- modeller_usage - salilab.org

Evaluating models with procheck
by HERBERT MAX VENTHUR PE¥A 21 May '13

21 May '13

Hello My name is Herbert Venthur, I'm PhD student from Universidad de La Frontera, Chile. I'm new and beginner with modeller, however, I can model a protein structure using the basic tutorial of modeller. The model structure that I have, I submitted to ProCheck to evaluate the model, my question is: Results indicate a 95% of residues in favoured regions. That valuew, it is enough to have a suitable model?, Could I perform a docking with this model then? Thank your very much Best regards Herbert -- *Herbert Venthur Peña Profesor de Estado en Ciencias con Mención en Química* *Estudiante de Doctorado en Ciencias de Recursos Naturales * *Laboratorio de Ecología Química Universidad de La Frontera Temuco, Chile * *08-3104992*

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Fwd: Customised Modeling - Template is NMR Structure
by Priya Chaudhary 10 May '13

10 May '13

Respected Sir I am new user of Modeller. *I don't have any background in python.* I have to use a template, whose PDB ID is 1APS. It is *NMR Model *with four models. I have to use only *first model of this NMR* structure. For this template, I have *50 Query sequences* in 50 separate ".fasta files" in PIR FORMAT. *Description of PIR Format of Query sequences:* *First line: *>1APS_1; Mutant_Y15M *Second Line:* I think this line is optional - I HAVE OMITTED THIS LINE. My second line is PROTEIN SEQUENCE in Capital letters ending with " * ". Can you guide me with* steps* of how to model 50 Query sequences with template 1APS (first model). I am mailing *ATTACHMENT* (in both .zip and .tar.gz format) containing 50 Query sequences and 1APS PDB file downloaded from Protein Databank. It would be of great help. Thanks a ton. Regards Priya

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Re: [modeller_usage] modeller_usage Digest, Vol 12, Issue 17
by aixintiankong 09 May '13

09 May '13

Dear, thanks for you help. should i use the the entire second template(loop is disordered) sequence or only part of the disordered sequence to aglian? >Message: 1 >Date: Fri, 03 May 2013 10:31:56 -0700 >From: Modeller Caretaker <modeller-care(a)salilab.org> >To: aixintiankong <aixintiankong(a)126.com> >Cc: modeller_usage(a)salilab.org >Subject: Re: [modeller_usage] how to build the loop of protein model > using modeller >Message-ID: <5183F48C.7010601(a)salilab.org> >Content-Type: text/plain; charset=ISO-8859-1; format=flowed > >On 4/29/13 8:25 PM, aixintiankong wrote: >> i don't know how to build a model that the protein, NAD+ and ligand >> coexsit and the loop of protein is disordered. > >One way to do this would be to align your model sequence with the first >template (loop is helix) for the entire sequence except the loop, and >the second template (loop is disordered) for the loop: >http://salilab.org/modeller/9.11/FAQ.html#1 > >Another way would be to just use the first template, and just unalign >the loop so Modeller builds it without template information: >http://salilab.org/modeller/9.11/FAQ.html#2 > > Ben Webb, Modeller Caretaker >-- >modeller-care(a)salilab.org http://www.salilab.org/modeller/ >Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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Error with the Mutate script
by Arjun Ray 08 May '13

08 May '13

Dear Sir, I am trying to mutate a residue THR61. Using the script provided on the website, I am getting following error: rayarjun$ python /usr/bin/mutate.py 1AV1.pdb 61 THR A > 1AV1.log File "/usr/bin/mutate.py", line 36 def refine(atmsel): ^ IndentationError: unindent does not match any outer indentation level Could you kindly help identifying the cause of it? Regards Arjun

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change restraints relative weights
by Pietro Sormanni 03 May '13

