May 2011 - modeller_usage

NADPH
by flavio seixas 25 May '11

25 May '11

Hi, I want to modelate a protein wit NADPH bonded. However, my template has NADH bonded. Here is parte the alignment file I am using with: >structure CCCCCCCCCCCCC4 >sequence BBBBBBBBBBBBB. Were "4" is NADH and "." will repeat NADH. My question is: Which is the align code for NADPH?? If there is no code, how can I replace NADH by NADPH with modeller? Thanks for any help. Flavio Augusto Vicente Seixas Professor Adjunto do Departamento de Bioquímica - DBQ Universidade Estadual de Maringá - UEM Av. Ângelo Moreira da Fonseca, 1800 - Zona 7 87506-370 - UMUARAMA - PR - BRAZIL

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Regarding multiple calls of align2d.py
by Ashish Runthala 24 May '11

24 May '11

Dear Modellers, FIRST and LAST string usage in align2d.py for Initial and final residue number specifier of the concerned template PDB chain generates errors. Why it is so? I should be simply able to alter PDB names in the same align2d.py script without specifying the first and last residue number of the concerned chain. SUGGEST ME THE SOLUTION. Thanks Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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Re: [modeller_usage] Loop modelling without changing structure
by Thomas Evangelidis 24 May '11

24 May '11

Yes, this happens quite often. Try to create many homology models without loop modeling (replace MyModel(loopmodel) with class MyModel(automodel), and omit lines starting with a.loop.*) using: a.library_schedule = autosched.slow a.max_var_iterations = 300 a.md_level = refine.very_slow Then chose one model with closed loop ends and use it as the initial conformation to start loop modeling, by following the instructions in my previous email. If the problem persists (probably in case you use multiple templates), paste your alignment here. Usually it's the alignment that requires aditing to make the loops close. Thomas On 24 May 2011 14:08, Matthias Schmidt <matthias.rene.schmidt(a)gmail.com>wrote: > Hi, > > Actually, the modelling works, but the result is not what I hoped for. > Despite having restraints everywhere except for on the loop, Modeller > alters the C-terminus, and it fails to close the loop. > > Hm... Have you seen this before? > > Cheers, > > Matthias > > On Tue, May 24, 2011 at 11:18 AM, Matthias Schmidt > <matthias.rene.schmidt(a)gmail.com> wrote: > > Hi Thomas, > > > > Thank you very much for the hint on the rigid_bodies constraints and > > for your scripts. > > > > It works well. > > > > Best, > > > > Matthias > > > > On Tue, May 24, 2011 at 10:07 AM, Thomas Evangelidis <tevang3(a)gmail.com> > wrote: > >> I'm sorry, I picked the wrong script. Please use the following corrected > >> version: > >> > >> > >> > >>>> class MyModel(loopmodel): > >>>> # This routine picks the residues to be refined by loop modeling > >>>> def select_loop_atoms(self): > >>>> return selection(self.residue_range('310:', '320:'), > >>>> self.residue_range('517:', '523:')) > >>>> > >>>> def special_restraints(self, aln): > >>>> rsr = self.restraints > >>>> # Keep whole model but loop atoms rigid > >>>> wholeSel = selection(self) - self.select_loop_atoms() > >>>> r = rigid_body(wholeSel) > >>>> rsr.rigid_bodies.append(r) > >>> > >>> Then use MyModel in the following way: > >>> > >>>> nv = environ() > >>>> env.io.hetatm = False > >>>> # directories for input atom files > >>>> env.io.atom_files_directory = ["../"] > >>>> a = MyModel(env, > >>>> alnfile = ALIGNMENT, # alignment filename > >>>> knowns = (template1, template2), # codes of the templates > >>>> assess_methods=(assess.DOPEHR,assess.normalized_dope), # > >>>> optionally assess the models on th fly > >>>> sequence=OUTPUT_MODEL_NAME) # code of the > >>>> target > >>>> a.starting_model = 1 # First homology model > >>>> a.ending_model = 1 # Last homology model > >> > >> > >> a.loop.starting_model = 1 # First loop model > >> a.loop.ending_model = 10 # Last loop model > >> a.loop.md_level = refine.very_slow # Loop model > >> refinement level > >>>> > >>>> > >>>> a.library_schedule = autosched.slow > >>>> a.max_var_iterations = 300 > >>>> # Very thorough MD optimization: > >>>> a.md_level = refine.very_slow > >>>> > >>>> a.make() > >>> > >>> > >> > >> In this way you will create a model from your template (if you already > have > >> a model then use it as the template), and then 10 loop decoys by keeping > the > >> rest of the structure rigid. Instead of loopmodel you could use the more > >> accurate dope_loopmodel or even dopehr_loopmodel. You could also start > from > >> an initial structure instead of building one, by using the inimodel > argument > >> within MyModel, i.e. > >> > >> a = MyLoopModel(env, > >> inimodel=initial_structure, > >> loop_assess_methods=assess.DOPEHR, > >> sequence=output_model_name) # code of the > target > >> a.loop.starting_model = 1 # First loop model > >> a.loop.ending_model = 10 # Last loop model > >> a.loop.md_level = refine.very_slow # Loop model refinement > >> level > >> a.make() > >> > >> > >> Whatever way you chose, the key is to define as rigid_body the part of > the > >> structure that you want to be fixed. > >> > >> > >> good luck, > >> Thomas > >> > >> > >>> > >>> > >>> On 24 May 2011 10:25, Matthias Schmidt < > matthias.rene.schmidt(a)gmail.com> > >>> wrote: > >>>> > >>>> Hi, > >>>> > >>>> how can I model a loop without changing the rest of the structure? > >>>> > >>>> Best, > >>>> > >>>> Matthias > >>>> _______________________________________________ > >>>> modeller_usage mailing list > >>>> modeller_usage(a)salilab.org > >>>> https://salilab.org/mailman/listinfo/modeller_usage > >>> > >> > >> > >> > >> Thomas Evangelidis > >> > >> PhD student > >> > >> Biomedical Research Foundation, Academy of Athens > >> > >> 4 Soranou Ephessiou , 115 27 Athens, Greece > >> > >> email: tevang(a)bioacademy.gr > >> > >> tevang3(a)gmail.com > >> > >> website: https://sites.google.com/site/thomasevangelidishomepage/ > >> > >> > > > -- ====================================================================== Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tevang(a)bioacademy.gr tevang3(a)gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/

