From owner-chemistry@ccl.net Fri Sep 3 01:20:00 2010 From: "W. Flak williamflak_-_yahoo.com" To: CCL Subject: CCL: Structure presentation software Message-Id: <-42667-100903011834-12566-ONKziC3c55mq4deZ1vtcAw%x%server.ccl.net> X-Original-From: "W. Flak" Date: Fri, 3 Sep 2010 01:18:26 -0400 Sent to CCL by: "W. Flak" [williamflak++yahoo.com] Dear CCL I was wondering which program do you use to present a protein structure in a paper? I use GaussView, but the picture looks sillly Thanks in advance W. Flak From owner-chemistry@ccl.net Fri Sep 3 02:47:00 2010 From: "laura S slaurami+/-yahoo.com" To: CCL Subject: CCL: Structure presentation software Message-Id: <-42668-100903024509-29003-qg7wiMGDx65Y0TFj817OWw]*[server.ccl.net> X-Original-From: laura S Content-Type: multipart/alternative; boundary="0-456382817-1283496301=:81260" Date: Thu, 2 Sep 2010 23:45:01 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: laura S [slaurami##yahoo.com] --0-456382817-1283496301=:81260 Content-Type: text/plain; charset=us-ascii Dear W. Flak, I recommend you to use DS Visualizer from Accelrys. http://accelrys.com/products/discovery-studio/visualization.html Best regards, Amalia-Laura Seff ------------------------------------------------ Research Assistant Babes-Bolyai University ________________________________ > From: W. Flak williamflak_-_yahoo.com To: "Seff, Amalia Laura " Sent: Fri, September 3, 2010 8:18:26 AM Subject: CCL: Structure presentation software Sent to CCL by: "W. Flak" [williamflak++yahoo.com] Dear CCL I was wondering which program do you use to present a protein structure in a paper? I use GaussView, but the picture looks sillly Thanks in advance W. Flakhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--0-456382817-1283496301=:81260 Content-Type: text/html; charset=us-ascii
Dear W. Flak,

I recommend you to use DS Visualizer from Accelrys.
http://accelrys.com/products/discovery-studio/visualization.html

Best regards,


 
Amalia-Laura Seff
------------------------------------------------
Research Assistant
Babes-Bolyai University


 


From: W. Flak williamflak_-_yahoo.com <owner-chemistry*ccl.net>
To: "Seff, Amalia Laura " <slaurami*yahoo.com>
Sent: Fri, September 3, 2010 8:18:26 AM
Subject: CCL: Structure presentation software


Sent to CCL by: "W.  Flak" [williamflak++yahoo.com]
Dear CCL
I was wondering which program do you use to present a protein structure in a
paper?
I use GaussView, but the picture looks sillly
Thanks in advance
W. Flak



