From owner-chemistry@ccl.net Mon Nov  1 10:17:00 2010
From: "Kshatresh Dutta Dubey kshatresh#,#gmail.com" <owner-chemistry_+_server.ccl.net>
To: CCL
Subject: CCL: trimer from monomer
Message-Id: <-43046-101101050752-4236-11sWUjOLKIwfb47/2t4nGQ_+_server.ccl.net>
X-Original-From: Kshatresh Dutta Dubey <kshatresh]![gmail.com>
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Date: Mon, 1 Nov 2010 14:37:45 +0530
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Sent to CCL by: Kshatresh Dutta Dubey [kshatresh ~ gmail.com]
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Dear all,

I want to model a simulate a protein which is found in trimeric form, but
unfortunately i have only monomer of that protein. Can anyone suggest me how
to model a trimer from a monomer. Kindly also suggest me modelling software
which can do this. I have maestro, chiemera and VMD.
Thanks in advance
Regards
Kshatresh Dutta Dubey

--0016363107613c79bd0493fa243a
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<div dir=3D"ltr">Dear all,<br><br>I want to model a simulate a protein whic=
h is found in trimeric form, but unfortunately i have only monomer of that =
protein. Can anyone suggest me how to model a trimer from a monomer. Kindly=
 also suggest me modelling software which can do this. I have maestro, chie=
mera and VMD. <br>
Thanks in advance<br>Regards<br>Kshatresh Dutta Dubey<br></div>

--0016363107613c79bd0493fa243a--


From owner-chemistry@ccl.net Mon Nov  1 11:20:00 2010
From: "Iain Moal Iain.Moal++cancer.org.uk" <owner-chemistry,server.ccl.net>
To: CCL
Subject: CCL: trimer from monomer
Message-Id: <-43047-101101105601-11397-uF/iNo5GcWLCce+QB+dQNQ,server.ccl.net>
X-Original-From: Iain Moal <Iain.Moal---cancer.org.uk>
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Date: Mon, 1 Nov 2010 14:54:44 +0000
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Sent to CCL by: Iain Moal [Iain.Moal!=!cancer.org.uk]
You should be able to download the biological assembly directly from the pdb.
________________________________________
> From: owner-chemistry+iain.moal==cancer.org.uk .. ccl.net [owner-chemistry+iain.moal==cancer.org.uk .. ccl.net] On Behalf Of Kshatresh Dutta Dubey kshatresh#,#gmail.com [owner-chemistry .. ccl.net]
Sent: 01 November 2010 09:07
To: Iain Moal
Subject: CCL: trimer from monomer

Dear all,

I want to model a simulate a protein which is found in trimeric form, but unfortunately i have only monomer of that protein. Can anyone suggest me how to model a trimer from a monomer. Kindly also suggest me modelling software which can do this. I have maestro, chiemera and VMD.
Thanks in advance
Regards
Kshatresh Dutta Dubey

This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a registered charity in England and Wales (1089464) and in Scotland (SC041666) and a company limited by guarantee registered in England and Wales under number 4325234. Our registered address is Angel Building, 407 St John Street, London, EC1V 4AD. Our central telephone number is 020 7242 0200.
 
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From owner-chemistry@ccl.net Mon Nov  1 12:33:00 2010
From: "Elaine Meng meng-$-cgl.ucsf.edu" <owner-chemistry : server.ccl.net>
To: CCL
Subject: CCL: trimer from monomer
Message-Id: <-43048-101101123136-16727-qDuag5A6UJPG0xB/iFt0aA : server.ccl.net>
X-Original-From: "Elaine  Meng" <meng+/-cgl.ucsf.edu>
Date: Mon, 1 Nov 2010 12:31:34 -0400


Sent to CCL by: "Elaine  Meng" [meng|a|cgl.ucsf.edu]
Hi Kshatresh,
In Chimera there are several ways to get the trimer from the monomer.  It depends what information is included in the PDB file.  The "biological unit" is supposed to be described in BIOMT records, but many PDB files do not have useful BIOMT records, only an identity matrix.

If the PDB file does contain useful BIOMT records (example: 1hxx), you can use the command sym or the "Multiscale Models" tool.  For example, if the structure is open as model 0 you can simply use the command:

sym #0

A PDB file can also contain various other matrices that describe crystallographic symmetry and the unit cell, which may or may not bear any relationship to the biological unit.  These other matrices can also be used by the sym command (it has options), the Multiscale Models tool, and the Unit Cell tool in Chimera. Those tools are under Tools... Higher-Order Structure in the menu.