03 May '13

dear Users, I am sorry for the naif question, but is there a way to change the relative importance of restraints? I am trying to add a secondary structure (both strand and sheet for H bonds) restraints to a model, in a region that do not align on the template structure (hence it shouldn't contain homology derived restraints). However only a few (up to 2) hydrogen bonds are formed rather than the whole beta sheet. In case you wish to delve further into this I attach at the end the piece of code that I use to add the restraints: Thank you very much for your help. Regards, Pietro from modeller import * from modeller.automodel import * # Load the automodel class # i tried also with automodel but there was no significant difference mdl = loopmodel(env, alnfile=already_done_alignment_filename, \ knowns = pdb_id, sequence = seq_id, \ loop_assess_methods=(assess.DOPE, assess.normalized_dope), \ assess_methods=(assess.DOPE, assess.normalized_dope) ) mdl.make_initial_model(aln) # Construct typical comparative modeling restraints mdl.mkhomcsr(selection(mdl), aln) mdl.restraints.add(secondary_structure.strand(mdl.residue_range('102:A', '108:A'))) # i know both of these regions are do align on anything (chain B is actually a 7 residues peptide I am adding, should be free to move anywhere). The residue numbering is read from initial model generated above mdl.restraints.add(secondary_structure.strand(mdl.residue_range('125:B:', '131:B'))) mdl.restraints.add(secondary_structure.sheet(mdl.atoms['N:102:A'], mdl.atoms['O:131:B'],sheet_h_bonds=-6)) mdl.restraints.make(selection(mdl), restraint_type='stereo', spline_on_site=False) mdl.restraints.condense() mdl.restraints.write(mdl.csrfile) # make the model env.edat.nonbonded_sel_atoms=1 # so that the selection interacts energetically with the unselected region. Actually I don't select anything manually, I added it just to be sure.. mdl.outputs = [] atmsel = mdl._check_select_atoms() mdl.multiple_models(atmsel) mdl.write_summary(mdl.outputs, 'models')

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how to build the loop of protein model using modeller
by aixintiankong 03 May '13

03 May '13

Dear, The last email have some errors please see this one. In my system ,the loop is part of the active pocket of the protein. when the ligand is absent, the loop is disordered. if the ligand is present , the loop can transform into helix. In order to simulate the disordered loop transform into helix , i should build a model that the ligand and cofactor are in the disoreded loop site. In my system, there is a NAD+ cofactor in the active site and interact with the ligand.when the ligand and cofactor NAD+ coexist, the disordered loop can transform into helix. In the PDB(protein date base) i find the complex with the liand,NAD+ and the state of the loop is helix. i also find a structure of the protein without the liand, NAD+ and the state of the loop is disordered. The sequences similarity of the two structure is 100% and the RMSD between the two structures of the protein is 0.275 . i don't know how to build a model that the protein, NAD+ and ligand coexsit and the loop of protein is disordered. could give me some advice and tell me how to do it detailed? thank you very much.

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how to build the loop of protein model using modeller
by aixintiankong 29 Apr '13

29 Apr '13

Dear, In my system ,the loop is part of the active pocket of the protein. when the ligand is absent, the loop is disordered and if the ligand is present , the loop can transform into helix. In order to simulate the disordered loop transform into helix , i should build a model that the ligand is in the disoreded loop site. In my system, there is a NAD+ cofactor in the active site and interact with the ligand.when the ligand and cofactor NAD+ coexist, the disordered loop can transform into helix. In the PDB(protein date base) i find the complex with the liand,NAD+ and the state of the loop is helix. i also find a protein structure without the liand, NAD+ and the state of the loop is disordered. The sequences similarity of the two structure is 100% and sturctue the the RMSD bettwen the two protein is 0.275 . i don't know how to build a model that the protein, NAD+ and ligand coexsit,but the loop of protein is disordered. could give me some advice and tell me how to do it detailed? thank you very much.

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How to get specified residue modelling
by Anogna 29 Apr '13

29 Apr '13

Dear friends, I have been struggling from past one week with the following kind of modelling.... I have a target sequence which is 97% identity with two PDB's (named A and B) I just want to make A as main template, but A has some residues missing, so i thought of making B as template for those missing residues in the "PDB A". But to go with this I am not able to get a python script file in which i can specify build residues. Can anyone can help me with this please. Thanking, Anogna

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Fwd: Run Modeller processes on multiple cpus
by Lalith Kumar 20 Apr '13

20 Apr '13

Hi, Greetings.... I am running mod9v11 on Intel Xeon with 12 cores processor. I have found that modeller is utilizing only single processor. Even though there are few older posts regarding the execution of modeller processors on multiple processors, I am unable to implement them. Sorry, I am newbie to python. It will be a great help if you could help me with a script or procedure to set up the running of modeller processes on multiple processors. This will save my lifetime. Please do the needful. Thank you Regards, Lalith -- Lalith Kumar K Research Associate, CADD Division, Dr. Reddy's Institute of Life Sciences (Formerly known as Institute of Life Sciences) University of Hyderabad Campus Gachibowli, Hyderabad 500046, India

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Modelling ofsymetric dimer
by James Starlight 15 Apr '13

15 Apr '13

Dear Modeller users! I want to model simple symmetric model of the TRP-repressor consist of 2 identical chains based on known PDB structure of that protein where some residues from N and C terms are absent in both monomers. Could you provide mewith some tutorial for such simple task ( as the input I'd like to define pdb consisting of the A and B chains as well as sequence of one monomer. As the output I'd like to obtain the same pdb with two chains included with the refined conformations of the N and C unstructured segments). Thanks for help James

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