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--0-456382817-1283496301=:81260-- From owner-chemistry@ccl.net Fri Sep 3 03:56:01 2010 From: "vadiraj kurdekar vadirajgcppc+/-yahoo.co.in" To: CCL Subject: CCL: Structure presentation software Message-Id: <-42669-100903035130-6990-gTFjY/jBE/pKXL9RFB0YNA-x-server.ccl.net> X-Original-From: vadiraj kurdekar Content-Type: multipart/alternative; boundary="0-429359943-1283500282=:62156" Date: Fri, 3 Sep 2010 13:21:22 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: vadiraj kurdekar [vadirajgcppc_._yahoo.co.in] --0-429359943-1283500282=:62156 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear W. Flak, I recommend you to use Yasara Visualizer =A0 http://www.yasara.org/ =A0 or pymol for http://www.pymol.org/ Best regards, =A0 Vadiraj Kurdekar, Research Scholar,=20 Pharmacy group, Birla Institute of Technology and Science-Pilani, Rajasthan, India. Mobile: + 91 9460763664=20 email: vadirajgcppc{:}yahoo.co.in --- On Fri, 3/9/10, W. Flak williamflak_-_yahoo.com wrote: > From: W. Flak williamflak_-_yahoo.com Subject: CCL: Structure presentation software To: "Kurdekar, Vadiraj " Date: Friday, 3 September, 2010, 10:48 AM Sent to CCL by: "W.=A0 Flak" [williamflak++yahoo.com] Dear CCL I was wondering which program do you use to present a protein structure in = a=20 paper? I use GaussView, but the picture looks sillly Thanks in advance W. Flak -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0Subscribe/Unsubscribe:=20 =A0 =A0 =A0Job: http://www.ccl.net/jobs=20=A0 =A0 =A0=0A=0A --0-429359943-1283500282=:62156 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
--0-429359943-1283500282=:62156-- From owner-chemistry@ccl.net Fri Sep 3 07:03:01 2010 From: "Francisco Hernandez-Guzman fhernand[#]accelrys.com" To: CCL Subject: CCL: Structure presentation software Message-Id: <-42670-100903070152-19033-2/seb8LrI7I1vdV4ipGQNQ _ server.ccl.net> X-Original-From: Francisco Hernandez-Guzman Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 3 Sep 2010 04:01:42 -0700 MIME-Version: 1.0 Sent to CCL by: Francisco Hernandez-Guzman [fhernand(0)accelrys.com] Hi William, You can try our free easy-to-use visualizer. It works great for visualization of protein, DNA/RNA, lipids and ligand structures. It is available for Windows and Linux. http://accelrys.com/products/discovery-studio/visualization-download.php Cheers, Francisco Product Manager Accelrys Inc. -----Original Message----- > From: owner-chemistry+fhernandez==accelrys.com,,ccl.net [mailto:owner-chemistry+fhernandez==accelrys.com,,ccl.net] On Behalf Of W. Flak williamflak_-_yahoo.com Sent: Thursday, September 02, 2010 10:18 PM To: Francisco Hernandez-Guzman Subject: CCL: Structure presentation software Sent to CCL by: "W.  Flak" [williamflak++yahoo.com] Dear CCL I was wondering which program do you use to present a protein structure in a paper? I use GaussView, but the picture looks silly Thanks in advance W. Flak                     From owner-chemistry@ccl.net Fri Sep 3 08:19:00 2010 From: "=?iso-8859-15?q?J=E9r=F4me_Pansanel?= j.pansanel:pansanel.net" To: CCL Subject: CCL: Structure presentation software Message-Id: <-42671-100903054421-24262-qGxR1eIxXknqcjiYFGtwRA() server.ccl.net> X-Original-From: =?iso-8859-15?q?J=E9r=F4me_Pansanel?= Content-Transfer-Encoding: 8bit Content-Type: Text/Plain; charset="iso-8859-15" Date: Fri, 3 Sep 2010 11:44:04 +0200 MIME-Version: 1.0 Sent to CCL by: =?iso-8859-15?q?J=E9r=F4me_Pansanel?