From owner-chemistry@ccl.net Sun Apr 12 02:18:00 2009 From: "Farhan Pasha pashafa=-=yahoo.co.in" To: CCL Subject: CCL: chemcraft, cubegen and density Message-Id: <-39065-090412021522-7416-S2Vr3CvhRXlKBoA0eyvlgQ .. server.ccl.net> X-Original-From: Farhan Pasha Content-Type: multipart/alternative; boundary="0-353746669-1239516897=:42824" Date: Sun, 12 Apr 2009 11:44:57 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: Farhan Pasha [pashafa]~[yahoo.co.in] --0-353746669-1239516897=:42824 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable hi =A0 have you tried keyword pop=3Dfull guess=3Dsave =A0 cheers=20 pasha Correspondence Address Dr. Syed Farhan Ahmad Pasha Room No. 5202 Institut de Biologie Structurale Laboratoire de Dynamique Moleculaire 41 rue Jules Horowitz 38027 Grenoble cedex France tel : (+33) (0)4 38 78 99 28 fax : (+33) (0)4 38 78 54 94 fpasha(~)rediffmail.com URL:www.geocities.com/pashafa www.ibs.fr --- On Sat, 11/4/09, Madi madi7sk _ gmail.com wro= te: > From: Madi madi7sk _ gmail.com Subject: CCL: chemcraft, cubegen and density To: "Pasha, Frahan Ahmad " Date: Saturday, 11 April, 2009, 9:08 PM Sent to CCL by: Madi [madi7sk-.-gmail.com] Hi All I am sorry about not wording the question properly. I meant to ask how to see regions of high and low electron densities. Right now i am able to see only one colored blob on the molecule. Thanks madi On Sat, Apr 11, 2009 at 9:53 AM, Madhavan Narayanan madi7sk_._gmail.com wrote: > > Sent to CCL by: "Madhavan =A0Narayanan" [madi7sk * gmail.com] > Hi, > > I converted my check point file to .fchk and then to .cube. > Then I tried opening it in chemcraft. When I opened it to view the electr= on density, I see only atoms with positive density. How do I get it to show= me both positive and negative regions? I am very new to this and would app= reciate any help. > > Thank you > Madi > > > > -=3D This is automatically added to each message by the mailing script = =3D-> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 = =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.c= cl.net/chemistry/sub_unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.tx= t> > > -- -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0=A0 =A0 =A0=A0 =A0 =A0=0A=0A=0A Add more friends to your messenger and enjoy! Go to http://m= essenger.yahoo.com/invite/ --0-353746669-1239516897=:42824 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
hi
 
have you tried keyword
pop=3Dfull guess=3Dsave
 
cheers
pasha

Correspondence Address
Dr. Syed Farhan Ahmad Pasha
= Room No. 5202
Institut de Biologie Structurale
Laboratoire de Dynamiq= ue Moleculaire
41 rue Jules Horowitz
38027 Grenoble cedex
Francetel : (+33) (0)4 38 78 99 28
fax : (+33) (0)4 38 78 54 94
fpasha(~)re= diffmail.com
URL:www.geocities.com/pashafa
www.ibs.fr

--- On <= B>Sat, 11/4/09, Madi madi7sk _ gmail.com <owner-chemistry(~)ccl.net>= wrote:

From: Madi madi7sk _ gmail.com <owner-chemistr= y(~)ccl.net>
Subject: CCL: chemcraft, cubegen and density
To: "Pasha= , Frahan Ahmad " <pashafa(~)yahoo.co.in>
Date: Saturday, 11 = April, 2009, 9:08 PM


Sent to CCL by: Madi [madi7sk-.-gmail.com]
Hi= All
I am sorry about not wording the question properly.
I meant to a= sk how to see regions of high and low electron densities.
Right now i am= able to see only one colored blob on the molecule.

