- modeller_usage - salilab.org

Parallel job with modeller on a machine with altinstall python2.3
by ashika torikora 20 Oct '15

20 Oct '15

Hi, I know there have been a million different and redundant questions asked concerning parallel jobs using modeller. However, after thoroughly reading through most of them (and the manual pages concerning parallel jobs) I still cannot run a modeller parallel job. I understand that in order to run parallel modeller one has to have the python2.3 modules. I have installed Python2.3.6 as an alternative install on my RHEL machine (the default Python for my machine is 2.7.5). However even after installing Python2.3.6 I still get the same error (no module named socket, although Python2.3.6 has the socket module --python2.7.5 does not--). Adding a shebang with the python2.3 location in the beginning of the input changes nothing. Here is my input: from modeller import * from modeller.automodel import * from modeller.parallel import * # Use 4 CPUs in a parallel job on this machine j = job() j.append(local_slave()) j.append(local_slave()) j.append(local_slave()) j.append(local_slave()) log.verbose() env = environ() env.io.atom_files_directory = ['.', './template_struc'] # Create a new class based on 'loopmodel' so that we can redefine # select_loop_atoms class MyLoop(dopehr_loopmodel): # This routine picks the residues to be refined by loop modeling def select_loop_atoms(self): # Two residue ranges (both will be refined simultaneously) return selection(self.residue_range('278:', '284:')) a = MyLoop(env, alnfile = 'alignment.ali', # alignment filename knowns = '2cjf_0', # codes of the templates sequence = '2cjf', # code of the target loop_assess_methods=assess.DOPE) # assess each loop with DOPE a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model a.loop.starting_model = 1 # First loop model a.loop.ending_model = 1000 # Last loop model a.loop.assess_methods=(assess.DOPE, assess.GA341, assess.normalized_dope) a.use_parallel_job(j) # Use the job for model building a.make() # do modeling and loop refinement And here is my error: Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] 'import site' failed; use -v for traceback Traceback (most recent call last): File "backup.py", line 4, in ? from modeller.parallel import * File "/usr/lib/modeller9.15/modlib/modeller/parallel/__init__.py", line 1, in ? from modeller.parallel.job import job File "/usr/lib/modeller9.15/modlib/modeller/parallel/job.py", line 1, in ? import socket, random, os, select ImportError: No module named socket

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Directly setting backbone dihedral angles (build an alpha helix)
by Ajasja Ljubetič 12 Oct '15

12 Oct '15

Dear all, I would like to build a perfect helix as an initial structure for some further manipulations. (Without a good initial structure the homology modelling part I apply later does not converge). Right now I'm using mdl.build_sequence(d.entire_sequence) to build the sequence, then I save it to a PDB, load it in VMD, set the backbone angles there (to get an alpha helix) save it to another PDB and load at back into modeller. So I guess my basic question is: *Is it possible to set backbone dihedral angles to a specific value? Or is there any other way to use mdl.build_sequence to get an alpha helix?* Thank you & best regards, Ajasja Ljubetič National Institute of Chemistry Slovenia

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Conformational Modelling
by Parker de Waal 02 Oct '15

02 Oct '15

Hi Modeller users, I have an interesting case where I have two known structures of related proteins A and B. A is in the inactive conformation while B is in the active conformation. Is it possible to use modeller to predict the active conformation of A using structure B as the template? Further, despite being in different conformations, only a handful of residues are important for this conformational change (the rest remain stable and are distal from the active site). Is it possible to hold the correct parts of protein A in place and only perform modelling on residues within the active site (taken from protein B as template)? Best, Parker

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Model Building
by Wong Li Zhe 02 Oct '15

02 Oct '15

Dear all, I am trying to build a protein model. Is it possible to build the model with the generated PDB files (with lowest DOPE score). There are 2 regions I which to build, where the first region consist of 1 template & the second region consists of 7 templates. I have built 100 models each for the 2 regions using single template approach and multiple template approach for the latter. >From the 100 models, I pick the best model with lowest DOPE score. With that, I have 1 model for first region & 1 model for second region. I would like to use the generated 2 models, combine them to build a final model. To my understanding, I can't proceed straight to the 'model building' command as it doesn't append PDB file. And I was trying to generate the alignment file for the 2 models but it won't work either. Could any of you enlighten me on this? Thank you & have a nice day! Best regards, Li Zhe [http://imu.edu.my/e-banner/sew-2015.jpg] Explore the endless possibilities in the field of medicine & health sciences. Register today at http://info.imu.edu.my/sew