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Loop modelling without changing structure
by Matthias Schmidt 24 May '11

24 May '11

Hi, how can I model a loop without changing the rest of the structure? Best, Matthias

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[Peptide Refinement] How to move R groups only?
by Ignacio Ibarra 23 May '11

23 May '11

Hello, I'm using mod9.9 to model a short peptide-protein complex. Once the model.pdb file is created, I would like to make a refinement without moving the protein (it should be fixed), and readjusting the R groups of the short peptide *with no movement of the backbone*. I don't want to modify the positions of the backbone at all. Currently I'm using the following code (short version). This one creates a model with no movement of the protein, but the short peptide is displaced several angstroms. class MyPeptide(loopmodel): def select_loop_atoms(self): # 13 residue selection return selection(self.residue_range('618:D', '630:D')) m = MyPeptide(env, inimodel='model.B99990001.pdb', # initial model of the target sequence='refinedModel') # code of the target m.loop.starting_model= 1 # index of the first loop model m.loop.ending_model = 1 # index of the last loop model m.loop.md_level = refine.slow m.make() I think that I should add restraints like the "max_ca_ca_distance" one, but I'm not sure if there's something more appropiate Greetings Ignacio

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Multi-model PDB file
by Thomas Holder 23 May '11

23 May '11

Hi, is it possible with modeller to read a particular model from a multi-model PDB file? Or to loop over all models in such a file? Thanks, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen

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retrieve fitted models after iterative_structural_align()
by Benjamin SCHWARZ 18 May '11

