From owner-chemistry@ccl.net Thu Mar 3 02:49:00 2011 From: "Adam Kubas ad.kubas()gmail.com" To: CCL Subject: CCL: software to visualize Gaussian cube files Message-Id: <-44042-110303024658-25501-ZYTHldgG3BcBP2czlrZ18Q!=!server.ccl.net> X-Original-From: Adam Kubas Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 3 Mar 2011 08:46:48 +0100 MIME-Version: 1.0 Sent to CCL by: Adam Kubas [ad.kubas.:.gmail.com] Dear Neranjan, you can try VMD: http://www.ks.uiuc.edu/Research/vmd/ you have to load your cube file to the xyz structure file and then create isosurface representation for both signs Adam From owner-chemistry@ccl.net Thu Mar 3 05:23:00 2011 From: "Vlad vvv900-$-anusf.anu.edu.au" To: CCL Subject: CCL:G: software to visualize Gaussian cube files Message-Id: <-44043-110303052122-24561-Uc3SV6Ky311L5FRce+lt5A()server.ccl.net> X-Original-From: Vlad Content-transfer-encoding: 7BIT Content-type: text/html; CHARSET=US-ASCII Date: Thu, 03 Mar 2011 21:20:17 +1100 MIME-version: 1.0 Sent to CCL by: Vlad [vvv900+*+anusf.anu.edu.au] Hi Neranjan,

> Hi all, I
> would like to know is there any software that can be used to
> visualize gaussian cube files which can show molecular orbitals?

Jamberoo can do it.

Regards,
Vlad
From owner-chemistry@ccl.net Thu Mar 3 07:54:00 2011 From: "Joaquin Calbo HimPhoenixCCL()gmail.com" To: CCL Subject: CCL:G: Lone pair location Message-Id: <-44044-110303050110-12739-ml7wDo7lnGCCvO5H0WS/1A(0)server.ccl.net> X-Original-From: "Joaquin Calbo" Date: Thu, 3 Mar 2011 05:01:08 -0500 Sent to CCL by: "Joaquin Calbo" [HimPhoenixCCL|-|gmail.com] Hello, I would like to know about if exists any calculations in Gaussian09 that help me to locate or visualize lone pair electrons in order to assign the atom hybridation (O, S, N..). I tried with NBO analysis but I can't extract that information from it. Thank you all. From owner-chemistry@ccl.net Thu Mar 3 08:29:00 2011 From: "Daniel Jana dfjana^gmail.com" To: CCL Subject: CCL:G: software to visualize Gaussian cube files Message-Id: <-44045-110303040819-4549-zXpn6U2Apgrkmte6mKz56A]|[server.ccl.net> X-Original-From: Daniel Jana Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 3 Mar 2011 10:08:11 +0100 MIME-Version: 1.0 Sent to CCL by: Daniel Jana [dfjana!^!gmail.com] Hello, VMD does a good job at displaying cube files: http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD You need to tell it to display a "Isosurface", choose a "Isovalue" (or two, one positive and one negative) and potentially choose "Solid Surface" in the "Draw" menu. Since VMD has really nice rendering capabilities and plugins (you can, for instance export to PovRAY or other raytracers, you get really good looking pictures. Depending on what you want to do and how much time you want to invest, OpenDX can also be a tool for it. The cube file format is very similar to the native format of OpenDX so it doesn't take long until you have something: http://www.opendx.org/ It does take substantially longer to do anything more than the basic isosurface observation, if you don't know how to use it... An example of what can be done (with a cube like file): http://mrna.ist.utl.pt/~jana/full.png Daniel On 2 March 2011 18:58, Neranjan Perera neranjan007^^gmail.com wrote: > > Sent to CCL by: "Neranjan  Perera" [neranjan007++gmail.com] > Hi all, > I would like to know is there any software that can be used to visualize gaussian cube files which can show molecular orbitals? > > I am using 09 and tried using gopenmol and molden to visualize but it doesn't work at all. In gopenmol, I created the *.plt file and the *.crd files and tried to visualize it but when i tried to import the *.plt file , the program crashed. > >  thanks for the help. > > neranjan>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Thu Mar 3 09:03:00 2011 From: "pascal boulet pascal.boulet]|[univ-provence.fr" To: CCL Subject: CCL:G: software to visualize Gaussian cube files Message-Id: <-44046-110303074158-15628-EcPAruBmMLVdpObB+93CAA]![server.ccl.net> X-Original-From: pascal boulet Content-Transfer-Encoding: 7bit Content-Type: text/html; charset=ISO-8859-1 Date: Thu, 03 Mar 2011 13:41:42 +0100 MIME-Version: 1.0 Sent to CCL by: pascal boulet [pascal.boulet%univ-provence.fr]
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Hash: SHA1

Hello,

There are many: molekel, VMD, gabedit, molden, ...

regards
Pascal


Le 03/03/2011 11:20, Vlad vvv900-$-anusf.anu.edu.au a écrit :
> Sent to CCL by: Vlad [vvv900+*+anusf.anu.edu.au] Hi Neranjan,
>
> > Hi all, I
>
> > would like to know is there any software that can be used to
>
> > visualize gaussian cube files which can show molecular
> orbitals?
>
>
> Jamberoo <http://sf.anu.edu.au/%7Evvv900/cct/appl/jmoleditor/index.html> can do it.
>
> Regards,
> Vlad
>E-mail to subscribers: CHEMISTRY[#]ccl.net or use: http://www.ccl.net/cgi-bin/ccl/send_ccl_message E-mail to administrators: CHEMISTRY-REQUEST[#]ccl.net or use http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtml Before posting, check wait time at: http://www.ccl.net Job: http://www.ccl.net/jobs Conferences: http://server.ccl.net/chemistry/announcements/conferences/ Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtmlhttp://www.ccl.net/spammers.txt RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/