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Problem in oligomer modelling
by Soong Jiaxin 29 Sep '15

29 Sep '15

Hi all, I'm modelling a dodecamer. Somehow, there seems to be a problem for some of the monomers to connect to the other monomers. The oligomer template I used has interdimeric contacts. However, the way my model connects among the monomers is different from the template I used. The tail for the monomer in concern goes in and out of the beta strands of the neighbour monomer instead of connecting by touching the C-terminal region interface of the next monomer. Is there a way to fix this or is this normal for a protein model? I have attached a copy of my modelling script as well. Thank you for your help in advance. Regards, Vanessa

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using DSS/BS crosslink information as restrain
by thereal sisterdot 08 Sep '15

08 Sep '15

Dear modeller users and "caretakers", i was using modeller to model a heterohexameric complex from mouse where the yeast orthologous structure is known. to evaluate the models i used the DOPE score and visualized a dozen available intersubunit DSS/BS crosslinks using Xlink Analyzer in chimera. for 2 neighbouring subunit 3 crosslinks indicate that the published heterohexameric complex appears to have a different arrangement in that part than the published one (crosslinked residues between subunits are around 60A apart) in order to obtain a model satisfying those crosslink restrains would one add the 3 crosslinks as below, or can you recommend a better approach: class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms # Constrain the distance between alpha carbons in residues 611 chain D # and 224 chain B to be less than 30 angstroms: rsr.add(forms.upper_bound(group=physical.xy_distance, feature=features.distance(a['CA:611:D'], a['CA:224:B']), mean=30., stdev=0.1)) thanks a lot!!!! Maria

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Import error
by GaoKyle 08 Sep '15

08 Sep '15

Hi,I'm running win7 64bit, and have both 32bit python3.4 and modeller9.15 installed. I'm getting this error when I tried to run a simple script:-------------------------------------Traceback (most recent call last): File "D:\学习\论文\Methylation\modeller\fasta2pir.py", line 1, in <module> from modeller import * File "C:\Program Files (x86)\Modeller9.15\modlib\modeller\__init__.py", line 93, in <module> import _modellerImportError: DLL load failed: 操作系统无法运行 %1。-------------------------------------------Please ignore the Chinese. I really have no idea of how to fix this problem.Please advise me.Thank you !

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Sequence difference between alignment and PDB
by Wong Li Zhe 08 Sep '15

08 Sep '15

Dear all, I edited the alignment file (SF3B1-Mult.ali) and would like to generate a protein model. Edited the templates sequence accordingly to start from position 610-1198. It is however, I keep getting the error message 'sequence difference between alignment and PDB'. Being the first time Modeller user, would anyone be kind enough to guide me as to how I should rectify the problem. Hereby I attached the alignment file along with this email. Thank you. Best regards, Li Zhe [http://imu.edu.my/e-banner/od-aug.jpg] Come join our INFO DAYS. Your journey in healthcare starts here! Find out more at http://info.imu.edu.my/open-day#infodays

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回复： using DSS/BS crosslink information as restrain
by S～star 08 Sep '15

08 Sep '15

dts 发自我的iPhone ------------------ 原始邮件 ------------------ 发件人: thereal sisterdot <therealsisterdot(a)gmail.com> 发送时间: 2015年09月08日 14:27 收件人: modeller_usage <modeller_usage(a)salilab.org> 主题: Re: [modeller_usage] using DSS/BS crosslink information as restrain

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alignment for multiple chain modelling
by thanj sal 31 Aug '15

31 Aug '15

Hello, For multichain modelling (ex. for a hetrodimer), Is it possible to force the alignment program in modeller to choose particular chain for the alignment?. For example use only template A chain for 1st chain in the sequence and template B chain for 2nd chain in the sequence. env = environ() aln = alignment(env) mdl = model(env, file=3gsn, model_segment=("FIRST:A, "LAST:B)) aln.append(file='seq.ali', align_codes='seq') aln.align2d() aln.write(file=align.ali, alignment_format='PIR') Thanks for any leads.. Sal

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