Thanks
madiOn Sat, Apr 11, 2009 at 9:53 AM, Madhavan Narayanan
madi7sk_._gmail.co= m <owner-chemistry[#]ccl.net> wrote:
>
> Sent to CCL by: = "Madhavan  Narayanan" [madi7sk * gmail.com]
> Hi,
>
>= ; I converted my check point file to .fchk and then to .cube.
> Then = I tried opening it in chemcraft. When I opened it to view the electron dens= ity, I see only atoms with positive density. How do I get it to show me bot= h positive and negative regions? I am very new to this and would appreciate= any help.
>
> Thank you
> Madi
>
>
>> -=3D This is automatically added to each message by the mailing script =3D->      http://www.ccl.net/cgi-bin/ccl/send_c= cl_message>      http://www.ccl.net/cgi-bin/ccl/send= _ccl_message>      http://www.ccl.net/chemistry/sub_uns= ub.shtml>      http://www.ccl.net/spammers.txt>
>
&g= t;



--



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=0A
Add more friends to your messenger an= d enjoy! Invite them now. --0-353746669-1239516897=:42824-- From owner-chemistry@ccl.net Sun Apr 12 13:00:00 2009 From: "Madi madi7sk^_^gmail.com" To: CCL Subject: CCL: chemcraft, cubegen and density Message-Id: <-39066-090412121627-6467-x3mP5+jP8Fd5l0jGtHKbAA]-[server.ccl.net> X-Original-From: Madi Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Sun, 12 Apr 2009 12:16:11 -0400 MIME-Version: 1.0 Sent to CCL by: Madi [madi7sk-,-gmail.com] Hi pasha I tried that. the converted fchk and then to cube and opened in chemcraft and it still does not work. thank you Madi On 4/12/09, Farhan Pasha pashafa=-=yahoo.co.in wrote: > hi > > have you tried keyword > pop=full guess=save > > cheers > pasha > > Correspondence Address > Dr. Syed Farhan Ahmad Pasha > Room No. 5202 > Institut de Biologie Structurale > Laboratoire de Dynamique Moleculaire > 41 rue Jules Horowitz > 38027 Grenoble cedex > France > tel : (+33) (0)4 38 78 99 28 > fax : (+33) (0)4 38 78 54 94 > fpasha .. rediffmail.com > URL:www.geocities.com/pashafa > www.ibs.fr > > --- On Sat, 11/4/09, Madi madi7sk _ gmail.com > wrote: > > >> From: Madi madi7sk _ gmail.com > Subject: CCL: chemcraft, cubegen and density > To: "Pasha, Frahan Ahmad " > Date: Saturday, 11 April, 2009, 9:08 PM > > > > Sent to CCL by: Madi [madi7sk-.-gmail.com] > Hi All > I am sorry about not wording the question properly. > I meant to ask how to see regions of high and low electron densities. > Right now i am able to see only one colored blob on the molecule. > > Thanks > madi > On Sat, Apr 11, 2009 at 9:53 AM, Madhavan Narayanan > madi7sk_._gmail.com wrote: >> >> Sent to CCL by: "Madhavan Narayanan" [madi7sk * gmail.com] >> Hi, >> >> I converted my check point file to .fchk and then to .cube. >> Then I tried opening it in chemcraft. When I opened it to view the >> electron density, I see only atoms with positive density. How do I get it >> to show me both positive and negative regions? I am very new to this and >> would appreciate any help. >> >> Thank you >> Madi> >> >> > > > > --> > > > Add more friends to your messenger and enjoy! Go to > http://messenger.yahoo.com/invite/ -- Asha for Education: Shall we labor so a child won't? http://www.workanhour.com From owner-chemistry@ccl.net Sun Apr 12 14:27:01 2009 From: "Close, David M. CLOSED##mail.etsu.edu" To: CCL Subject: CCL: chemcraft, cubegen and density Message-Id: <-39067-090412142224-13087-hz6zSyWO8BcAFu4LKT3poQ!A!server.ccl.net> X-Original-From: "Close, David M." Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Sun, 12 Apr 2009 14:22:01 -0400 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED(0)mail.etsu.edu] Madi: When you open the .cube file, does a work area appear on the left that = says "Electron Density from Spin" ? If so, move down to the choice = "Show Isosurface, and then click on the "Both Signed" option to the = right. You still may not see what you want because the Contour Value is = too big. Click on the Contour Value to make it below say 0.0008, and = you should see positive and negative spin densities. Regards, Dave Close. -----Original Message----- > From: owner-chemistry+closed=3D=3Detsu.edu()ccl.net = [mailto:owner-chemistry+closed=3D=3Detsu.edu()ccl.net] On Behalf Of Madi = madi7sk _ gmail.com Sent: Saturday, April 11, 2009 11:38 AM To: Close, David M. Subject: CCL: chemcraft, cubegen and density Sent to CCL by: Madi [madi7sk-.