From owner-chemistry@ccl.net Thu Aug 26 12:09:00 2010
From: "Roy Jensen JensenRH-,-MacEwan.ca" <owner-chemistry]~[server.ccl.net>
To: CCL
Subject: CCL: Drawing Software
Message-Id: <-42616-100826120019-25980-pkh4Q+TsxFUo46uGSni0Zw]~[server.ccl.net>
X-Original-From: Roy Jensen <JensenRH ~ MacEwan.ca>
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Date: Thu, 26 Aug 2010 09:59:34 -0600
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Sent to CCL by: Roy Jensen [JensenRH : MacEwan.ca]
Excel is not free, but ubiquitous. 
* Copy the structures from your drawing program. 
* Use the row heights to scale as the actual energies (this takes a
bit of getting use to)
* Use the border tools to draw heavy lines for the energy levels and
lighter diagonal lines for the reaction coordinate.

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



On Wed, 25 Aug 2010 19:08:16 -0400, you wrote:

>
>Sent to CCL by: "W  Flak" [williamflak{=}yahoo.com]
>Dear CCL
>I was wondering if there is a free software to draw the reaction mechanism, 
>energy levels of reactants, transition state and products, where I use chemdraw 
>but the graph is not organised well.
>Thanks in advance
>Flak>


From owner-chemistry@ccl.net Thu Aug 26 13:44:00 2010
From: "RD Miles rdmsgl__gmail.com" <owner-chemistry_+_server.ccl.net>
To: CCL
Subject: CCL: Drawing Software
Message-Id: <-42617-100826124739-6680-WP29zbg7pUH/vTYl1lkD1g_+_server.ccl.net>
X-Original-From: RD Miles <rdmsgl]![gmail.com>
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Date: Thu, 26 Aug 2010 12:47:10 -0400
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Sent to CCL by: RD Miles [rdmsgl^^^gmail.com]
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I use gnuplot for most of my graphing. It is free, highly customizable, and
easy to use for basic plotting, but it has a learning curve if preparing
professional looking plots.

I don't recommend it for 3d projection plots however.

-Randy


On Wed, 25 Aug 2010 19:08:16 -0400, you wrote:

>
>Sent to CCL by: "W  Flak" [williamflak{=}yahoo.com]
>Dear CCL
>I was wondering if there is a free software to draw the reaction mechanism,
>energy levels of reactants, transition state and products, where I use
chemdraw
>but the graph is not organised well.
>Thanks in advance
>Flak>

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I use gnuplot for most of my graphing. It is free, highly customizable, and=
 easy to use for basic plotting, but it has a learning curve if preparing p=
rofessional looking plots.<br clear=3D"all"><div><br></div><div>I don&#39;t=
 recommend it for 3d projection plots however.</div>

<div><br></div>-Randy<br>
<br><br><div class=3D"gmail_quote">On Wed, 25 Aug 2010 19:08:16 -0400, you =
wrote:<br><br>&gt;<br>&gt;Sent to CCL by: &quot;W =A0Flak&quot; [williamfla=
k{=3D}<a href=3D"http://yahoo.com" target=3D"_blank">yahoo.com</a>]<br>&gt;=
Dear CCL<br>

&gt;I was wondering if there is a free software to draw the reaction mechan=
ism,<br>&gt;energy levels of reactants, transition state and products, wher=
e I use chemdraw<br>&gt;but the graph is not organised well.<br>&gt;Thanks =
in advance<br>

&gt;Flak&gt;</div>

--001636417c1f0a15d1048ebcc136--


From owner-chemistry@ccl.net Thu Aug 26 14:18:00 2010
From: "Chris Swain swain[a]mac.com" <owner-chemistry|-|server.ccl.net>
To: CCL
Subject: CCL: Drawing Software
Message-Id: <-42618-100826141436-22549-ND5QMa9A0JucFBORaK/eFA|-|server.ccl.net>
X-Original-From: Chris Swain <swain_._mac.com>
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Sent to CCL by: Chris Swain [swain=-=mac.com]

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It might be worth contacting iChemLabs (http://www.ichemlabs.com/) I've found them very responsive to adding new features to ChemDoodle

Chris

http://www.macinchem.org


On 26 Aug 2010, at 17:47, RD Miles rdmsgl__gmail.com wrote:

> I use gnuplot for most of my graphing. It is free, highly customizable, and easy to use for basic plotting, but it has a learning curve if preparing professional looking plots.
> 
> I don't recommend it for 3d projection plots however.
> 
> -Randy
> 
> 
> On Wed, 25 Aug 2010 19:08:16 -0400, you wrote:
> 
> >
> >Sent to CCL by: "W  Flak" [williamflak{=}yahoo.com]
> >Dear CCL
> >I was wondering if there is a free software to draw the reaction mechanism,
> >energy levels of reactants, transition state and products, where I use chemdraw
> >but the graph is not organised well.
> >Thanks in advance
> >Flak>