- --
Dr. pascal Boulet, computational chemist
University of Aix-Marseille I
Laboratoire Chimie Provence, UMR 6264
Group of Theoretical Chemistry
Avenue Normandie-Niemen
13397 Marseille Cedex 20
France
**********
Tel. (+33) (0)491.63.71.17
Fax. (+33) (0)491.63.71.11
**********
http://www.lc-provence.fr
https://sites.google.com/a/univ-provence.fr/pb-comput-chem
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From owner-chemistry@ccl.net Thu Mar 3 10:49:00 2011 From: "Fuming Ying fmying**gmail.com" To: CCL Subject: CCL:G: software to visualize Gaussian cube files Message-Id: <-44047-110303075206-2776-g1HPLHiiW5mZlgPUlPutBw---server.ccl.net> X-Original-From: Fuming Ying Content-Type: multipart/alternative; boundary="------------040708060804020602010109" Date: Thu, 03 Mar 2011 20:51:49 +0800 MIME-Version: 1.0 Sent to CCL by: Fuming Ying [fmying**gmail.com] This is a multi-part message in MIME format. --------------040708060804020602010109 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit ? 2011?03?03? 18:20, Vlad vvv900-$-anusf.anu.edu.au ??: > Sent to CCL by: Vlad [vvv900+*+anusf.anu.edu.au] Hi Neranjan, > > > Hi all, I > > > would like to know is there any software that can be used to > > > visualize gaussian cube files which can show molecular > orbitals? > > > Jamberoo > can do it. > > Regards, > Vlad > -= This is automatically added to each message by the mailing script > =- To recover the email address of the author of the message, please > change the strange characters on the top line to the -#- sign. You can > alsoE-mail to > subscribers: CHEMISTRY-#-ccl.net or use:E-mail to > administrators: CHEMISTRY-REQUEST-#-ccl.net or useBefore posting, check > wait time at: http://www.ccl.net> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ Search > Messages: http://www.ccl.net/chemistry/searchccl/index.shtml If your > mail bounces from CCL with 5.7.1 error, check:RTFI: > http://www.ccl.net/chemistry/aboutccl/instructions/ I will recommend VMD, which is totally free to download and use. --------------040708060804020602010109 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit 于 2011年03月03日 18:20, Vlad vvv900-$-anusf.anu.edu.au 写道:
Sent to CCL by: Vlad [vvv900+*+anusf.anu.edu.au] Hi Neranjan,

> Hi all, I

> would like to know is there any software that can be used to

> visualize gaussian cube files which can show molecular
orbitals?


Jamberoo can do it.

Regards,
VladCHEMISTRY-#-ccl.net or use: http://www.ccl.net/cgi-bin/ccl/send_ccl_message E-mail to administrators: CHEMISTRY-REQUEST-#-ccl.net or use http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtml Before posting, check wait time at: http://www.ccl.net Job: http://www.ccl.net/jobs Conferences: http://server.ccl.net/chemistry/announcements/conferences/ Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtmlhttp://www.ccl.net/spammers.txt RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/
I will recommend VMD, which is totally free to download and use.
--------------040708060804020602010109-- From owner-chemistry@ccl.net Thu Mar 3 17:54:00 2011 From: "Robin A Haw robin.haw{=}oicr.on.ca" To: CCL Subject: CCL: Reactome Pathway Database User Survey Message-Id: <-44048-110303153251-15974-qg8k9Ry9dySwVVTKSBKMWA#server.ccl.net> X-Original-From: "Robin A Haw" Date: Thu, 3 Mar 2011 15:32:48 -0500 Sent to CCL by: "Robin A Haw" [robin.haw_-_oicr.on.ca] We appreciate your assistance in evaluating Reactome. Your responses will give us an indication of the effectiveness of the Reactome website and tools, and areas in which improvement could be made. We would like to know a bit about your background and research interests and welcome your written comments and suggestions. The survey should take about 5 minutes to complete. The information you provide will never be made publicly available or shared with third parties. Participation in the survey is optional. However, five lucky participants who complete the survey will receive a Reactome T-shirt. You can access the survey at: https://www.surveymonkey.com/s/RV63355 Thank you for taking part. Regards, Robin Haw Robin Haw, PhD Scientific Associate Manager of Reactome Outreach Ontario Institute for Cancer Research MaRS Centre, South Tower 101 College Street, Suite 800 Toronto, Ontario, Canada M5G 0A3 Tel: 647-260-7985 Toll-free: 1-866-678-6427 http://www.oicr.on.ca http://www.reactome.org This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization. From owner-chemistry@ccl.net Thu Mar 3 20:18:00 2011 From: "Wojciech Kolodziejczyk dziecial,icnanotox.org" To: CCL Subject: CCL: software to visualize Gaussian cube files Message-Id: <-44049-110303200655-11542-7Z8Unu67elR0eX/wrmpP6w~!~server.ccl.net> X-Original-From: Wojciech Kolodziejczyk Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 4 Mar 2011 02:06:48 +0100 MIME-Version: 1.0 Sent to CCL by: Wojciech Kolodziejczyk [dziecial]^[icnanotox.org] The programs that can visualize cube files are molden or gmolden (openGL version of molden) and of course GaussView The second is better and you can make it easier W.