= [j.pansanel!A!pansanel.net] Dear William, I am using PyMOL. J. Pansanel Le vendredi 3 septembre 2010 07:18:26, vous avez écrit : > Sent to CCL by: "W. Flak" [williamflak++yahoo.com] > Dear CCL > I was wondering which program do you use to present a protein structure in > a paper? > I use GaussView, but the picture looks sillly > Thanks in advance > W. Flak-- Jerome Pansanel IPHC 23, rue du Loess BP 28 F-67037 STRASBOURG CEDEX 2 Tel: +33 (0)3 88 10 66 24 Fax: +33 (0)3 88 10 62 34 From owner-chemistry@ccl.net Fri Sep 3 08:54:00 2010 From: "Jerome Pansanel jerome.pansanel]=[iphc.cnrs.fr" To: CCL Subject: CCL: Structure presentation software Message-Id: <-42672-100903024804-10078-p6aXGvYBHq/1KgFeroNVtA]|[server.ccl.net> X-Original-From: Jerome Pansanel Content-Transfer-Encoding: 8bit Content-Type: Text/Plain; charset="iso-8859-15" Date: Fri, 3 Sep 2010 08:47:47 +0200 MIME-Version: 1.0 Sent to CCL by: Jerome Pansanel [jerome.pansanel-$-iphc.cnrs.fr] Dear William, I am using PyMOL. J. Pansanel Le vendredi 3 septembre 2010 07:18:26, vous avez écrit : > Sent to CCL by: "W. Flak" [williamflak++yahoo.com] > Dear CCL > I was wondering which program do you use to present a protein structure in > a paper? > I use GaussView, but the picture looks sillly > Thanks in advance > W. Flak-- Jerome Pansanel IPHC 23, rue du Loess BP 28 F-67037 STRASBOURG CEDEX 2 Tel: +33 (0)3 88 10 66 24 Fax: +33 (0)3 88 10 62 34 From owner-chemistry@ccl.net Fri Sep 3 09:29:01 2010 From: "Francisco Hernandez-Guzman fhernand^accelrys.com" To: CCL Subject: CCL: Structure presentation software Message-Id: <-42673-100903065818-6089-5QGIKkhQf/0u6MisCydo7g|,|server.ccl.net> X-Original-From: Francisco Hernandez-Guzman Content-Language: en-US Content-Type: multipart/related; boundary="_004_55AC410F3302E740AC9EC50011F73E8F01D1D1CC5EEXCH1COLOacce_"; type="multipart/alternative" Date: Fri, 3 Sep 2010 03:58:06 -0700 MIME-Version: 1.0 Sent to CCL by: Francisco Hernandez-Guzman [fhernand()accelrys.com] --_004_55AC410F3302E740AC9EC50011F73E8F01D1D1CC5EEXCH1COLOacce_ Content-Type: multipart/alternative; boundary="_000_55AC410F3302E740AC9EC50011F73E8F01D1D1CC5EEXCH1COLOacce_" --_000_55AC410F3302E740AC9EC50011F73E8F01D1D1CC5EEXCH1COLOacce_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hi William, You can try our free easy-to-use visualizer. It works great for visualizati= on of protein, DNA/RNA, lipids and ligand structures. It is available for W= indows and Linux. http://accelrys.com/products/discovery-studio/visualization-download.php Cheers, Francisco [cid:image001.gif : 01CB4B1B.BBAABC40] Francisco G. Hernandez-Guzman, Ph.D. Product Manager, Life Sciences Accelrys, Inc. 10188 Telesis Court, Suite 100 San Diego, CA 92121, USA T: +1 858 799 5606 C: +1 858 361 3020 F: +1 858 799 5100 fhernand : accelrys.com Customer Support Hotline (800) 756-4674 - Americas (+44) 1223-228822 - EU (+81) 3-3578-3861 - AP support : accelrys.com http://customer.accelrys.com Smarter Science. Better Business. 2010 European User Group Meeting Barcelona, Spain, 26-28 October Learn new applications & techniques > from colleagues, experts and partners Register Here >> Website | Communities | Blog | Twitter | LinkedIn | = Facebook -----Original Message----- > From: owner-chemistry+fhernandez=3D=3Daccelrys.com : ccl.net [mailto:owner-ch= emistry+fhernandez=3D=3Daccelrys.com : ccl.net] On Behalf Of W. Flak williamf= lak_-_yahoo.com Sent: Thursday, September 02, 2010 10:18 PM To: Francisco Hernandez-Guzman Subject: CCL: Structure presentation software Sent to CCL by: "W. Flak" [williamflak++yahoo.com] Dear CCL I was wondering which program do you use to present a protein structure in = a paper? I use GaussView, but the picture looks sillly Thanks in advance W. Flak -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--_000_55AC410F3302E740AC9EC50011F73E8F01D1D1CC5EEXCH1COLOacce_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hi William,

 

You can try our free easy-to-use visualizer. It wor= ks great for visualization of protein, DNA/RNA, lipids and ligand structures. = It is available for Windows and Linux.

