- modeller_usage - salilab.org

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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questions about model refinement protocol
by albert 06 Jul '10

06 Jul '10

Hello: I am reading Modeller9v8 manual and found in Page 14, 2.2.2, it is said that models could be refined by VTFM with conjugated gradients(CG) methods. In fact CG is usually applied to correct subtle errors and steepest gradient (SG) is effective for some big erros. I am wondering why not import SG for model refinement? In fact, I found that may people would like to do SG before CG when they are doing model refinement. Thank you very much.

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job running error
by albert 06 Jul '10

06 Jul '10

Hello: I am running modeller job by "python model-parall.py" based on the following scrips. But it is said in the termial which seems that modeller coundn't find the template pdb file. However, my template pdb file is already in the same working directory which named pt6A.pdb. I don't why it said couldn't find it. Would you please give me some advices? File "/soft/python2.5/lib/python2.5/site-packages/modeller/automodel/automodel.py", line 98, in make self.homcsr(exit_stage) File "/soft/python2.5/lib/python2.5/site-packages/modeller/automodel/automodel.py", line 411, in homcsr aln = self.read_alignment() File "/soft/python2.5/lib/python2.5/site-packages/modeller/automodel/automodel.py", line 401, in read_alignment aln.append(file=self.alnfile, align_codes=self.knowns+[self.sequence]) File "/soft/python2.5/lib/python2.5/site-packages/modeller/alignment.py", line 81, in append allow_alternates) _modeller.ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = pt6 ---------------------------------------------------------------------------------------- # Homology modeling by the automodel class, using multiple processors from modeller import * from modeller.automodel import * # Load the automodel class from modeller.parallel import * # Use 2 CPUs in a parallel job on this machine j = job() j.append(local_slave()) j.append(local_slave()) 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'] a = automodel(env, alnfile = 'a8-pt6.ali', # alignment filename knowns = 'pt6', # codes of the templates sequence = 'a8') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 5 # index of the last model # (determines how many models to calculate) a.use_parallel_job(j) # Use the job for model building a.make() # do the actual homology modeling

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Re: [modeller_usage] questions about loop refinement
by David Hall 05 Jul '10

05 Jul '10

http://www.salilab.org/modeller/manual/node90.html ? -David On Jul 4, 2010, at 10:25 AM, albert <leuven(a)yeah.net> wrote: Hello I have see the ppt in Modeller website and it is said that in Modeller9V8 has a new method for loop building and refinement, i.e: Newer DOPE + GB/SA protocol("dope_loopmodel"). However, in the lastest Modeller manual I don't find such kind of function. I would be very appreciated if someone could tell me how to use this new function or where I can find a scrips of Modeller. Thank you _______________________________________________ modeller_usage mailing list modeller_usage(a)salilab.org https://salilab.org/mailman/listinfo/modeller_usage

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questions about loop refinement
by albert 04 Jul '10

04 Jul '10

Hello I have see the ppt in Modeller website and it is said that in Modeller9V8 has a new method for loop building and refinement, i.e: Newer DOPE + GB/SA protocol("dope_loopmodel"). However, in the lastest Modeller manual I don't find such kind of function. I would be very appreciated if someone could tell me how to use this new function or where I can find a scrips of Modeller. Thank you

1 0

questions on loopmodel in the presence of a ligand
by Diane Lynch DLLYNCH 02 Jul '10

02 Jul '10

2 1