from modeller import * from modeller.parallel import * from modeller.automodel import * log.verbose() j = sge_pe_job() env = environ() a = automodel(env, alnfile='2NT2-mult.ali', knowns=('1m3gA','2wgpA','2hxpA'), sequence='2NT2', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 25 a.use_parallel_job(j) a.make() However, once I submit the job (using the parallel environment mpich), the job runs on the master node fine but fails on all the slave nodes. The error is also ambiguous: within the slave1 output file (identical for all other output files except the slave0 one which runs fine): error: executing task of job 76003 failed: Thanks in advance for the help! -Charles Xue

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Re: [modeller_usage] have you solved the problem with installation under Windows XP
by Modeller Caretaker 23 Jul '10

23 Jul '10

On 7/23/10 1:59 PM, Andrew Voronkov wrote: > Here is modenv.bat from 64 bit system. I got no item in Start menu. Your batch file is fine - it's the same as mine. The Modeller shortcut in the Start menu simply runs command.com /E:8192 /K "C:\Program Files\Modeller9v8\bin\modenv.bat" i.e. it starts a command prompt and runs that batch file to set up the environment so that Modeller will work. (If you run a regular command prompt, it won't have the paths set up properly, and Modeller won't work.) I don't know why the Start menu shortcut isn't being installed on your system - although you have to run the installer as an admin user in order for it to do that (it should warn you if you don't) - but you can make your own shortcut to Modeller in this case. 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] have you solved the problem with installation under Windows XP
by Modeller Caretaker 23 Jul '10

23 Jul '10

On 7/23/10 12:48 PM, Andrew Voronkov wrote: > Actually indeed only one PC where I don't have this problem is 32 bit > NoteBook, btw I also have some troubles with rpm usage for 64-bit. What sort of troubles? I can't help you if I don't know what your problem is. > So what can be a soluation for 64 bit system? How batch file is > called? I can't find anything with *batch* in the search. The Modeller batch file is called modenv.bat and lives in the 'bin' directory under whichever directory you installed Modeller in (C:\Program Files\Modeller9v8 by default). On a successful install, it looks like: @echo off set MODINSTALL9v8=C:\Program Files\Modeller9v8 set PYTHONPATH=C:\Program Files\Modeller9v8\modlib; set LIB_ASGL=C:\Program Files\Modeller9v8\asgl set BIN_ASGL=C:\Program Files\Modeller9v8\bin set PATH=%MODINSTALL9v8%\bin;%PATH% cd C:\Program Files\Modeller9v8 echo You can find many useful example scripts in the echo examples\automodel directory. echo Type 'mod9v8' to run Modeller. What does yours look like? 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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have you solved the problem with installation under Windows XP
by Andrew Voronkov 20 Jul '10

20 Jul '10

Dear Modeller administration, there is definitely a problem with installation of Modeller uinder windows XP 64 bit. I have installed it on different PCs in different places, I don't get icon in Start menu and when I run it using command line there is an error message about environment which is not set properly. I don't know if there is such a problem with Windows XP 32 bit as well, but this is definitely a bug with Windows XP 64 bit. If you have such a system or any of users have it - please test Mod9v8 and confirm that it doesn't install properly. Sincerely yours, Andrew

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model generate error
by albert 20 Jul '10

20 Jul '10

Hello: I am trying to use my own mutiple alignment to generate model, but it faild, it is said : ---------------log---------------------------------------- Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 4) = protein Here is parameter in my model-changeopt.py: ---------------model-changeopt.py---------------------- a = automodel(env, alnfile='man.ali', knowns=('1A','2A','3A'), sequence='protein', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model =1 a.ending_model = 4 ....... Here is my alignment file, man.ali: ------------------------man.ali------------------------------- >P1; protein sequence:ttl: : : : ::: 0.00: 0.00 aaaaaaaaaaaaaabbbbbbbbbbbbbbcccccccccccccccccccc* >P1;1A structureX:1: 1 :A:+14 :A:::-1.00:-1.00 aaaaaaaaaaaaaa--------------------------------------------* >P1;2A structureX:2: 1 :A:+16 :A:::-1.00:-1.00 -----------------aabbbbbbbbbbbbbb--------------------------* >P1;3A structureX:3: 1 :A:+20 :A:::-1.00:-1.00 --------------------------------------cccccccccccccccccccc* I have 1.pdb 2.pdb 3.pdb and 1_fit.pdb 2_fit.pdb 3_fit.pdb in the same directory. could you please give me some advices please? Thank you very much

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A followup question to Re: questions on loopmodel in the presence of a ligand
by Diane Lynch DLLYNCH 19 Jul '10

19 Jul '10

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difference side chain dihedrals of identical residues in model and the template
by rsachdeva＠imtech.res.in 15 Jul '10