 

http://accelrys.com/products/discovery-studio/visualization-download= .php

 

 

Cheers,

 

Francisco

 

Dear W. Flak,

I recommend you to = use Yasara Visualizer
 
 
or pymol for http://= www.pymol.org/<= BR>
Best regards,
 
Vadiraj Kurdekar,
Research Scholar,
Pharmacy group,
Rajasthan,
India.
Mobile: + 91 9460763664
email: vadirajgcppc{:}yahoo.co.in


--- On = Fri, 3/9/10, W. Flak williamflak_-_yahoo.com <owner-chemistry{:}ccl.= net> wrote:

From: W. Flak williamflak_-_yahoo.com <owner-c= hemistry{:}ccl.net>
Subject: CCL: Structure presentation software
To= : "Kurdekar, Vadiraj " <vadirajgcppc{:}yahoo.co.in>
Date: Fr= iday, 3 September, 2010, 10:48 AM


Sent to CCL by: "W.  Flak" [williamflak++ya= hoo.com]
Dear CCL
I was wondering which program do you use to present= a protein structure in a
paper?
I use GaussView, but the picture lo= oks sillly
Thanks in advance
W. Flak



-=3D This is auto= matically added to each message by the mailing script =3D-
To recover th= e email address of the author of the message, please change
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3Dsig-accl-logo-st

 

Francisco G. Hernandez-Guzman, Ph= .D.
Product Manager, Life Sciences

Accelrys, Inc.
10188 Telesis Court, Suite 100
San Diego, CA 92121, USA
T:  +1 858 799 5606
C:  +1 858 361 3020
F:  +1 858 799 5100
fhernand : accelrys.com

Customer Support Hotline
(800) 756-4674 - Americas
(+44) 1223-228822 - EU
(+81) 3-3578-3861 - AP
support : accelrys.com
http://customer.accelrys.com

S= marter Science. Better Business.

2010 European User G= roup Meeting
Barcelona, Spain, 26-28 October

Learn new applicatio= ns & techniques
from colleagues, experts and partners

Register Here >>

Website   |   Communities   |   Blog   |   = Twitter  |   LinkedIn  |   Facebook

 =

 

 

 

 

 

-----Original Message-----
> From: owner-chemistry+fhernandez=3D=3Daccelrys.com : ccl.net [mailto:owner-chemistry+fhernandez=3D=3Daccelrys.com : ccl.net] On Behalf Of = W. Flak williamflak_-_yahoo.com
Sent: Thursday, September 02, 2010 10:18 PM
To: Francisco Hernandez-Guzman
Subject: CCL: Structure presentation software

 

 

Sent to CCL by: "W.  Flak" [williamflak++yahoo.com]

Dear CCL

I was wondering which program do you use to present= a protein structure in a

paper?

I use GaussView, but the picture looks sillly<= /o:p>

Thanks in advance

W. Flak

 

 

 

-=3D This is automatically added to each message by= the mailing script =3D-

the strange characters on the top line to the : sig= n. You can also

look up the X-Original-From: line in the mail heade= r.

 

     

 

E-mail to administrators: CHEMISTRY-REQUEST : ccl.net= or use

     

 

     

 

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If your mail bounces from CCL with 5.7.1 error, che= ck:

     

 

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--_000_55AC410F3302E740AC9EC50011F73E8F01D1D1CC5EEXCH1COLOacce_-- --_004_55AC410F3302E740AC9EC50011F73E8F01D1D1CC5EEXCH1COLOacce_ Content-Type: image/gif; name="image001.gif" Content-Description: image001.gif Content-Disposition: inline; filename="image001.gif"; size=940; creation-date="Fri, 03 Sep 2010 03:58:08 GMT"; modification-date="Fri, 03 Sep 2010 03:58:08 GMT" Content-ID: Content-Transfer-Encoding: base64 R0lGODlhXwAkAMQAAK/C22iNu9zk7+Tq84elynaYwqO51pqz0kd0rSNanfr7/dTf7FqDtvH0+DNl pMLR5LzM4ZKtzuvw9j1sqc7a6VJ9svX4+x9Wmy1hojlqp015sCleoMjV50Bvqv///xxUmiH5BAAA AAAALAAAAABfACQAAAX/4CeOZGmeaKqubOu+cCzPdG3feK7vfO//wKBwSCwagxtRBTCQQAiOo5R0 CVQuBIvnwUgkpuBPBJAoeDyGy4cRMUQqw41mYktoOrGAB+EQeAQJCBxaZw0AUUAaAwY1ZQAHMAkP Ax96HgUZfh4WCw8CCguIPhoKjDQYBwAEMAgSFBdmewRnAB1qHxoPZCMOE19UDqIiwb/DGSMIDaYi GBi3JRdqCRPHHwVuMAweDRuxFQwLEY4GBV4RGh8ZABSdBSNLAgKHHwgGAwIQdBMGC/II9A0ioKpQ YAEEBwTEidhAbs2DBRQgMKAnjIWGBh4CdMAI5xiCM2cedEjgEQADBgAU/wRYI0FAgQK1OgwYQABm BQzxCgTgEGpjhAkWZh4oB8DDRFweCLSSGOBABBkIMFD4M6FCgGIYAAggFErEMwdoPlAYgMgLAAvo PkQ7YAEOvUsOAjoY0OCfCA0eIIlp0GGW3Q9JYkCa9SdtCQwdioYdFiACBwUHJjRYNSKDhWUfEnxi t2CBXAkR5mK+8DAKhVcVJNC8OUNAhw0QzqAtweCBu1kCjhUYsOAAgwERtK0cgZfyMAkcvp2skMHn XL0j9Fy18HSNVg8L3MKg8CABBnuuSxg4s/JBW8sAkiRQ8HMyCaCYE0h4YCJZ6AHQF8orIOEo43vP uGAGBOhMEAwC0lyQjP8HFCTAgALfKOCONXldMJYoG5xl11ptjZDABskcIJoJBChwzxfFfABAAym2 AJsHCkT0gAQWXAVBKONZ4IBMUTVRgGMDQHABAw0M8BIXEwggQU22bUBBAwcEQAAHDCBQSgYSAGBC Jh5UFwAEBbAB5QwTPAASSN+cQRCMEyCQ3gcV3AhBB1J+oQEAnR2AwQf7QATAMRhEwA4FBExjQACB BhCgCAd44BYGBAxKwKIvbEDAjREF4CSMGehhQQYa+JcZCgksGo0JLapwAQQDtJhqDFFcEMwFWdEi hgccNEMpEVVFcIkPDkRAwDcEDHAGBQ5ollEYIjBA4wGv4qCOsWdkmewpeAfsasQFHVTkQwc/KpVA BQa4pC2z6Kar7rrstuvuu/DGK++89NZLbwgAOw== --_004_55AC410F3302E740AC9EC50011F73E8F01D1D1CC5EEXCH1COLOacce_-- From owner-chemistry@ccl.net Fri Sep 3 10:04:00 2010 From: "fabiana caporuscio andfadeout++gmail.com" To: CCL Subject: CCL: Structure presentation software Message-Id: <-42674-100903042557-31800-R17FX30mhgMTYdONdglFaQ-,-server.ccl.net> X-Original-From: fabiana caporuscio Content-Type: multipart/alternative; boundary=000e0cd4d758b5aaa7048f56ad3f Date: Fri, 3 Sep 2010 10:25:51 +0200 MIME-Version: 1.0 Sent to CCL by: fabiana caporuscio [andfadeout-*-gmail.com] --000e0cd4d758b5aaa7048f56ad3f Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear William, do you mean a software to make good pictures of proteins? I generally use PyMol http://www.pymol.org/ and/or Maestro http://www.schrodinger.com/products/14/12/ Maestro is the interface for all Schr=F6dinger software but if you are an academic researcher you can download it at no charge. Best regards, Fabiana Caporuscio, PhD On 3 September 2010 07:18, W. Flak williamflak_-_yahoo.com < owner-chemistry-$-ccl.net> wrote: > > Sent to CCL by: "W. Flak" [williamflak++yahoo.com] > Dear CCL > I was wondering which program do you use to present a protein structure i= n > a > paper? > I use GaussView, but the picture looks sillly > Thanks in advance > W. Flak > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --000e0cd4d758b5aaa7048f56ad3f Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear William,
do you mean a software to make good pictures of proteins?
I general= ly use PyMol http://www.pymol.org/=A0= and/or Maestro http:= //www.schrodinger.com/products/14/12/=A0
Maestro is=A0the interface for all Schr=F6dinger software but if you a= re an academic researcher you can download it at no charge.
Best regards,
=A0
Fabiana Caporuscio, PhD