If none of the information in the PDB file makes the trimer, you might also try fetching the predicted biological unit for that PDB entry from the PQS database.  That can be done using Fetch by ID in Chimera (see the File menu).

Documentation:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemulti.html
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/unitcell.html
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/fetch.html

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco


From owner-chemistry@ccl.net Mon Nov  1 15:05:00 2010
From: "Niels Johan Christensen njc~!~life.ku.dk" <owner-chemistry,+,server.ccl.net>
To: CCL
Subject: CCL: trimer from monomer
Message-Id: <-43049-101101115357-13841-9RcC0W859CjylMy+pE63nw,+,server.ccl.net>
X-Original-From: "Niels Johan Christensen" <njc\a/life.ku.dk>
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Date: Mon, 01 Nov 2010 16:53:42 +0100
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Sent to CCL by: "Niels Johan Christensen" [njc%%life.ku.dk]
This is a MIME message. If you are reading this text, you may want to 
consider changing to a mail reader or gateway that understands how to 
properly handle MIME multipart messages.

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Dear Kshatresh

If you want to make a symmetrical trimer, you could try this online =
resource:

http://bioinfo3d.cs.tau.ac.il/SymmDock/

If you have some kind of restraints for your model, Haddock may be more =
suitable:

http://www.nmr.chem.uu.nl/haddock/

Best

Niels Johan Christensen
Postdoctoral Research Associate
Phone: +45 353-32405
E-mail: njc-at-life.ku.dk
Bioinorganic Chemistry
Department of Basic Sciences and Environment
Faculty of Life Sciences
University of Copenhagen
Thorvaldsensvej 40
1871 Frederiksberg C
Denmark


>>> "Kshatresh Dutta Dubey kshatresh#,#gmail.com"  01-11-10 16:09 >>>
Dear all,

I want to model a simulate a protein which is found in trimeric form, but =
unfortunately i have only monomer of that protein. Can anyone suggest me =
how to model a trimer from a monomer. Kindly also suggest me modelling =
software which can do this. I have maestro, chiemera and VMD.=20
Thanks in advance
Regards
Kshatresh Dutta Dubey



--=__Part9EB31196.0__=
Content-Type: text/html; charset=US-ASCII
Content-Transfer-Encoding: quoted-printable
Content-Description: HTML

<html><head><meta http-equiv=3DContent-Type content=3D"text/html; =
charset=3Diso-8859-1"><META name=3D"Author" content=3D"Novell GroupWise =
WebAccess"></head><body style=3D'font-family: Tahoma, sans-serif; =
font-size: 13px; '>Dear Kshatresh<br><br>If you want to make a symmetrical =
trimer, you could try this online resource:<br><br>http://bioinfo3d.cs.tau.=
ac.il/SymmDock/<br><br>If you have some kind of restraints for your model, =
Haddock may be more suitable:<br><br>http://www.nmr.chem.uu.nl/haddock/<br>=
<br>Best<br><br>Niels Johan Christensen<br><font style=3D"font-size: 8pt;" =
face=3D"Arial">Postdoctoral Research Associate<br>
Phone: +45 353-32405<br>
E-mail: njc-at-life.ku.dk<br>
Bioinorganic Chemistry<br>
Department of Basic Sciences and Environment<br>
Faculty of Life Sciences<br>
University of Copenhagen<br>
Thorvaldsensvej 40<br>
1871 Frederiksberg C<br>
Denmark</font><br><br><br>&gt;&gt;&gt; "Kshatresh Dutta Dubey kshatresh#,#g=
mail.com" <owner-chemistry:+:ccl.net> 01-11-10 16:09 &gt;&gt;&gt;<br>
<div dir=3D"ltr">Dear all,<br><br>I want to model a simulate a protein =
which is found in trimeric form, but unfortunately i have only monomer of =
that protein. Can anyone suggest me how to model a trimer from a monomer. =
Kindly also suggest me modelling software which can do this. I have =
maestro, chiemera and VMD. <br>
Thanks in advance<br>Regards<br>Kshatresh Dutta Dubey<br></div>
</owner-chemistry:+:ccl.net></body></html>

