- modeller_usage - salilab.org

Modelling Molybdenum atom
by belal najjar 12 Jul '05

12 Jul '05

Dear all, I am trying to model an enzyme containing the molybdenum (Mo) atom , this atom contains in the template as well. however, the atom type for the Mo is not in the restype.lib. i want to add the atom type in the library and from what i read in the FAQ, i need to follow the steps suggested by question number 10. i'm a new user to modeller and i just want to know is there any other way that i could do to define my own atom type? or i would have to follow all the consecutive four steps in the FAQ? please advice me on this.. thank you very much in advance regards, belal __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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determination of symmetry
by rathankar rao 11 Jul '05

11 Jul '05

Dear sir Iam in to modelling assignment of a zinc finger protein, which has nearly 6 zinc fingers The nearest template (1MEY) to it covers only 50% of the sequence length and has 3 fingers corresponding to 3 chains in the template. 1. i would like to know the method of representing the alignment in .ali file for chain breaks 2. i modelled this in a different manner. I aligned the query with the template for only 50% of the sequence and assumed that these chains belong to different pdb files and hence modelled the query protein like what we do for a chimeric protein(without DNA chains). Outcome: i got a 3D Model which did not represent the actual template, since the coordinates of DNA was not incorporated in it. I dont know why DNA was not built and as a result, the protein appeared to be bent. (a) Can this be correlated to confirmational changes taking place bcoz of the absence of DNA binding to the protein (b) Or is this an error. Then i tried to model the same protein with nucleotides, but how do we represent the nucleotides in the target sequence, as it consists of only aminoacids. should there be a delimiter like a { , } to separate the dna sequence from the amino acid sequence. 3. The three fingers in the template are exactly identical from the sequence point of view. Hence when i looked in to the structure, there appeared to be a symmetric element in which the first and second zinc fingers where displaced. (a) How do i infer that symmetric element (b) after obtaining that symmetric element can i now generate one more 4more fingers so that i can cover my full sequence. (c) after building such a model, will it be biologically valid. plz answer modeller_usage-request(a)salilab.org wrote: Send modeller_usage mailing list submissions to modeller_usage(a)salilab.org To subscribe or unsubscribe via the World Wide Web, visit http://salilab.org/mailman/listinfo/modeller_usage or, via email, send a message with subject or body 'help' to modeller_usage-request(a)salilab.org You can reach the person managing the list at modeller_usage-owner(a)salilab.org When replying, please edit your Subject line so it is more specific than "Re: Contents of modeller_usage digest..." Today's Topics: 1. Re: Terminal patching (acetylation/amidation) in Modeller 7.7 (Modeller Caretaker) 2. NOC 2.0 released (Chenmengen) 3. Some theoretical questions (Dmitry Osolodkin) 4. Re: Some theoretical questions (Modeller Caretaker) ---------------------------------------------------------------------- Message: 1 Date: Mon, 27 Jun 2005 17:16:29 -0700 From: Modeller Caretaker Subject: Re: [modeller_usage] Terminal patching (acetylation/amidation) in Modeller 7.7 To: "Niels Johan Christensen" , modeller_usage(a)salilab.org Message-ID: <42C096DD.4080603(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed "Niels Johan Christensen" 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 ------------------------------ Message: 2 Date: Mon, 27 Jun 2005 23:56:12 +0800 From: "Chenmengen" Subject: [modeller_usage] NOC 2.0 released To: "ccp4bb" Message-ID: <20050628035249.A85391C23E(a)noc.ibp.ac.cn> Content-Type: text/plain; charset="gb2312" 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 ------------------------------ Message: 3 Date: Thu, 30 Jun 2005 16:35:30 +0400 From: Dmitry Osolodkin Subject: [modeller_usage] Some theoretical questions To: modeller_usage(a)salilab.org Message-ID: <200506301635.30643.divanych(a)rambler.ru> Content-Type: text/plain; charset="us-ascii" 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. ------------------------------ Message: 4 Date: Thu, 30 Jun 2005 10:45:55 -0700 From: Modeller Caretaker Subject: Re: [modeller_usage] Some theoretical questions To: Dmitry Osolodkin Cc: modeller_usage(a)salilab.org Message-ID: <42C42FD3.50701(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Dmitry Osolodkin wrote: > 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? You shouldn't need to do any further optimization - Modeller has already done CG minimization and MD simulated annealing for you. In fact, running an ordinary MD simulation of a Modeller model will often end up making the model worse, as you're throwing away the homology-derived restraints. > 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? Each model is built from a different randomized starting model, so they'll all differ slightly. You should build multiple models to allow for the possibility that the optimizer gets stuck in a local minimum. > 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? If you build one subunit, you'll be ignoring interactions between subunits, so your model will likely be incorrect. You can build a model of the whole system and use Modeller's symmetry restraints to ensure that each subunit has similar structure. Modeller has no facility to build new coordinates using symmetry operations. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage ------------------------------ _______________________________________________ modeller_usage mailing list modeller_usage(a)salilab.org http://salilab.org/mailman/listinfo/modeller_usage End of modeller_usage Digest, Vol 4, Issue 62 ********************************************* --------------------------------- Yahoo! Mail Stay connected, organized, and protected. Take the tour

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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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