On 3 September 2010 07:18, W. Flak williamflak_-_yahoo.com <owner-chemistry-$-ccl.net= > wrote:

Sent to CCL by: "W. =A0= Flak" [williamflak++ya= hoo.com]
Dear CCL
I was wondering which program do you use to present a protein s= tructure in a
paper?
I use GaussView, but the picture looks silllyThanks in advance
W. Flak



-=3D This is automatically add= ed to each message by the mailing script =3D-look= up the X-Original-From: line in the mail header.

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--000e0cd4d758b5aaa7048f56ad3f-- From owner-chemistry@ccl.net Fri Sep 3 10:39:00 2010 From: "Johannes Salewski Johannes.Salewski a tu-berlin.de" To: CCL Subject: CCL: Structure presentation software Message-Id: <-42675-100903032052-30580-EV16zmG/JrE6hstG/BVXJA],[server.ccl.net> X-Original-From: Johannes Salewski Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Fri, 03 Sep 2010 09:20:39 +0200 MIME-Version: 1.0 Sent to CCL by: Johannes Salewski [Johannes.Salewski]~[tu-berlin.de] Hello W. Flak, I use *vmd* to prepare pretty pictures of proteins or cofactors in pockets You can adjust a huge amount of parameters like color, opacity, drawing style (alpha-helices, beta-sheets, etc), bonds, atom labels, ... You can download it for free at http://www.ks.uiuc.edu/Research/vmd/, just have a look! I hope that I could help you, Best Regards, Johannes W. Flak williamflak_-_yahoo.com schrieb: > Sent to CCL by: "W. Flak" [williamflak++yahoo.com] > Dear CCL > I was wondering which program do you use to present a protein structure in a > paper? > I use GaussView, but the picture looks sillly > Thanks in advance > W. Flak From owner-chemistry@ccl.net Fri Sep 3 11:13:00 2010 From: "Marcin =?iso-8859-2?Q?Kr=F3l?= mykrol[*]cyf-kr.edu.pl" To: CCL Subject: CCL: Structure presentation software Message-Id: <-42676-100903075144-26899-35fPAQyuEpBo8i2akzbSsg:server.ccl.net> X-Original-From: Marcin =?iso-8859-2?Q?Kr=F3l?= Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-2 Date: Fri, 3 Sep 2010 13:51:32 +0200 MIME-Version: 1.0 Sent to CCL by: Marcin =?iso-8859-2?Q?Kr=F3l?= [mykrol^^^cyf-kr.edu.pl] I always used VMD (http://www.ks.uiuc.edu/Research/vmd/), it makes nice pictures (especially when linked with Povray) and is great to work with MD trajectories. best Marcin >> From: owner-chemistry+fhernandez==accelrys.com{}ccl.net >> [mailto:owner-chemistry+fhernandez==accelrys.com{}ccl.net] On Behalf Of >> W. Flak williamflak_-_yahoo.com > Sent: Thursday, September 02, 2010 10:18 PM > To: Francisco Hernandez-Guzman > Subject: CCL: Structure presentation software > > > Sent to CCL by: "W.  Flak" [williamflak++yahoo.com] > Dear CCL > I was wondering which program do you use to present a protein structure in > a > paper? > I use GaussView, but the picture looks silly > Thanks in advance > W. Flak                     > > From owner-chemistry@ccl.net Fri Sep 3 11:48:00 2010 From: "Sayed Mesa elsayed.elmes- -yahoo.com" To: CCL Subject: CCL: Antiferromagnetism and multiplicity Message-Id: <-42677-100903110551-14212-iSDXAwG9+Y3dcfOOjtc64Q(a)server.ccl.net> X-Original-From: "Sayed Mesa" Date: Fri, 3 Sep 2010 11:05:39 -0400 Sent to CCL by: "Sayed Mesa" [elsayed.elmes_-_yahoo.com] Dear CCL community I measured experimentally the magnetic properties of some dinuclear transition-metal complexes for example [Co2L]4+ where L is macrocyclic ligand. I found most of them exhibit "Antiferromagnetic character". I want to optimize the geometries of these complexes but I am confused how can I define the multiplicity in such case? It is worth mentioned that the total number of electrons for the complex or for the ligand is even. Thanks in advance Sayed From owner-chemistry@ccl.net Fri Sep 3 12:23:00 2010 From: "Reichert, David reichertd[*]mir.wustl.edu" To: CCL Subject: CCL: Structure presentation software Message-Id: <-42678-100903100634-13148-EyKEL0Uy92B9fDZaKfwoew ~~ server.ccl.net> X-Original-From: "Reichert, David" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 3 Sep 2010 09:06:24 -0500 MIME-Version: 1.0 Sent to CCL by: "Reichert, David" [reichertd*_*mir.wustl.edu] For proteins I highly recommend UCSF Chimera. -david David E. Reichert, PhD. Asst. Professor of Radiology Washington University School of Medicine e-mail: reichertd|-|wustl.edu voice: 314-362-8461 fax: 314-362-9940 web: http://scoobie.wustl.edu/ -----Original Message----- > From: owner-chemistry+reichertd==mir.wustl.edu|-|ccl.net [mailto:owner-chemistry+reichertd==mir.wustl.edu|-|ccl.net] On Behalf Of W. Flak williamflak_-_yahoo.com Sent: Friday, September 03, 2010 12:18 AM To: Reichert, David Subject: CCL: Structure presentation software Sent to CCL by: "W. Flak" [williamflak++yahoo.com] Dear CCL I was wondering which program do you use to present a protein structure in a paper? I use GaussView, but the picture looks sillly Thanks in advance W. Flakhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThe material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. From owner-chemistry@ccl.net Fri Sep 3 12:58:00 2010 From: "jaleel uc jaleel.uc]=[gmail.com" To: CCL Subject: CCL: Structure presentation software Message-Id: <-42679-100903112517-4263-IY0NyV7+o80CQH+/S8gyow ~~ server.ccl.net> X-Original-From: jaleel uc Content-Type: multipart/alternative; boundary=000e0cd567de2e9975048f5c894b Date: Fri, 3 Sep 2010 20:55:07 +0530 MIME-Version: 1.0 Sent to CCL by: jaleel uc [jaleel.uc++gmail.com] --000e0cd567de2e9975048f5c894b Content-Type: text/plain; charset=ISO-8859-1 Dear friend In addition to pymol, VMD , schrodinger , hyperchem Please check yasara http://www.yasara.org/ JALEEL On Fri, Sep 3, 2010 at 12:50 PM, Johannes Salewski Johannes.Salewski a tu-berlin.de wrote: > > Sent to CCL by: Johannes Salewski [Johannes.Salewski]~[tu-berlin.de] > Hello W. Flak, > > I use *vmd* to prepare pretty pictures of proteins or cofactors in pockets > You can adjust a huge amount of parameters like color, opacity, drawing > style (alpha-helices, beta-sheets, etc), bonds, atom labels, ... > You can download it for free at http://www.ks.uiuc.edu/Research/vmd/, just > have a look! > > I hope that I could help you, > Best Regards, > Johannes > > > W. Flak williamflak_-_yahoo.com schrieb: > > Sent to CCL by: "W. Flak" [williamflak++yahoo.com] >> Dear CCL >> I was wondering which program do you use to present a protein structure in >> a paper? >> I use GaussView, but the picture looks sillly >> Thanks in advance >> W. Flakhttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > -- Dr U.C.A.Jaleel. Asst Professor in cheminformatics Cheminformatics Division( UGC) Malabar Christian College Calicut University --000e0cd567de2e9975048f5c894b Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear friend
=A0
=A0
In addition to pymol, VMD , schrodinger , hyperchem=A0 Please check ya= sara
=A0
=A0
JALEEL

On Fri, Sep 3, 2010 at 12:50 PM, Johannes Salews= ki Johannes.Salewski a tu-berlin.de <owner-chemist= ry|,|ccl.net> wrote:

Sent to CCL by: Johannes Sal= ewski [Johannes.Salewski]~[tu-berlin.de]
Hello W. Flak,

I use *vmd* to prepare pretty pictures of proteins or= cofactors in pockets
You can adjust a huge amount of parameters like co= lor, opacity, drawing style (alpha-helices, beta-sheets, etc), bonds, atom = labels, ...
You can download it for free at http://www.ks.uiuc.edu/Research/vmd/, just have= a look!

I hope that I could help you,
Best Regards,
Johannes<= br>

W. Flak williamflak_-_yahoo.com schrieb:=20

Sent to CCL by: "W. =A0Flak= " [williamflak++yahoo.= com]
Dear CCL
I was wondering which program do you use to present a protein s= tructure in a paper?
I use GaussView, but the picture looks sillly
Th= anks in advance
W. Flak