-gmail.com] Hi All I am sorry about not wording the question properly. I meant to ask how to see regions of high and low electron densities. Right now i am able to see only one colored blob on the molecule. Thanks madi On Sat, Apr 11, 2009 at 9:53 AM, Madhavan Narayanan madi7sk_._gmail.com wrote: > > Sent to CCL by: "Madhavan =A0Narayanan" [madi7sk * gmail.com] > Hi, > > I converted my check point file to .fchk and then to .cube. > Then I tried opening it in chemcraft. When I opened it to view the = electron density, I see only atoms with positive density. How do I get = it to show me both positive and negative regions? I am very new to this = and would appreciate any help. > > Thank you > Madi > > > > -=3D This is automatically added to each message by the mailing script = =3D-> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 = =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 = =A0http://www.ccl.net/chemistry/sub_unsub.shtml> =A0 =A0 = =A0http://www.ccl.net/spammers.txt> > > -- -=3Dhis is automatically added to each message by the mailing script =3Dhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Sun Apr 12 16:56:00 2009 From: "Madi madi7sk]^[gmail.com" To: CCL Subject: CCL: chemcraft, cubegen and density Message-Id: <-39068-090412165200-12566-MQwEw5E67ds5F8ifYeK1aA_+_server.ccl.net> X-Original-From: Madi Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Sun, 12 Apr 2009 16:51:46 -0400 MIME-Version: 1.0 Sent to CCL by: Madi [madi7sk]*[gmail.com] Hi David, It says "Electron density from Total SCF Density" on the left work area. Is there a command line that i need to use during the making of cube file to get "electron density from spin"?. I tried changing the contour value to 0.0008. the blob gets much bigger. when I go to higher contour values, size of the blobs become smaller. The blob stays in single colour though. There are other parameters such as values range and scale. Are there appropriate settings for those that i need to use? Thank you for your help Madi On Sun, Apr 12, 2009 at 2:22 PM, Close, David M. CLOSED##mail.etsu.edu wrote: > > Sent to CCL by: "Close, David M." [CLOSED(0)mail.etsu.edu] > Madi: > =A0When you open the .cube file, does a work area appear on the left that= says "Electron Density from Spin" ? =A0If so, move down to the choice "Sho= w Isosurface, and then click on the "Both Signed" option to the right. =A0Y= ou still may not see what you want because the Contour Value is too big. = =A0Click on the Contour Value to make it below say 0.0008, and you should s= ee positive and negative spin densities. > =A0Regards, Dave Close. > > -----Original Message----- >> From: owner-chemistry+closed=3D=3Detsu.edu**ccl.net [mailto:owner-chemis= try+closed=3D=3Detsu.edu**ccl.net] On Behalf Of Madi madi7sk _ gmail.com > Sent: Saturday, April 11, 2009 11:38 AM > To: Close, David M. > Subject: CCL: chemcraft, cubegen and density > > > Sent to CCL by: Madi [madi7sk-.-gmail.com] > Hi All > I am sorry about not wording the question properly. > I meant to ask how to see regions of high and low electron densities. > Right now i am able to see only one colored blob on the molecule. > > Thanks > madi > On Sat, Apr 11, 2009 at 9:53 AM, Madhavan Narayanan > madi7sk_._gmail.com wrote: >> >> Sent to CCL by: "Madhavan =A0Narayanan" [madi7sk * gmail.com] >> Hi, >> >> I converted my check point file to .fchk and then to .cube. >> Then I tried opening it in chemcraft. When I opened it to view the elect= ron density, I see only atoms with positive density. How do I get it to sho= w me both positive and negative regions? I am very new to this and would ap= preciate any help. >> >> Thank you >> Madi >> >> >> >> -=3D This is automatically added to each message by the mailing script = =3D-> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 = =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.c= cl.net/chemistry/sub_unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.tx= t> >> >> > > > > -- > > > > -=3Dhis is automatically added to each message by the mailing script =3Dh= ttp://www.ccl.net/cgi-bin/ccl/send_ccl_messageJob: h= ttp://www.ccl.net/jobs> > > - This is automatically added to each message by the mailing script -> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.txt> > >