- modeller_usage - salilab.org

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

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

02 Jul '10

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Cross Species Dimer
by Fuhrman, Kit 02 Jul '10

02 Jul '10

Dear Modellers, I am looking for some insight into modeling a heterodimeric complex in a single species. The original crystal structure was solved with Chain A and Chain B from two different species. Chain A is from humans and Chain B is from mice. I would like to model the whole complex in the mouse form. Chain A is about 77% conserved between mice and humans. Here's my basic protocol. 1) I edited my sequences to contain only the portions modeled in the PDB. 2) I used align2d to create my PIR and PAP files 3) I used automodel and subclassed it to only select chain A for modeling The final structure looks ok visually. The DOPE score per residue actually decreased by about .01 for a few regions between the crystallographically solved structure and final homology model. Otherwise is looks about the same. Does this protocol sound correct? Is there anything else I should have done? or other potential problems I should look out for? My main concern is that the dimer interface be as close to the real deal as possible. I ran one of the models through PDBsum and a couple of Gamma turns were lost. One turn had the same sequence in both human and mouse, but no did not show up as having the secondary structure. Any help would be greatly appreciated. Best regards, Kit Kit Fuhrman IDP Graduate Student Department of Pathology, Immunology and Laboratory Medicine University of Florida College of Medicine kit.fuhrman(a)pathology.ufl.edu

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structure refinement and loop optimization protocol
by Thomas Evangelidis 24 Jun '10

24 Jun '10

Dear Modellers, I've read previous posts on the same topic and concluded that it is better to generate multiple models with moderate refinement and loop optimization level, rather that a few with very thorough parameterization. I've also noticed myself that with the thorough parameterization parts of the secondary structure are distorted. I have concluded about the optimum alignment after a lot of experimentation and would like to set up a very effective optimization process. However I'm not sure about the output files. My code looks like this: a = MyLoopModel(env, alnfile=alignment, > knowns=known_templates, > assess_methods=(assess.DOPEHR,assess.normalized_dope), > sequence='target') > a.starting_model = 1 > a.ending_model = 2 > # Normal VTFM model optimization: > a.library_schedule = autosched.normal > a.max_var_iterations = 200 ## 200 by default > # Very thorough MD model optimization: > a.md_level = refine.slow > a.repeat_optimization = 1 > > a.loop.starting_model = 1 # First loop model > a.loop.ending_model = 5 # Last loop model > a.loop.md_level = refine.slow # Loop model refinement > level > Which generates the following pdb files: target.B99990001.pdb target.B99990002.pdb target.BL00040002.pdb > target.IL00000001.pdb target.IL00000002.pdb > I thought the above should perform model refinement twice and write 5 different conformations (loop optimization) for each. So my questions are the following: 1) Can you explain what's happening with the .pdb files? 2) I 'd like to ask your opinion about the most effective way to find a near-native protein conformation in low sequence identity levels. How should the parameters shown above be set? I don't care if it's running a day or so as long as I get good results. 3) I also attempted to cluster the models with a.cluster(cluster_cut=1.5), which generated a representative structure with the parts of the protein that remained similar in most of the models but without the variable parts (files cluster.ini and cluster.opt). Does it make sense to select the model that is closer to that consensus structure? If yes is there a way to do it with Modeller? I know it can been found with Maxcluster program. Or alternatively, do you reckon it is better to select the based model based on the normalized DOPE z-score? Hope to get some answers on these question cause I've been strangling to find the best refinement/optimization protocol for several weeks. thanks, Thomas

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wrong asparagine and glutamine side chains
by David Rodríguez 24 Jun '10

24 Jun '10

>From time to time I find in generated models wrong asparagine and glutamine side chains (see attached PDB for a glutamine example), either with automodel or loopmodel classes. It is not reproducible, it happens in certain runs, and within the same one it only happens in one residue of one model. I've been looking for it to be documented, but I found nothing related. In order to overcome this, I used the "mutate_model.py" script, to try the trick of mutating glutamine for itself, but didn't work. I wonder if anyone know a way to detect and/or correct those residues with a Modeller script (I know other programs that can do it, but using an exclusively Modeller pipeline will make things much easier). Thanks in advance, -- David Rodríguez Díaz, PhD Student Fundación Pública Galega de Medicina Xenómica (SERGAS) E-mail: david.rodriguez.diaz at usc dot es

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