-=3D This is automat= ically added to each message by the mailing script =3D-
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--
Dr = U.C.A.Jaleel.
Asst Professor in cheminformatics
Cheminformatics Divi= sion( UGC)
Malabar Christian College
Calicut University
--000e0cd567de2e9975048f5c894b-- From owner-chemistry@ccl.net Fri Sep 3 13:33:00 2010 From: "Elaine Meng meng:cgl.ucsf.edu" To: CCL Subject: CCL: Structure presentation software Message-Id: <-42680-100903120514-20264-nNANnDMaM45OZj1PrNQ6CQ++server.ccl.net> X-Original-From: "Elaine Meng" Date: Fri, 3 Sep 2010 12:05:05 -0400 Sent to CCL by: "Elaine Meng" [meng%%cgl.ucsf.edu] Hi W, There are many programs to do this -- you could also consider Chimera. It is free for noncommercial use (downloads available for Windows, Mac, Linux), and there is a full set of documentation including tutorials. Chimera homepage: http://www.cgl.ucsf.edu/chimera/index.html See links to download, User's Guide, tutorials, image gallery, etc. Best, 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 Fri Sep 3 14:08:00 2010 From: "=?ISO-8859-1?Q?Carlos_Javier_N=FA=F1ez?= carlosjavierna|gmail.com" To: CCL Subject: CCL: Structure presentation software Message-Id: <-42681-100903130651-23923-hScSqkiBlLHfV91k1KEFzQ+/-server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Carlos_Javier_N=FA=F1ez?= Content-Type: multipart/alternative; boundary=001636c5a8be5362b0048f5df417 Date: Fri, 3 Sep 2010 12:06:40 -0500 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Carlos_Javier_N=FA=F1ez?= [carlosjavierna##gmail.com] --001636c5a8be5362b0048f5df417 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi, MolSoft-ICM-Browser is another option: http://www.molsoft.com/ Chimera can do an excelent picture: http://www.cgl.ucsf.edu/chimera/ both have free-software options. Regards, Carlos Javier El 3 de septiembre de 2010 00:18, W. Flak williamflak_-_yahoo.com < owner-chemistry^^^ccl.net> escribi=F3: > > Sent to CCL by: "W. Flak" [williamflak++yahoo.com] > Dear CCL > I was wondering which program do you use to present a protein structure i= n > a > paper? > I use GaussView, but the picture looks sillly > Thanks in advance > W. Flak > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --001636c5a8be5362b0048f5df417 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi,

MolSoft-ICM-Browser is another option:

Chimera can do an excelent picture:

both have free-software options.=

Regards,
Carlos Javier






El 3 de septiembre de 2010 00:18, W. Flak williamflak_-_yahoo.com &l= t;owner-chemistry^^^ccl.net>= ; escribi=F3:

Sent to CCL by: "W. =A0Flak" [williamflak++yahoo.com]
Dear CCL
I was wondering which program do you use to present a protein structure in = a
paper?
I use GaussView, but the picture looks sillly
Thanks in advance
W. Flak