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<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">It might be worth contacting iChemLabs (<a href="http://www.ichemlabs.com/">http://www.ichemlabs.com/</a>) I've found them very responsive to adding new features to ChemDoodle<div><br></div><div>Chris</div><div><div><span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div><br></div><div><a href="http://www.macinchem.org">http://www.macinchem.org</a></div><br class="Apple-interchange-newline"></span>
</div>
<br><div><div>On 26 Aug 2010, at 17:47, RD Miles rdmsgl__gmail.com wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">I use gnuplot for most of my graphing. It is free, highly customizable, and easy to use for basic plotting, but it has a learning curve if preparing professional looking plots.<br clear="all"><div><br></div><div>I don't recommend it for 3d projection plots however.</div>

<div><br></div>-Randy<br>
<br><br><div class="gmail_quote">On Wed, 25 Aug 2010 19:08:16 -0400, you wrote:<br><br>&gt;<br>&gt;Sent to CCL by: "W &nbsp;Flak" [williamflak{=}<a href="http://yahoo.com/" target="_blank">yahoo.com</a>]<br>&gt;Dear CCL<br>

&gt;I was wondering if there is a free software to draw the reaction mechanism,<br>&gt;energy levels of reactants, transition state and products, where I use chemdraw<br>&gt;but the graph is not organised well.<br>&gt;Thanks in advance<br>

&gt;Flak&gt;</div>
</blockquote></div><br></div></body></html>

--Boundary_(ID_LdjV/Ce9/vhGS0yWscNRdA)--


From owner-chemistry@ccl.net Thu Aug 26 14:53:00 2010
From: "N. Sukumar nagams^rpi.edu" <owner-chemistry-*-server.ccl.net>
To: CCL
Subject: CCL: Literature of current status and perspective of comp. chemistry
Message-Id: <-42619-100826143147-553-MSquwZAphOneGZ3KEO+lqA-*-server.ccl.net>
X-Original-From: "N. Sukumar" <nagams{=}rpi.edu>
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Date: Thu, 26 Aug 2010 14:31:36 -0400
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Sent to CCL by: "N. Sukumar" [nagams+/-rpi.edu]
For brief and current reports and perspectives, check out the latest or
recent issue(s) of Annual Reports in Computational Chemistry (distributed 
free to all members of the Division of Computers in Chemistry of the
American Chemical Society [ACS COMP], as part of the membership benefits).

Dr. N. Sukumar
Rensselaer Exploratory Center for Cheminformatics Research
http://reccr.chem.rpi.edu/ --------------------------
"It is nice to know that the computer understands the problem. But I
would like to understand it too." -- Eugene P. Wigner

==============Original message text===============
On Tue, 24 Aug 2010 15:30:36 EDT "William Wei william.lh.wei,+,gmail.com" 
wrote:


Sent to CCL by: "William  Wei" [william.lh.wei**gmail.com]
Dear All,

I am looking for some literature on the current status and perspective of 
computational chemistry.  Could anybody suggest some papers?

Thank you very much,
Williamhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt===========End of original message text===========


From owner-chemistry@ccl.net Thu Aug 26 15:30:01 2010
From: "david hose anthrax_brothers#,#hotmail.com" <owner-chemistry*_*server.ccl.net>
To: CCL
Subject: CCL: Drawing Software
Message-Id: <-42620-100826152902-29866-rrEaF90sNQl/QqND2fmxUg*_*server.ccl.net>
X-Original-From: "david  hose" <anthrax_brothers===hotmail.com>
Date: Thu, 26 Aug 2010 15:28:57 -0400


Sent to CCL by: "david  hose" [anthrax_brothers.:.hotmail.com]
Flak,

I don't know of a package that will do this directly for you, but you can use Excel (or your favorite 
graph drawing package) to draw you energy profiles with the typical truncated sawtooth pattern.

Consider the reaction A -> B -> C, where the energy change for A -> B is 10 kcal, and B -> C is -
30 kcal.  In your favorite package set up the following table;

0
0
10
10
-20
-20

Plotting the data as a line graph will produce the typical truncated sawtooth plot.  Play around with 
the formating of the individual points to produce segments of the line that is thicker or thinner as 
required.

If you want to have a different spacing on the x-axis, set up this table;

1.0   0
2.0   0
3.5   10
4.5   10
6.0   -20
7.0   -20

Then plot the data as a scatter plot and format the points/line segments as required.

If you are using Excel, you can paste chemical structures into the graph from most (2D) chemical 
drawing packages, or picture of your 3D structure.

Of course if you are using a spreadsheet, you could create a table of energy changes for each step, 
and then get Excel to create the forementioned tables.  I've set up my own template for these graphs 
with all the calculations and formatting already done which saves a lot of effort.

Hope that helps.

Regards,

Dave.


>Sent to CCL by: "W  Flak" [williamflak{=}yahoo.com]
>Dear CCL
>I was wondering if there is a free software to draw the reaction mechanism,
>energy levels of reactants, transition state and products, where I use chemdraw
>but the graph is not organised well.
>Thanks in advance
>Flak>