May 2013 - modeller_usage

Select and remove atoms from automodel
by Ignacio Ibarra 04 Mar '14

04 Mar '14

Hello, Currently I am generating nucleic acid models using the MODELLER suite. I would like to remove the initial phosphate group declared in the first residue of each nucleic acid chain. Those atoms should not be present in real structures. I would like to do it without writing new text in the .lib files that are into the modlib folder I read about a pick_atoms() method in an older version of MODELLER, but it is not commented in the 9v11 manual ( http://binf.gmu.edu/software/MODELLER/node131.html) Is there something similar currently available for removing atoms from the model in the automodel or another class? Regards, Ignacio

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Question about huge gaps
by Daron Standley 30 May '13

30 May '13

Hi- Although I'm not a very regular user of modeller, I believe it is well known that long gaps, especially terminal gaps, look strange when modeled using default options. I was wondering, would be possible to add an Rg restraint so that such regions at least stay nearby the rest of the (well-modeled) protein? This is not just a problem of aesthetics. When I try to superimpose such structures using structural alignment, sometimes the long gappy regions throw the superpositioning calculation off. I could just write a script to try to cut them out, but it would be nice if I could fix the problem at the source. My suggestion of using an Rg restrain would be basically "if distance of residue x from center is greater than some huge value (2-3x the predicted Rg, based on sequence length), add a bias to the potential for x toward the center of the protein" This kind of restraint should leave the "good" parts of the alone and just pull the "bad" parts closer to the rest of the protein. Any thoughts on whether this can be done? Thanks for your advice and apologies if I have raised a already well-discussed topic. Regards, Daron

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Doubt Regarding multiple X, Y, Z coordinates for same atoms
by Priya Chaudhary 24 May '13

24 May '13

Respected Sir DOUBT REGARDING MULTIPLE X,Y,Z COORDINATES FOR same ATOMS During Modeling via automodel model-full.py script Which coordinates are used while modeling in case multiple coordinates for same atom and residue at a position are mentioned in PDB file ? On what basis are the coordinates for modeling selected if more than one coordinate set is present for same atom? Thanks

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Amount of models
by HERBERT MAX VENTHUR PE¥A 24 May '13

24 May '13

Hello I've read papers where the amount of models generated are not indicated, however, indicate that more than 1 model was obtained. The script of the tutorial of modeller provides 5 models. My question is, Is there any effect in the quality of the model if I generate several models? for example, 200 models versus 5 models? Thank you 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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Urgent Query . Please do reply. Thanks a ton.
by Priya Chaudhary 21 May '13

21 May '13

Using automodel model-full python script, 1. Do we get any changes in side chain conformations or coordinates if the query sequence is perfectly aligned with template sequence at sequence level. Because upon point mutations, there is no change in sequence alignment. Whole query sequence is perfectly aligned with template. I calculated no. of contacts of wild type residues and mutant residues, there is no change at all. I used only distance between C-alpha atoms(CA) while calculating . Is there any change in side chain conformations in the modeled structures by using this script. 2. Can I get to know the details of a.make() and a.auto_align() commands used in this script. I WANT TO KNOW STEP WISE THE INSIDE DETAILS AND WORKING OF THIS SCRIPT. PLEASE HELP. URGENT !!! Please bear up with me as I don't know Python.. *Example: examples/automodel/model-full.py<http://salilab.org/modeller/9.11/examples/automodel/model-full.py> * # A sample script for fully automated comparative modeling from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] a = automodel(env, # file with template codes and target sequence alnfile = 'alignment.seg', # PDB codes of the templates knowns = ('5fd1', '1fdn', '1fxd', '1iqz'), # code of the target sequence = '1fdx') a.auto_align() # get an automatic alignment a.make() # do homology modeling

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Residues missing !!! How to specify NMR MODEL - 2
by Priya Chaudhary 21 May '13

21 May '13

Sir I used automodel - model-full.py script. I have NMR Structure. Some residues are missing in NMR MODEL no.1. I wish to use NMR Model No 2 as template. How and where to make necessary changes ?

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HETATM modelling query -reg
by venkatesh s 21 May '13

21 May '13

Respected Sir i am trying to add my model one zinc HETATM, but my efforts are failed , *iam getting *ATOM in my file pdb instead HETATM in the template structure Experimentally solved Residues Region *191-609* , protein Total Length: *419* in that Five residue are Missing Residue Here i mentioned Alignment file >P1;2DW0 structureX:2DW0.pdb: 196 :A:+414 :A:MOL_ID 1; MOLECULE CATROCOLLASTATIN; CHAIN A, B; FRAGMENT RESIDUES 191-609; SYNONYM VAP2, VASCULAR APOPTOSIS-INDUCING PROTEIN-2, CATROCOLLASTATIN/VAP2B:MOL_ID 1; ORGANISM_SCIENTIFIC CROTALUS ATROX; ORGANISM_COMMON WESTERN DIAMONDBACK RATTLESNAKE; ORGANISM_TAXID 8730: 2.15: 0.17 PFRFVELVLVVDKAMVTKNNGDLDKIKTRMYEIVNTVNEIYRYMYIHVALVGLEIWSNEDKITVKPEAGYTLNAF GEWRKTDLLTRKKHDNAQLLTAIDLD-RVIGLAYVGSMCHPKRSTGIIQDYSEINLVVAVIMAHEMGHNLGINHD SGYCSCGDYACIMRPEISPEPSTFFSNCSYFECWDFIMNHNPECILNEPLGTDIISPPVCGNELLEVGEECDCGT PENCQNECCDAATCKLKSGSQCGHGDCCEQCKFSKSGTECRASMSECDPAEHCTGQSSECPADVFHKNGQPCLDN YGYCYNGNCPIMYHQCYDLFGADVYEAEDSCFERNQKGNYYGYCRKENGNKIPCAPEDVKCGRLYCKDNSPGQNN PCKMFYSNEDEHKGMVLPGTKCADGKVCSNGHCVDVATAY.* >P1;TvLDH sequence:TvLDH: : : : ::: 0.00: 0.00 P-RYIELVIVADRAMVTKNNGDLTAIRTWVHQIVNDMTVMYRDLNIHITLAAVVIWNKRDLITVTSSAEDTLNLF GTWRETKYLKHRKHDNAQLLTGIILDDDTIGLAYVGGMCDPKKSVGIIEDHSTEHLLVAATMAHEMGHNLGMNHD ANQCNCGANGCVMSATLTEQTSYQFSDCSKDEYQNYLTDHNPQCILNQPLRTD-T-P-VSRNELLQ-NSAHPC-- --------CDPVTCQPK--RFCVSGPCCENCQFVRAGTVCNPAKGD-WMDDYCTGISSDCPRNPL---------- -----NGFR------------------------------------------------------------------ ----------------------------------------.* and Model Ligand python script which i used as followed # Homology modeling with ligand transfer from the template from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class 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'] # Read in HETATM records from template PDBs env.io.hetatm = True a = automodel(env, alnfile = 'TvLDH-2DW0A.ali', # alignment filename knowns = '2DW0', # codes of the templates sequence = 'TvLDH') # 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.make() # do the actual homology modeling kindly give provide your valuable suggestion regarding error -- Regards,* *S.VENKATESH,

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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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