- modeller_usage - salilab.org

mutant protein
by silefra＠libero.it 11 Jul '05

11 Jul '05

hi i need to create a mutant protein (ex.substitute a single amino acid) is this possible with modeller? which script file do i need, which input files? i found on the website this script # Example for: MUTATE_MODEL # This will read a PDB file, change its sequence a little, build new # coordinates for any of the additional atoms using only the internal # geometry, and write the mutant PDB file. It can be seen as primitive, # but rapid comparative modeling for substitution mutants. For insertion # and deletion mutants, follow the standard comparative modeling procedure. # Read the topology library with non-hydrogen atoms only: READ_TOPOLOGY FILE = '$(LIB)/top_heav.lib', TOPOLOGY_MODEL = 3 # To produce a mutant with all hydrogens, uncomment this line: # READ_TOPOLOGY FILE = '$(LIB)/top.lib', TOPOLOGY_MODEL = 1 # Read the CHARMM parameter library: READ_PARAMETERS FILE = '$(LIB)/par.lib' # Read the original PDB file and copy its sequence to the alignment array: READ_MODEL FILE = '1fas' SEQUENCE_TO_ALI ADD_SEQUENCE = on, ATOM_FILES = '1fas', ALIGN_CODES = '1fas' # Select the residues to be mutated: in this case all ASP residues: PICK_ATOMS RES_TYPES = 'ASP' # The second example is commented out; it selects residues '1' and '10'. # SET SELECTION_SEARCH = 'SEGMENT', SELECTION_FROM = 'ALL' # PICK_ATOMS SELECTION_SEGMENT = '1' '1', SELECTION_STATUS = 'INITIALIZE' # PICK_ATOMS SELECTION_SEGMENT = '10' '10', SELECTION_STATUS = 'ADD' # Mutate the selected residues into HSD residues (neutral HIS): MUTATE_MODEL RESIDUE_TYPE = 'HSD' # Add the mutated sequence to the alignment arrays (it is now the second # sequence in the alignment): SEQUENCE_TO_ALI ADD_SEQUENCE = on, ALIGN_CODES = ALIGN_CODES '1fas-1' # Generate molecular topology for the mutant: GENERATE_TOPOLOGY SEQUENCE = '1fas-1' # Transfer all the coordinates you can from the template native structure # to the mutant (this works even if the order of atoms in the native PDB # file is not standard): TRANSFER_XYZ # Build the remaining unknown coordinates for the mutant: BUILD_MODEL INITIALIZE_XYZ = off # Write the mutant to a file: WRITE_MODEL FILE = '1fas-1.atm' but..how using it? thanks frà ____________________________________________________________ 6X velocizzare la tua navigazione a 56k? 6X Web Accelerator di Libero! Scaricalo su INTERNET GRATIS 6X http://www.libero.it

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alignment file?
by Rozana Othman 07 Jul '05

07 Jul '05

Hie. What does: " _modeller.error: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = 1jxp " mean? The code for my template is 1jxp. Thank you. Rozana Othman -------------------------------------- 'Sambutan 100 Tahun Universiti Malaya' http://www.um.edu.my

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adding loops while retaining template structure
by Peter C. Lai 06 Jul '05

06 Jul '05

Hi everybody - I'm modelling a membrane protein and I have externally refined my helices. Now I want to have modeller build ab initio interhelical loops using modeller but my primary functional requirement is to keep the helices in the target exactly the same as the template. The default parameters for the model.build method aren't linking up the loops; the strands are just flying outwards from the helical bundle. I am guessing I need to define a whole set of restraints? Using anything other than INTERNAL_COORDINATES for build_method is making a complete mess of the model. (I cannot use the automodel superclass because at the end, it is altering my helical structures in order to fit the loops.) model.py: log.verbose() env = environ() #all hydrogen model env.libs.topology.read(file='$(LIB)/top_allh.lib') env.libs.parameters.read(file='$(LIB)/par.lib') #instantiate new alignment aln = alignment(env) aln.append(file='assem.ali', align_codes=('or17209h_helix', 'or17209h')) #instantiate new model mdl = model(env) mdl.generate_topology(aln, sequence='or17209h') #xfer the template coords mdl.transfer_xyz(aln) #build ab initio loops mdl.build(initialize_xyz=False, build_method='INTERNAL_COORDINATES') mdl.write(file='test.ini') The way the .ali is arranged is that the template has the loops gapped out, and the sequence is the complete protein. Any ideas on how to get the loops to connect? I don't care about optimization since I will be running MD in parameterized solvent anyway. TIA Peter -- Peter C. Lai Yale University School of Medicine SenseLab

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Some theoretical questions
by Dmitry Osolodkin 30 Jun '05

30 Jun '05

Dear colleagues, I recently started working with Modeller8v0, so I have some questions about the authenticity of the models which I get. First of all, if I use optimisation of my structure (exactly as described in Manual section 1.8.7.), do I need to minimise this system, for example, in Sybyl to get better model? Or the model which I get is good enough for using it without any further optimisation such as energy minimisation or molecular dynamics? Second, Modeller can build number of models by one script. For what can it be useful? And is there any difference between obtained models? What's the reason for such a difference? Third, is modelling of homomeric protein using the heteromeric template authentical? All subunits of heteromer have the same folding as my homomer and are homologous to my protein. Or can I build a model of one subunit of my protein using the best template subunit and then build a pentamer using the symmetry operations (rotation about C5 axis)? Is there such feature in Modeller? Hope for help, Dmitry Osolodkin.

