Subject: [modeller_usage] determination of symmetry
From: rathankar rao <>
Date: Sat, 9 Jul 2005 08:14:41 -0700 (PDT)
Cc:
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.
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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)
"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 -- http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
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Message: 2 Date: Mon, 27 Jun 2005 23:56:12 +0800 From: "Chenmengen" <> Subject: [modeller_usage] NOC 2.0 released To: "ccp4bb" <> Message-ID: <> 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
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Message: 3 Date: Thu, 30 Jun 2005 16:35:30 +0400 From: Dmitry Osolodkin <> Subject: [modeller_usage] Some theoretical questions To: Message-ID: <> 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.
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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: Message-ID: <> 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 -- http://www.salilab.org/modeller/ Modeller mail list:
http://salilab.org/mailman/listinfo/modeller_usage
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