determination of symmetry

9 Jul 2005

      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
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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)
----------------------------------------------------------------------
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@salilab.org
Message-ID: 42C096DD.4080603@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@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@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@salilab.org
Message-ID: 200506301635.30643.divanych@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@salilab.org
Message-ID: 42C42FD3.50701@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@salilab.org http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

------------------------------

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