15 Jul '10

Dear All, I have built a homology model of my protein using a single template sharing 38% sequence identity. Some of the functionally important residues of target protein are conserved in the template. These residues are well aligned in the input sequence alignment file. In the top most model so obtained, I found difference in side chain dihedral angles of such identical residues. Since both target as well as template contain a few identical residues, their secondary structure is also same, then why these conserved residues in the model adopt rotamers different from those of the template. Following is comparison of side chain dihedrals of arginine conserved in both target as well as template. chi1 chi2 chi3 chi4 chi5 template 169 -100 179 -80 0 model 65 81 75 -96 0 Here, chi1, chi2 and chi3 are drastically different Can anybody please explain why this is so? Thanks Ruchi

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based on intial model failed
by albert 09 Jul '10

09 Jul '10

I try to build a model with my own intial model, but it failed, here is the log file: Traceback (most recent call last): File "single.py", line 36, in ? a.make() File "/usr/lib64/python2.4/site-packages/modeller/automodel/automodel.py", line 98, in make self.homcsr(exit_stage) File "/usr/lib64/python2.4/site-packages/modeller/automodel/automodel.py", line 427, in homcsr self.make_initial_model(aln) File "/usr/lib64/python2.4/site-packages/modeller/automodel/automodel.py", line 441, in make_initial_model self.generate_method(self, aln) File "/usr/lib64/python2.4/site-packages/modeller/automodel/generate.py", line 46, in read_xyz mdl.transfer_xyz(a, cluster_cut=-1.0) File "/usr/lib64/python2.4/site-packages/modeller/model.py", line 200, in transfer_xyz cluster_method) _modeller.ModellerError: rdpdb___303E> No atoms were read from the specified input PDB file, since the starting residue number and/or chain id in MODEL_SEGMENT (or the alignment file header) was not found; requested starting position: residue number " ", chain " "; atom file name: loop.pdb

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retrieve model object
by Andrea Coletta 09 Jul '10

09 Jul '10

Hi everybody, it is possible to retrieve the model(s) object from the automodel.make() instance, instead of writing a pdb(s) and subsequenlty open it with a model.read() ? Thanks Andrea Coletta

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loop refinement error
by albert 07 Jul '10

07 Jul '10

Hello: I try to do loop refinement by loop.py using mutiple CPU, but it doesn't work. Here is the scrips and log file. Could anybody give me some advices? scrips: ------------------------------------------------------------ from modeller import * from modeller.automodel import * from modeller.parallel import * j = job() j.append(local_slave()) j.append(local_slave()) j.append(local_slave()) j.append(local_slave()) env = environ() log.verbose() # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] # Create a new class based on 'loopmodel' so that we can redefine # select_loop_atoms (necessary) class dope_loopmodel(loopmodel): # This routine picks the residues to be refined by loop modeling def select_loop_atoms(self): # One loop from residue 19 to 28 inclusive return selection(self.residue_range('238:', '241:')) m = dope_loopmodel(env, inimodel='backbone', # initial model of the target sequence='a8') # code of the target m.loop.starting_model= 1 # index of the first loop model m.loop.ending_model = 100 # index of the last loop model m.loop.md_level = refine.slow # loop refinement method m.use_parallel_job(j) m.make() logfile --------------------------------------------------------------------------------------------------- Traceback (most recent call last): File "loop.py", line 34, in ? m.make() File "/usr/lib64/python2.4/site-packages/modeller/automodel/loopmodel.py", line 34, in make self.build_seq(self.inimodel, 1) File "/usr/lib64/python2.4/site-packages/modeller/automodel/loopmodel.py", line 146, in build_seq self.parallel_loop_models(atmsel, ini_model, num, sched) File "/usr/lib64/python2.4/site-packages/modeller/automodel/loopmodel.py", line 164, in parallel_loop_models self.loop.outputs.extend(job.run_all_tasks()) File "/usr/lib64/python2.4/site-packages/modeller/parallel/job.py", line 130, in run_all_tasks for task in self._finish_all_tasks(): File "/usr/lib64/python2.4/site-packages/modeller/parallel/job.py", line 163, in _finish_all_tasks task = self._process_event(obj, s) File "/usr/lib64/python2.4/site-packages/modeller/parallel/job.py", line 179, in _process_event task = obj.task_results() File "/usr/lib64/python2.4/site-packages/modeller/parallel/slave.py", line 61, in task_results r = self.get_data(allow_heartbeat=True) File "/usr/lib64/python2.4/site-packages/modeller/parallel/communicator.py", line 84, in get_data (cmdtype, obj) = self._recv() File "/usr/lib64/python2.4/site-packages/modeller/parallel/communicator.py", line 125, in _recv raise RemoteError(obj.exc, self) modeller.parallel.communicator.RemoteError: AttributeError: 'module' object has no attribute 'MyLoop' from <Slave on localhost>

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