--=__Part9EB31196.0__=--


From owner-chemistry@ccl.net Mon Nov  1 18:55:01 2010
From: "Roy Jensen JensenRH++MacEwan.ca" <owner-chemistry ~~ server.ccl.net>
To: CCL
Subject: CCL: question on Born-Oppenheimer approx.
Message-Id: <-43050-101101165928-2554-sLwFJNyxHuUB6bFbuRLrqw ~~ server.ccl.net>
X-Original-From: Roy Jensen <JensenRH__MacEwan.ca>
Content-Transfer-Encoding: 8bit
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Date: Mon, 01 Nov 2010 14:59:20 -0600
MIME-Version: 1.0


Sent to CCL by: Roy Jensen [JensenRH.]=[.MacEwan.ca]
Well, according to the formation enthalpies at 298 K, ethanol is 51.0
kJ/mol lower energy.

Run at both B3LYP/6-311++G** and M06/6-311++G**, ethanol is 47 kJ/mol
lower energy (uncorrected). I was able to find a transition state with
B3LYP/6-311++G** (a concerted O-C flip with simultaneous H migration)
at 517 kJ/mol. Amazingly, there is only one negative frequency! Not
sure if associative recombination is lower energy.

 Dr. Roy Jensen
(==========)-----------------------------------------¤
 Chemistry, Grant MacEwan University
 Room 5-172J, 10700-104 Avenue
 Edmonton, AB    T5J 4S2
 780.633.3915



On Sat, 30 Oct 2010 15:19:02 -0700, you wrote:

>
>
>Thanks for all the responses so far.
>
>Ulf, please say a little more about super-selection rules etc.  The  
>last time I spoke about this topic at a conference in London on  
>"Emergence", a philosopher of physics also brought up super-selection  
>but did not go into any detail.
>
>And what is the difference in the energies of these two isomers?  Can  
>anyone help?
>
>
>eric scerri
>
>---------------
>
>
>
>------------------------------------------------------------------------ 
>------------------------------------------------------------------------ 
>------------------------------------------------------------------------ 
>--------------------
>The Periodic Table: Its Story and Its Significance, by Eric Scerri,  
>Oxford University Press, 2007.
>
>named as an "outstanding academic book of 2007" by Choice Library  
>magazine.
>
>Reviews:
>"An absolutely gorgeous book.  I put it on my bedside table and then  
>stayed up half the night reading it - it is immensely readable."
>---Oliver Sacks, author of The Man Who Mistook his wife for a Hat,  
>Awakenings etc.
>
>“As the author of "The Periodic System of Chemical Elements: A  
>History of the First Hundred Years" (1969), I consider Scerri's "The  
>Periodic Table: Its Story and Its Significance" a worthy successor. I  
>declare his new book a must, not only for all historians of chemistry  
>and the other natural sciences, but also for the scientists and  
>pupils thereof.--- Jan W. van Spronsen, author of "The Periodic  
>System of Chemical Elements: A History of the First Hundred Years"
>
>“Few concepts are more important in chemistry than the periodic  
>table, and Eric Scerri's book offers a wonderfully thorough, lucid,  
>and provocative introduction for both chemists and the scientifically  
>literate to this major cultural contribution. Anyone interested in  
>the foundations of chemistry will take delight, inspiration, and  
>information from this highly approachable book.” ----- Peter Atkins,  
>author of "The Periodic Kingdom", "Molecules" etc.
>
>
>
>On Oct 30, 2010, at 12:57 AM, Ulf Ekström ulfek+/-few.vu.nl wrote:
>
>>
>> Sent to CCL by: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= [ulfek*few.vu.nl]
>>
>> On Sat, Oct 30, 2010 at 2:20 AM, Eric Scerri scerri.:.chem.ucla.edu
>> <owner-chemistry.-*-.ccl.net> wrote:
>>> They claim that applying the approximation amounts to writing the  
>>> structure
>>> of a molecule in 'by hand' rather than the structure being  
>>> inherent in the
>>> quantum formalism.
>>> They cite examples such as C2H5OH and CH3OCH3 which share the same
>>> Hamiltonian and conclude that structure cannot therefore be  
>>> deduced from QM
>>> in an ab initio fashion.
>>
>> Does this analysis properly take the environment into account? I  
>> would expect
>> that if the tunneling time between the isomers is long enough then the
>> "classical"
>> structures would be superselected by the environment (i.e. quantum  
>> mechanical
>> decoherence). If the isomers would have similar energies this would  
>> be a kind of
>> spontaneous symmetry breaking.
>>
>> Sincerely,
>> Ulf Ekstrom
>>
>>
>>
>> -= This is automatically added to each message by the mailing  
>> script =-
>> To recover the email address of the author of the message, please  
>> change> Conferences: http://server.ccl.net/chemistry/announcements/ 
>> conferences/>
>>
>
>
>


