- modeller_usage - salilab.org

[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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Need help regarding alteration of align2d.py parameters
by Ashish Runthala 02 May '11

02 May '11

Dear Modellers, Align2d.py the pairwise alignment is not working i want it to. Will somebody please tell me where are the options to change the considered score matrix and other gap based parameters. Thanks Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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High energy in template-based parts of the model
by Lilit Nersisyan 02 May '11

02 May '11

Hi, I am building a protein model based on templates and secondary structure restraints. My protein is 781 amino acids long, and it has two homology derived templates in the 1-92 and 394-412 segments. The 590-781 segment has a solved crystallographic structure. I have given the corresponding templates to these three segments. I have also added secondary structure restraints to the remaining parts of the protein based on secondary structure predictions. The problem is that when I plot the DOPE profiles of the generated models, I see that the template-based segments (especially the 590-781 segment) have the highest energy. This makes it impossible to refine only the parts of the model with high energy, since the refinement will destroy the structures that must be present in the protein. I have used the standard scripts for model making and restraint-adding incorporated in Modeller examples. I would like to know the reasons for getting high energy in the part of the protein, which has a solved crystallographic structure. I will appreciate any advice. Thank you. -- Lilit Nersisyan Institute of Molecular Biology NAS RA E-mail: txgt.lilit.nersisyan(a)gmail.com Tel.: +37494 601703

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batch model building
by Vagmita Pabuwal 02 May '11

02 May '11

Hi, I was wondering if we can build models in batch if we are using same template, but different alignment, so for each alignment we have new model. And this could be automated.I have to build around 300 models with same template but different alignment for each model i generate. I would really appreciate if anybody could help me on this. Otherwise it takes a long time if I build them using automodel, as each time i have to change the .ali filename and also the sequence name in there. ThanksVagmita

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B value
by Sanger 28 Apr '11

28 Apr '11

Dear friends, I have some questions about the B value, generated from the Modeller along with the homology model. I am not sure how the temperature factor (Beta) is calculated (by MD simulation?). Since many homology modeling program didn't supply the information of B value, or just used it as a temporary space to fill up data, I am curious how serious the Modeller deals with it? Is it a proper data to estimate the flexibility of residues? Any suggestions or comments are greatly appreicated. Your sincerely, Xinhao Ye ---------- PhD candidate Department of Biological Systems Engineering, Virginia Tech Blacksburg, VA 24061 USA

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