--001636c5a8be5362b0048f5df417-- From owner-chemistry@ccl.net Fri Sep 3 14:44:00 2010 From: "Nuno A. G. Bandeira nuno.bandeira[a]ist.utl.pt" To: CCL Subject: CCL: Antiferromagnetism and multiplicity Message-Id: <-42682-100903131827-2341-DUxjutQWQLGgcy5ZkTtgow~!~server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="ISO-8859-1"; format=flowed Date: Fri, 3 Sep 2010 18:18:20 +0100 MIME-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira() ist.utl.pt] On 03-09-2010 16:05, Sayed Mesa elsayed.elmes- -yahoo.com wrote: > Sent to CCL by: "Sayed Mesa" [elsayed.elmes_-_yahoo.com] > Dear CCL community > I measured experimentally the magnetic properties of some dinuclear transition-metal complexes for example [Co2L]4+ where L is macrocyclic ligand. I found most of them exhibit "Antiferromagnetic character". I want to optimize the geometries of these complexes but I am confused how can I define the multiplicity in such case? It is worth mentioned that the total number of electrons for the complex or for the ligand is even. The multiplicity is always singlet but you should attempt use what is called the broken symmetry technique (Google or WoK it for the relevant literature). Tipically you start with the highest multiplicity and then mix the SOMOs to produce the singlet. -- Nuno A. G. Bandeira, AMRSC Laboratoire de Chimie LR6 Ecole Normale Superieure de Lyon 46, Allee d'Italie 69364 Lyon Cedex 07 - France http://cqb.fc.ul.pt/intheochem/nuno/ -- From owner-chemistry@ccl.net Fri Sep 3 15:18:00 2010 From: "=?utf-8?Q?Walter_Ca=C3=B1=C3=B3n_Mancisidor?= wcanon===ciq.uchile.cl" To: CCL Subject: CCL: Antiferromagnetism and multiplicity Message-Id: <-42683-100903150441-20455-+OoiMN6fSgbzGqkl1RuueA|,|server.ccl.net> X-Original-From: =?utf-8?Q?Walter_Ca=C3=B1=C3=B3n_Mancisidor?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Fri, 3 Sep 2010 14:38:44 -0400 (CLT) MIME-Version: 1.0 Sent to CCL by: =?utf-8?Q?Walter_Ca=C3=B1=C3=B3n_Mancisidor?= [wcanon.:.ciq.uchile.cl] Sayed, look the work of Eliseo Ruiz from the university of barcelona. They used the broken simmetry aprouch. Walter ----- Mensaje original ----- De: "Sayed Mesa elsayed.elmes- -yahoo.com" Para: "Walter Alberto CaƃĀ±on" Enviados: Viernes, 3 de Septiembre 2010 11:05:39 Asunto: CCL: Antiferromagnetism and multiplicity Sent to CCL by: "Sayed Mesa" [elsayed.elmes_-_yahoo.com] Dear CCL community I measured experimentally the magnetic properties of some dinuclear transition-metal complexes for example [Co2L]4+ where L is macrocyclic ligand. I found most of them exhibit "Antiferromagnetic character". I want to optimize the geometries of these complexes but I am confused how can I define the multiplicity in such case? It is worth mentioned that the total number of electrons for the complex or for the ligand is even. Thanks in advance Sayedhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt-- Walter Alberto CaĆ±Ć³n Mancisidor QuĆ­mico, Licenciado en QuĆ­mica Candidato a Doctor en QuĆ­mica Laboratorio de Magnetismo Molecular Facultad de Ciencias QuĆ­micas y FarmacĆ©utica Universidad de Chile Tel: 56 (2) 978-2987 wcanon**ciq.uchile.cl From owner-chemistry@ccl.net Fri Sep 3 19:54:00 2010 From: "Jorge H. Rodriguez jhrodrig,,purdue.edu" To: CCL Subject: CCL: Antiferromagnetism and multiplicity Message-Id: <-42684-100903174350-6702-/v+xx9bGiZCspVRx/QjS1g[*]server.ccl.net> X-Original-From: "Jorge H. Rodriguez" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 3 Sep 2010 17:43:43 -0400 MIME-Version: 1.0 Sent to CCL by: "Jorge H. Rodriguez" [jhrodrig~~purdue.edu] Dear Sayed: You may want to consider the following: 1.If the two metals in the binuclear complex have the same nominal oxidation and spin state and the complex is in fact antiferromagnetic, then the overall spin multiplicity M (M = 2S + 1) of the system is 1 (M = 2X0 + 1 = 1). 2.In mixed valence binuclear complexes where the nominal oxidation and spin state of each metal ion is different and the system is antiferromagnetic, the overall spin of the system (S) is S = S1 - S2 (S1 minus S2) and the overall system spin multiplicity is M = 2S + 1. For example, if S = 1/2, then M = 2. 3.Within the single Slater determinant representation of the Kohn Sham wavefunction you can converge to the broken symmetry state which only mimics some properties of the actual ground state of the binuclear system but is not strictly equivalent. Therefore, the geometry that you obtain from a broken symmetry calculation (which depends on the broken symmetry energy energy) is only a (generally good) approximation to that of the actual binuclear system in its actual ground state. 4. The quality of the final geometry you obtain from a broken symmetry optimization, as it is also true for a conventional geometry optimization, is somewhat dependent on the particular exchange-correlation functional and basis set you choose. Best regards, Jorge H. Rodriguez Quoting "Sayed Mesa elsayed.elmes- -yahoo.com" : > > Sent to CCL by: "Sayed Mesa" [elsayed.elmes_-_yahoo.com] > Dear CCL community > I measured experimentally the magnetic properties of some dinuclear > transition-metal complexes for example [Co2L]4+ where L is macrocyclic > ligand. I found most of them exhibit "Antiferromagnetic character". I want to > optimize the geometries of these complexes but I am confused how can I define > the multiplicity in such case? It is worth mentioned that the total number of > electrons for the complex or for the ligand is even. > > Thanks in advance > Sayed> > > From owner-chemistry@ccl.net Fri Sep 3 20:29:00 2010 From: "Ian Grant Ian.Grant]_[ruhr-uni-bochum.de" To: CCL Subject: CCL: Structure presentation software Message-Id: <-42685-100903122607-12959-iYojhSRCLxzS1BfyIEW5/Q _ server.ccl.net> X-Original-From: "Ian Grant" Content-Type: multipart/alternative; boundary="------------050505020908010407060807" Date: 3 Sep 2010 18:25:58 +0200 MIME-Version: 1.0 Sent to CCL by: "Ian Grant" [Ian.Grant^ruhr-uni-bochum.de] This is a multi-part message in MIME format. --------------050505020908010407060807 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit I use PyMOL (http://www.pymol.org/) a lot, but if you are interested producing images using a space-filling vdW spheres representation, then QuteMol (http://qutemol.sourceforge.net/) produces some very nice pictures with little effort. The PyMOL wiki contains instructions how to replicate this effect (ambient occlusion shading) in PyMOL, and you can probably do it VMD too, but I don't know how myself. In fact, you definitely can reproduce the effect in VMD, as illustrated in this article: http://biostumblematic.wordpress.com/2009/12/02/rendering-proteins-in-pymol/ (which also demonstrates the different ray-tracing modes available in PyMOL). Regards, Ian. On 03/09/10 07:18, W. Flak williamflak_-_yahoo.com wrote: > Sent to CCL by: "W. Flak" [williamflak++yahoo.com] > Dear CCL > I was wondering which program do you use to present a protein structure in a > paper? > I use GaussView, but the picture looks sillly > Thanks in advance > W. Flak > -- ------------------------------------------------------------------------ Dr. Ian M. Grant [ian.grant**ruhr-uni-bochum.de] Centre for Theoretical Chemistry Ruhr-Universität Bochum 44780 Bochum, Germany Office: NC 03/51 --- Tel.: +49 234 32 26751 --------------050505020908010407060807 Content-Type: multipart/related; boundary="------------040308040909080504040101" --------------040308040909080504040101 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit I use PyMOL (http://www.pymol.org/) a lot, but if you are interested producing images using a space-filling vdW spheres representation, then QuteMol (http://qutemol.sourceforge.net/) produces some very nice pictures with little effort.
The PyMOL wiki contains instructions how to replicate this effect (ambient occlusion shading) in PyMOL, and you can probably do it VMD too, but I don't know how myself.
In fact, you definitely can reproduce the effect in VMD, as illustrated in this article: http://biostumblematic.wordpress.com/2009/12/02/rendering-proteins-in-pymol/ (which also demonstrates the different ray-tracing modes available in PyMOL).

Regards,

Ian.


On 03/09/10 07:18, W. Flak williamflak_-_yahoo.com wrote: 
Sent to CCL by: "W.  Flak" [williamflak++yahoo.com]
Dear CCL
I was wondering which program do you use to present a protein structure in a 
paper?
I use GaussView, but the picture looks sillly
Thanks in advance
W. Flak
--

