- modeller_usage - salilab.org

Re: [modeller_usage] Atom index is out of range
by Modeller Caretaker 20 Nov '06

20 Nov '06

andreyvoronkov wrote: > Dear MADELLER administration and MODELLER users, my MODELLER job, > using modeller for "initial model" procedure failed. I wanted to > replace a part of protein by the data of X-ray analysis and used > initial model procedure. I've got the error: > > "nselat__596E> Atom index is out of range (iatm,natm): 5009 > 5008" > > What might be the problem? I've browsed archives and found same > question, but there the problem was in mismatch of number of atoms. I > don't have such mismatch. The initial model is assumed to be produced by a previous Modeller run, which is not the case for your example. It has the wrong number of atoms, in the incorrect order. You can fix this problem by first reading your model into Modeller, 'correcting' it, and then writing it out again, with a script similar to that below (similar to examples/commands/energy.py): env = environ() env.libs.topology.read(file='$(LIB)/top_heav.lib') env.libs.parameters.read(file='$(LIB)/par.lib') aln = alignment(env) code = "FZD1" mdl = model(env, file=code) aln.append_model(mdl, atom_files=code, align_codes=code) aln.append_model(mdl, atom_files=code+'.ini', align_codes=code+'-ini') mdl.generate_topology(aln, sequence=code+'-ini') mdl.transfer_xyz(aln) mdl.build(initialize_xyz=False, build_method='INTERNAL_COORDINATES') mdl.write(file='new%s.pdb' % code) 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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_modeller.errorS
by Tamas Hegedus 20 Nov '06

20 Nov '06

Hi, I'm using mod8v2 on RH AS4. ************************************************** I have an alignment file with 7 proteins (including the 'sequence'). I got the following error: _modeller.error: crsplin_223E> Internal error: array too small: MAXSPL current maximum, current need: 400 488 My guess: you have some hard coded buffer size, and I have too many and large (?) proteins in the alignment file... ************************************************** If I have 1XMI in the alignment file, I have the following error: _modeller.error: rdpir___648E> Alignment sequence not found in PDB file: 1 ./pdb/1XMI.pdb I checked for extra spaces, numbering, sequence, but I do not find the problem... You can find my script, alignment and pdb files at: http://www.biohegedus.org/modNbd2.py http://www.biohegedus.org/testB.pir http://www.biohegedus.org/1XMI.pdb *********** Thanks for your help in advance, Tamas -- Tamas Hegedus, PhD | phone: (1) 919-966 0329 UNC - Biochem & Biophys | fax: (1) 919-966 5178 6107 Thurston-Bowles Bldg | mailto:hegedus@med.unc.edu Chapel Hill, NC, 27599-7248 | http://biohegedus.org

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make_chains problem
by Nicolas Fusseder 17 Nov '06

17 Nov '06

Hello, When I run my make_chains.py script to generate a .chn file from a pdb file I have been encountering an issue. It works perfectly for pdb files where the chains are denoted as letters (A, B, C, D, ...) but pdb files where numerics are used to denote chains (1, 2, 3, 4, ...) no .chn file output. Below is the make_chains.py script I have been using: -------------------------------------------------- env = environ() mdl = model(env, file='c:/pdb/pdb1d3e.ent') mdl.make_chains(file='1D3E', minimal_chain_length=30, minimal_resolution=4.0, minimal_stdres=30, chop_nonstd_terminii=True, structure_types='structureN structureX', alignment_format='PIR') ---------------------------------------------------- for pdb id 1d3e (uses numerics): NO .CHN FILE OUTPUT for pdb id 1e3l (uses letters): WORKS, 2 .chn files are output Thank you for your help, -- Nicolas Fusseder

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(no subject)
by doppelt olivia 17 Nov '06

17 Nov '06

Hello, I've been using MODELLER 2 ways : first with only one template second with 2 templates Is the Objective Function of the modeles generated comparable ? and if so, how ? The first is around 600, and the second around 3000 for a 151 residus query sequence. Thanks in advance for your help, Olivia Doppelt ___________________________________________________________________________ Découvrez une nouvelle façon d'obtenir des réponses à toutes vos questions ! Profitez des connaissances, des opinions et des expériences des internautes sur Yahoo! Questions/Réponses http://fr.answers.yahoo.com

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Re: [modeller_usage] can't bond disulfide
by Modeller Caretaker 16 Nov '06

16 Nov '06

jitrayut jitonnom wrote: > I want to bond two disulfides (residue 20 and residue 66, res 105 > and res 164) by using script below. But i did not bond any > disulfides so why ? ... > a = automodel(env, alnfile='CD147-mult.ali', > knowns=('1F97A','1NBQA','1EPFB'), sequence='CD147') This line should start as a = mymodel(env, ... rather than a = automodel(env, ... so that you use the newly-defined 'mymodel' class, with the disulfide restraints. 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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cyclic peptide modeling
by Giacomo Bastianelli 16 Nov '06

16 Nov '06

Dear users, I am modelling mutations and insertions of an original cyclic peptide sequence. However, when I run the modeling, I always loose my cyclization. Does modeller recognize cyclic peptides for the modeling? Thanks in advance, Giacomo Bastianelli

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question
by Widjaja, Linda 15 Nov '06

15 Nov '06

I am new to modeler. How do I convert my target sequence to PIR format?

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Hole in models
by hori koshii 13 Nov '06

13 Nov '06

(sorry this is a repeated question but it was missed and there was no answer to this) Hi everybody. I am wondering if anyone has got holes in many of the homology models generated? Any ways to control this? Thanks for answering. Good day. Sincerely, (P.S> the pdb was attached, you may select the "resid 165 to 185" and view as SURF on vmd, and you may see the hole I was referring to, thanks) --------------------------------- Cheap Talk? Check out Yahoo! Messenger's low PC-to-Phone call rates.

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Incorporation of hetero atom
by 서주현 13 Nov '06

13 Nov '06

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Re: [modeller_usage] How to use model.patch_ss_templates() ?
by Modeller Caretaker 08 Nov '06

08 Nov '06

jitrayut jitonnom wrote: > I am new for this program and i doubt on how to use > model.patch_ss_templates() in order to model disulfide bond of our model > from templates. As i read the FAQ no. 3, i am stil not understand that > where *_patch_disulfides.py_* be used. Since I know from the advanced > tutorials that there are many steps to run multiple template such as > salign.py , align2d_mult.py, model_mult.py, and evaluate_model.py. So, > which steps should be insertedt the patch_disulfides.py ? salign.py and align2d_mult.py are for alignment, and evaluate_model.py is for model evaluation. In all of these cases the definition of disulfide bonds is not required. model.patch_ss_templates() adds disulfide bonds in the model, if it is aligned with a template which has a disulfide. This is called automatically for you for 'automodel' so you don't generally need to worry about it. An example is given in FAQ #3 of how to add specific disulfide bonds in the 'automodel' procedure, using model.patch(). This only applies to the model building step, of course - model_mult.py in your case. 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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