18 May '11

Can someone tell me what is the (best) way to extract fitted models after an iterative_structural_align() ? I have tried something like : 1 aln = alignment( env ); for model in models : aln.append_model( model ) 2 salign.iterative_structural_align( aln ) 3 aln.salign(write_fit=True) 4 aln.write(alignment.ali) The structural alignment seems OK, but the alignment file alignment.ali doesn't reflect the observed structural alignment. I then realized the salign call probably messes up with the alignment. I thus switched lines 3 and 4, and the resulting alignment seems OK. In fact it resembles what I was expecting according to the structural alignment, and this puzzles me a lot since I somehow expect that after an salign call, the fitted structure and the alignment would be connected. I also tied something like : 3 aln.write(alignment1.ali) 4 aln.salign(write_fit=True, improve_alignment=False, feature_weights=[0]*6) 5 aln.write(alignment2.ali) The fitted structures are unchanged but alignment2.ali is totally messed up compared to alignment.ali when I expected the two to be similar. In the end, I am not sure anymore that the fitted models I retrieve are the ones coming out from the salign.iterative_structural_align() or if my salign() call does something in-between... I'd be glad if someone can give me the best way to retrieve my fitted models. Some hints to explain the observed behavior would be appreciated to. --Ben

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align-template.py command erorr
by Sajad Ahrari 18 May '11

18 May '11

hello dears I am trying to build a model of protein1 with MG-ATP(naturally 1 holds ADP instead of MG-ATP in it's structure) , based on protein2 structure witch holds MG-ATP in it's structure(2 is considered as template). in fact I want only hetero-atoms of protein2 be considered and finally be added to the structure of 1, by modeller. i have prepared the PDB file of both 1and2 .but after running the command"mod9v8 align-templates" , I am faced with this erorr " import site' failed; use -v for traceback". could you please let me know what is wrong?( I have attached the "align-templates.py" file, to be considered for any possible mistakes in it) thanks in advance! sajad

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Re: [modeller_usage] Problem in mGeneThreader link
by Bishwajit Das 16 May '11

16 May '11

On Mon, May 16, 2011 at 11:06 PM, Bishwajit Das <das.bishwajit(a)gmail.com>wrote: > Dear modeller > i want to submit my sequence into mGeneThreader,but i doin't > get the link.please send me the mGeneThreader server link where i submit my > query to finding fold assignment. > > Thanking You. > > -- > * > > > BISHWAJIT DAS*** > KOLKATA > > -- * BISHWAJIT DAS* *+91-9433237920* KOLKATA

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FATAL ERROR: MODINSTALL9v9 environment variable not set: incomplete MODELLER installation on Ubuntu 10.4
by crina ionescu 10 May '11

10 May '11

Hi. I am trying to run Modeller under Ubuntu and I am getting the following output: ----------- Running calculation: /usr/lib/modeller9.9/bin/mod9.9_i386-intel8 model.py MODELLER outputs: FATAL ERROR: MODINSTALL9v9 environment variable not set: incomplete MODELLER installation ---------- I had a look through the archives for similar issues, but the solution was posted only for Windows. Either I'm the only one who managed to mess it up under Linux, or I'm the only one who isn't able to fix it. In any case, I'd love some help. I installed Modeller in the following way. I downloaded the corresponding package (modeller_9.9-1_i386.deb) and just opened it. The package manager ran the installation itself (I did not do it in the terminal). ------ Selecting previously deselected package modeller. (Reading database ... 307463 files and directories currently installed.) Unpacking modeller (from .../modeller_9.9-1_i386.deb) ... Setting up modeller (9.9-1) ... Modeller installed, but not licensed. Please visit the Modeller web site at http://salilab.org/modeller/ to get a license key, and then edit the file /usr/lib/modeller9.9/modlib/modeller/config.py to set the key, i.e. the line license = 'xxx' should be changed to read license = 'MYKEY' where MYKEY is the key you obtained. ------- I then got a key and edited the respective file accordingly. Was I supposed to run anything else after this? All the best. Crina

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