From owner-chemistry@ccl.net Mon Nov  1 22:16:00 2010
From: "Francisco Hernandez-Guzman Francisco.Hernandez_-_accelrys.com" <owner-chemistry^^server.ccl.net>
To: CCL
Subject: CCL: trimer from monomer
Message-Id: <-43051-101101212511-5740-hALsTO8mydhbJ0/uuACf7Q^^server.ccl.net>
X-Original-From: Francisco Hernandez-Guzman <Francisco.Hernandez,accelrys.com>
Content-Language: en-US
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	boundary="_000_55AC410F3302E740AC9EC50011F73E8F0207B2A08FEXCH1COLOacce_"
Date: Mon, 1 Nov 2010 18:24:57 -0700
MIME-Version: 1.0


Sent to CCL by: Francisco Hernandez-Guzman [Francisco.Hernandez{:}accelrys.com]
--_000_55AC410F3302E740AC9EC50011F73E8F0207B2A08FEXCH1COLOacce_
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Hello Kshatresh,

Your task is not trivial since you have to determine which are the contacts=
 that need to be present in your trimer. Depending on the shape of your pro=
tein, certain contacts may make more sense than others. Definitely having s=
ome additional information regarding the trimer form would be helpful, i.e.=
 residues involved in protein-protein interactions.

You can use a protein-protein docking program like Rosetta Dock or ZDOCK to=
 look at various poses that could make sense. You could also use standard s=
ymmetry methods to build a trimer using a P3 cell, but this will be tricky =
since you still will have lots of options on how to orient the asymmetric u=
nit, and it will be an arduous trial and error task.

Lastly, if you suspect high homology to another system that you're lucky en=
ough to find as a trimer, either a trimer in the asymmetric unit or a symme=
try related trimer, then you can simply superimpose your system and hope th=
at such an arrangement may lead to the proper protein-protein contacts to m=
ake your model meaningful. Of course after superimposition you will need to=
 optimize the contacts.

 As I said at the beginning, this is a fairly tricky and not easy task if y=
ou want to do this in a meaningful way. Our tools (Discovery Studio) can be=
 helpful in your search so feel free to contact me directly if you need mor=
e information.

Good luck!

Francisco

Product Manager, Life Sciences
Accelrys, San Diego, CA
fhernandez]=[accelrys.com<mailto:fhernandez]=[accelrys.com>
858-799-5606


> From: owner-chemistry+fhernandez=3D=3Daccelrys.com]=[ccl.net [mailto:owner-ch=
emistry+fhernandez=3D=3Daccelrys.com]=[ccl.net] On Behalf Of Kshatresh Dutta =
Dubey kshatresh#,#gmail.com
Sent: Monday, November 01, 2010 2:08 AM
To: Francisco Hernandez-Guzman
Subject: CCL: trimer from monomer

Dear all,

I want to model a simulate a protein which is found in trimeric form, but u=
nfortunately i have only monomer of that protein. Can anyone suggest me how=
 to model a trimer from a monomer. Kindly also suggest me modelling softwar=
e which can do this. I have maestro, chiemera and VMD.
Thanks in advance
Regards
Kshatresh Dutta Dubey

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<p class=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Calibri",=
"sans-serif";
color:#1F497D'>Hello Kshatresh,<o:p></o:p></span></p>

<p class=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Calibri",=
"sans-serif";
color:#1F497D'><o:p>&nbsp;</o:p></span></p>

<p class=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Calibri",=
"sans-serif";
color:#1F497D'>Your task is not trivial since you have to determine which a=
re
the contacts that need to be present in your trimer. Depending on the shape=
 of
your protein, certain contacts may make more sense than others. Definitely
having some additional information regarding the trimer form would be helpf=
ul,
i.e. residues involved in protein-protein interactions.<o:p></o:p></span></=
p>

<p class=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Calibri",=
"sans-serif";
color:#1F497D'><o:p>&nbsp;</o:p></span></p>