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Re: [modeller_usage] Terminal patching (acetylation/amidation) in Modeller 7.7
by Modeller Caretaker 27 Jun '05

27 Jun '05

"Niels Johan Christensen" <s991418(a)student.dtu.dk> wrote: > A good deal of my previous work (calculation of various electronic > properties) is based on structures from non terminal patched MODELLER > 7.7 models. To be consistent, I would like to introduce the terminal > acetylation/amidation with MODELLER 7.7 and subsequently calculate > properties for (fragments of) these models. > > (Regarding "consistency", I am mainly considering the fact that I get > slightly different models from versions 7.7 and 8.1 despite using the > same template/sequence. The only difference in the input conditions, > is that in the former case I use TOP scipting while in the latter I > use Python.) Your reasoning is incorrect; the difference between Modeller 7v7 and 8v1 is that they were built with different Fortran compiler versions. Over time, the way the compiler vendors optimize code (e.g. the ordering of floating point operations) leads to very small changes in the results. You'll also notice that if you build models on a Windows machine, for example, that they'll differ from those built on a Linux box, for the same reason. The Python and TOP interfaces to Modeller give the same results (for equivalent scripts, on the same machine and Modeller version) and in fact are tested precisely to ensure this. Your script doesn't work in Modeller 7v7 because the patch residue CT2 in ${LIB}/top_heav.lib incorrectly adds hydrogens. This was one of the bugs fixed in Modeller 8v1. You can fix it yourself by comparing the top_heav.lib file from the two versions, and correcting the 7v7 copy. 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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NOC 2.0 released
by Chenmengen 27 Jun '05

27 Jun '05

http://noc.ibp.ac.cn New features: Structure factors calculation and R factor validation Electron density synthesis MTZ(CCP4 format),CIF(PDB format),CV(CNS format)reflection data parsing Interface to RCSB PDB bug fixed: CCP4 format Map parsing Picture output Side-chain map-fitting

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no alignment
by Arnout Voet 26 Jun '05

26 Jun '05

dear modellers i am just starting with modeller and i want to make a model using different templates i have my template files, i have the sequence aligned and checked manually but the program gives me an error File "C:\Program Files\Modeller8v1\modlib\modeller\util\top.py", line 37, in check_alignment return _modeller.check_alignment(aln, io, libs, *args) modeller.error: check_a_335E> No alignment. i guess automodel does not like my aligment (although i only want this alignment) could someone please tell me how to cut out the alligment and only use the aligment i have (i have my templates as a pdb (6 different) and i have my aligment in the regular file format (file.ali) kind regards arnout voet

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Re: [modeller_usage] problem!
by vivek sharma 26 Jun '05

26 Jun '05

Hello Benn, > > -------------------------- > > > > 1536 637 READ_TOPOLOGY FILE = TOPLIB > > > > openf5__224_> Open 11 OLD SEQUENTIAL > > ${MODINSTALL7v7}/modlib//top_heav.lib > > read_to_241E> Residue type defined multiple times: ALA > > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > Two possibilities: either your top_heav.lib file really does have ALA > defined multiple times, or you set ADD_TOPOLOGY to 'on' at some point > (it should be set to 'off'). If it isn't either of these, then I'd have > to see your input files to figure out what the problem is. Thanks, problem was: I was using the ADD_TOPOLOGY = 'on', although I needed to, but made few changes and it works fine. > > P.S. Please consider using a more descriptive subject for your mails > rather than "problem!" every time. ;) No problem!, there will be no 'problem' after this, this is the last time. ;-) Regards, Vivek -- VIVEK SHARMA HBG BI "Basic research is what I'm doing when I don't know what I'm doing." - Werner von Braun

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problem!
by vivek sharma 25 Jun '05

25 Jun '05

Dear Ben, I am regular user of MODELLER, I am still using 7v7 as I dont know Python much. I suddenly got an strange error while I was doing the loop modelling, I couldnt found any such previous email too which is in concern to this, so I need you help/comments in this concern. The whole structures are generated normally but when loop modelling procedure starts, it stops with following error. -------------------------- 1536 637 READ_TOPOLOGY FILE = TOPLIB openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib//top_heav.lib read_to_241E> Residue type defined multiple times: ALA recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 52416487 51187.977 49.988 Starting time : 2005/06/25 09:49:26.337 Closing time : 2005/06/25 10:44:12.188 -------------------------- I dont see any such multiple definition of ALA residue in my top_heav.lib file. Although the same top_heav file was read finely by program when it began generating topology. PLease place your comments. Regards, Vivek Sharma -- VIVEK SHARMA HBG BI "Basic research is what I'm doing when I don't know what I'm doing." - Werner von Braun

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violation of restraints
by Marsita M 25 Jun '05

25 Jun '05

hello everybody i'm a new user and i just would like to know, is there any units for the violation restraints? ( i calculated the total of the violations, and i just wondering if there is any units for that? ) thank you _________________________________________________________________ Undgå pop-ups med MSN Toolbar - http://toolbar.msn.dk hent den gratis!

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