Dr. Ian M. Grant [ian.grant**ruhr-uni-bochum.de]
Centre for Theoretical Chemistry
Ruhr-Universität Bochum
44780 Bochum, Germany
Office: NC 03/51 — Tel.: +49 234 32 26751
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Content-class: urn:content-classes:message Content-Type: multipart/mixed; boundary="----_=_NextPart_001_01CB4B86.2C6B6834" Date: Fri, 3 Sep 2010 12:31:49 -0400 MIME-Version: 1.0 Sent to CCL by: "Gutsev, Gennady L." [gennady.gutsev+*+famu.edu] This is a multi-part message in MIME format. ------_=_NextPart_001_01CB4B86.2C6B6834 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Sayed, a free Co2 dimer possesses antiferoomagnetic singlet and antiferrimagnetic triplet states [CPL 345, 481 (2001)]. Your complex is likely in an AF singlet state, where occupied 3d-subshells on Co atoms are antiferromagnetically coupled. However, to get this state using, e.g., G03 could be rather tricky. =20 -----Original Message----- > From: owner-chemistry+gennady.gutsev=3D=3Dfamu.edu%a%ccl.net on behalf of = Sayed Mesa elsayed.elmes- -yahoo.com Sent: Fri 9/3/2010 11:05 AM To: Gutsev, Gennady L. Subject: CCL: Antiferromagnetism and multiplicity =20 Sent to CCL by: "Sayed Mesa" [elsayed.elmes_-_yahoo.com] Dear CCL community I measured experimentally the magnetic properties of some dinuclear = transition-metal complexes for example [Co2L]4+ where L is macrocyclic = ligand. I found most of them exhibit "Antiferromagnetic character". I = want to optimize the geometries of these complexes but I am confused how = can I define the multiplicity in such case? It is worth mentioned that = the total number of electrons for the complex or for the ligand is even. = Thanks in advance Sayed -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt------_=_NextPart_001_01CB4B86.2C6B6834-- From owner-chemistry@ccl.net Fri Sep 3 21:39:01 2010 From: "Eduard Matito ematito{}gmail.com" To: CCL Subject: CCL: soft for molecular construction Message-Id: <-42687-100903125907-15440-EBDBcjz64yYBfQ+sGABRNA#%#server.ccl.net> X-Original-From: Eduard Matito Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Fri, 3 Sep 2010 18:58:54 +0200 Mime-Version: 1.0 (Apple Message framework v936) Sent to CCL by: Eduard Matito [ematito-#-gmail.com] Hi, Can anyone recommend me a good *free* software to build up molecules? I would need it to run under Mac and deal with large molecules (say hundreds of atoms). So far I was using molden, but now capabilities such as copy-paste, rotation of translation of small fragments in the molecule would be highly desirable. Thanks in advance, Eduard -- Eduard Matito Postdoctoral researcher Institute of Physics University of Szczecin Wielkopolska 15 70451 Szczecin (Poland) Phone: +48914441436 http://ematito.webs.com From owner-chemistry@ccl.net Fri Sep 3 22:13:01 2010 From: "Serge Gorelsky gorelsky-,-gmail.com" To: CCL Subject: CCL:G: Antiferromagnetism and multiplicity Message-Id: <-42688-100903213220-3661-POE+HMywT4oVjPdm1VBwFw{=}server.ccl.net> X-Original-From: Serge Gorelsky Content-Type: multipart/alternative; boundary=001485f1e28a1d6863048f6504b7 Date: Fri, 3 Sep 2010 21:32:10 -0400 MIME-Version: 1.0 Sent to CCL by: Serge Gorelsky [gorelsky__gmail.com] --001485f1e28a1d6863048f6504b7 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable The issue of generating a proper initial guess for electronic states with antiferromagnetically-coupled metal ions has been discussed in CCL before. For Gaussian 03 calculations, the procedure is fairly straightforward and described in Appendix II of the AOMix manual http://www.sg-chem.net/aomix/AOMix-manual.pdf On Fri, Sep 3, 2010 at 12:31 PM, Gutsev, Gennady L. gennady.gutsev ~ famu.edu wrote: > > Sayed, > > a free Co2 dimer possesses antiferoomagnetic singlet > and antiferrimagnetic triplet states [CPL 345, 481 (2001)]. > Your complex is likely in an AF singlet state, where > occupied 3d-subshells on Co atoms are antiferromagnetically coupled. > However, to get this state using, e.g., G03 could be > rather tricky. > > > -----Original Message----- > > From: owner-chemistry+gennady.gutsev=3D=3Dfamu.edu=C3=8Cl.neton behalf of Sayed Mesa elsayed.elmes- - > yahoo.com > Sent: Fri 9/3/2010 11:05 AM > To: Gutsev, Gennady L. > Subject: CCL: Antiferromagnetism and multiplicity > > > Sent to CCL by: "Sayed Mesa" [elsayed.elmes_-_yahoo.com] > Dear CCL community > I measured experimentally the magnetic properties of some dinuclear > transition-metal complexes for example [Co2L]4+ where L is macrocyclic > ligand. I found most of them exhibit "Antiferromagnetic character". I wan= t > to optimize the geometries of these complexes but I am confused how can I > define the multiplicity in such case? It is worth mentioned that the tota= l > number of electrons for the complex or for the ligand is even. > > Thanks in advance > Sayed > > > > -=3D This is automatically added to each message by the mailing script = =3D-Job= : > http://www.ccl.net/jobs------__NextPart_001_01CB4B86.2C6B6834-- > > > > - This is automatically added to each message by the mailing script -> > --=20 Best regards, Serge Gorelsky --001485f1e28a1d6863048f6504b7 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
The issue of generating a proper initial guess for electronic states w= ith antiferromagnetically-coupled=C2=A0metal ions=C2=A0has been discussed i= n CCL before. For Gaussian 03 calculations, the procedure is fairly straigh= tforward and described in Appendix II of the AOMix manual
=C2=A0
On Fri, Sep 3, 2010 at 12:31 PM, Gutsev, Gennady= L. gennady.gutsev ~ famu.edu <owner-chemistry*ccl.net= > wrote:

Sayed,

a free Co2 dim= er possesses antiferoomagnetic singlet
and antiferrimagnetic triplet sta= tes [CPL 345, 481 (2001)].
Your complex is likely in an AF singlet state, where
occupied 3d-subshel= ls on Co atoms are antiferromagnetically coupled.
However, to get this s= tate using, e.g., G03 could be
rather tricky.


-----Original M= essage-----
> From: owner-chemistry+gennady.gutsev=3D=3Dfamu.edu=C3=8Cl.net on behalf of Sayed = Mesa elsayed.elmes- -yahoo.= com
Sent: Fri 9/3/2010 11:05 AM
To: Gutsev, Gennady L.
Subject: CCL: Antiferromagnetism and multiplicity=


Sent to CCL by: "Sayed =C2=A0Mesa" [elsayed.elmes_-_yahoo.com]
Dear CCL community
I measured experimentally the magnetic properties of = some dinuclear transition-metal complexes for example [Co2L]4+ where L is m= acrocyclic ligand. I found most of them exhibit "Antiferromagnetic cha= racter". I want to optimize the geometries of these complexes but I am= confused how can I define the multiplicity in such case? It is worth menti= oned that the total number of electrons for the complex or for the ligand i= s even.

Thanks in advance
Sayed



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--
Best regards,
= =C2=A0 Serge Gorelsky
--001485f1e28a1d6863048f6504b7--