<p class=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Calibri",=
"sans-serif";
color:#1F497D'>You can use a protein-protein docking program like Rosetta D=
ock
or ZDOCK to look at various poses that could make sense. You could also use
standard symmetry methods to build a trimer using a P3 cell, but this will =
be
tricky since you still will have lots of options on how to orient the
asymmetric unit, and it will be an arduous trial and error task.<o:p></o:p>=
</span></p>

<p class=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Calibri",=
"sans-serif";
color:#1F497D'><o:p>&nbsp;</o:p></span></p>

<p class=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Calibri",=
"sans-serif";
color:#1F497D'>Lastly, if you suspect high homology to another system that =
you&#8217;re
lucky enough to find as a trimer, either a trimer in the asymmetric unit or=
 a symmetry
related trimer, then you can simply superimpose your system and hope that s=
uch
an arrangement may lead to the proper protein-protein contacts to make your
model meaningful. Of course after superimposition you will need to optimize=
 the
contacts.<o:p></o:p></span></p>

<p class=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Calibri",=
"sans-serif";
color:#1F497D'><o:p>&nbsp;</o:p></span></p>

<p class=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Calibri",=
"sans-serif";
color:#1F497D'>&nbsp;As I said at the beginning, this is a fairly tricky an=
d
not easy task if you want to do this in a meaningful way. Our tools (Discov=
ery
Studio) can be helpful in your search so feel free to contact me directly i=
f
you need more information.<o:p></o:p></span></p>

<p class=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Calibri",=
"sans-serif";
color:#1F497D'><o:p>&nbsp;</o:p></span></p>

<p class=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Calibri",=
"sans-serif";
color:#1F497D'>Good luck!<o:p></o:p></span></p>

<p class=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Calibri",=
"sans-serif";
color:#1F497D'><o:p>&nbsp;</o:p></span></p>

<p class=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Calibri",=
"sans-serif";
color:#1F497D'>Francisco<o:p></o:p></span></p>

<p class=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Calibri",=
"sans-serif";
color:#1F497D'><o:p>&nbsp;</o:p></span></p>

<p class=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Calibri",=
"sans-serif";
color:#1F497D'>Product Manager, Life Sciences<o:p></o:p></span></p>

<p class=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Calibri",=
"sans-serif";
color:#1F497D'>Accelrys, San Diego, CA<o:p></o:p></span></p>

<p class=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Calibri",=
"sans-serif";
color:#1F497D'><a href=3D"mailto:fhernandez]=[accelrys.com">fhernandez]=[accelr=
ys.com</a><o:p></o:p></span></p>

<p class=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Calibri",=
"sans-serif";
color:#1F497D'>858-799-5606<o:p></o:p></span></p>

<p class=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Calibri",=
"sans-serif";
color:#1F497D'><o:p>&nbsp;</o:p></span></p>

<p class=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Calibri",=
"sans-serif";
color:#1F497D'><o:p>&nbsp;</o:p></span></p>

<div style=3D'border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in =
0in 0in'>

<p class=3DMsoNormal><b><span style=3D'font-size:10.0pt;font-family:"Tahoma=
","sans-serif"'>From:</span></b><span
style=3D'font-size:10.0pt;font-family:"Tahoma","sans-serif"'>
owner-chemistry+fhernandez=3D=3Daccelrys.com]=[ccl.net
[mailto:owner-chemistry+fhernandez=3D=3Daccelrys.com]=[ccl.net] <b>On Behalf =
Of </b>Kshatresh
Dutta Dubey kshatresh#,#gmail.com<br>
<b>Sent:</b> Monday, November 01, 2010 2:08 AM<br>
<b>To:</b> Francisco Hernandez-Guzman<br>
<b>Subject:</b> CCL: trimer from monomer<o:p></o:p></span></p>

</div>

<p class=3DMsoNormal><o:p>&nbsp;</o:p></p>

<div>

<p class=3DMsoNormal>Dear all,<br>
<br>
I want to model a simulate a protein which is found in trimeric form, but
unfortunately i have only monomer of that protein. Can anyone suggest me ho=
w to
model a trimer from a monomer. Kindly also suggest me modelling software wh=
ich
can do this. I have maestro, chiemera and VMD. <br>
Thanks in advance<br>
Regards<br>
Kshatresh Dutta Dubey<o:p></o:p></p>

</div>

</div>

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