From owner-chemistry $#at#$ ccl.net Fri May 15 06:08:01 2009 From: "laxmikanth rao lkjoshiji*|*yahoo.com" To: CCL Subject: CCL: Generating symmetry from where it almost exists... Message-Id: <-39328-090514064715-27505-cXrf0+yYosJwJg32kxlvPQ|server.ccl.net> X-Original-From: laxmikanth rao Content-Type: multipart/alternative; boundary="0-1428823028-1242294417=:66482" Date: Thu, 14 May 2009 15:16:57 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: laxmikanth rao [lkjoshiji- -yahoo.com] --0-1428823028-1242294417=:66482 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Sten=0A=0AGood morning=0A=0AI am a ccl subscribers. Regularly I check = the mails.=0A=0AAs suggusted by use I am able to select the point group and= then I saved the coordinates of the=A0selected symmetry of the molecule us= ing "file/save strucutre in xyz format".=A0=0A=0ATo check symmetry of the t= he saved geom,=A0I used gaussview program, to my surprise it have given sam= e initial symmetry=A0of the molecule not the chemcraft saved symmetry molec= ule.=0A=0APlease suggest how to save the symmetry in chemcraft.=0A=0AThanks= in advance=0A=0ADr. Joshi Laxmikanth Rao=A0=0AIICT, Hyderabad. India=0A=0A= =0A=0A=0A________________________________=0AFrom: Sten Nilsson Lill stenil]= *[chem.gu.se =0ATo: "Rao, J.laxmikanth " <= lkjoshiji-*-yahoo.com>=0ASent: Wednesday, 13 May, 2009 1:32:19 PM=0ASubject: = CCL: Generating symmetry from where it almost exists...=0A=0A=0ASent to CCL= by: "Sten Nilsson Lill" [stenil=3D-=3Dchem.gu.se]=0AJohn,=0A=0A> from my e= xperience Chemcraft is very useful for symmetrizing molecules.=0A=0AYou can= download the program at http://www.chemcraftprog.com/ and it works=0Afor W= indows and Linux.=0A=0AIf you go to the Edit menu there's an option called = "Set Point Group". I=0Anormally let the program suggest the symmetry by usi= ng the "Auto"=0Afunction. There you will get a few point group options to s= elect from. If=0Athe program doesn't include your specific symmetry you can= directly define=0Ait to set the point group you are searching for, just pi= ck it in the menu.=0A=0AHope that helps,=0A=0ASten=0A=0A=0A=0A=0A> Folks,= =0A>=0A> I have a bunch of cartesian geometries that have "almost" C2 symme= try.=0A> Graphical inspection says yhey should be C2 but the code I'm using= won't=0A> generate C2, even with large "out-of-symmetry" threshold values.= =A0 Can=0A> anyone=0A> point me to a simple utility that could be used to c= lean these structures=0A> up?=0A>=0A> Thanks!=0A>=0A> John McKelvey=0A>=0A= =0A=0APh. D. Sten Nilsson Lill=0ADep. of Chemistry=0AUniversity of Gothenbu= rg=0AKemig=E5rden 4=0AS-412 96 G=F6teborg, Sweden=0APhone: +46-31-772 2873= =0AFax: +46-31-772 3840=0AE-mail: stenil{}chem.gu.se=0AAlternative e-mail: = stenil{}physto.se=0A=0A=0A=0A-=3D This is automatically added to each messa= ge by the mailing script =3D-=0ATo recover the email address of the author = of the message, please change=0Athe strange characters on the top line to t= he -*- sign. You can also=0Alook up the X-Original-From: line in the mail hea= der.=0A=0A=0A=A0 =A0 =A0 ht= tp://www.ccl.net/cgi-bin/ccl/send_ccl_message=0A=0AE-mail to administrators= : CHEMISTRY-REQUEST-*-ccl.net or use=0A=A0 =A0 =A0 http://www.ccl.net/cgi-bin= /ccl/send_ccl_message=0A=0A=0A=A0 =A0 =A0 http://www= .ccl.net/chemistry/sub_unsub.shtml=0A=0ABefore posting, check wait time at:= http://www.ccl.net=0A=0A=0AConferences: http:= //server.ccl.net/chemistry/announcements/conferences/=0A=0ASearch Messages:= http://www.ccl.net/chemistry/searchccl/index.shtml=0A=0AIf your mail bounc= es from CCL with 5.7.1 error, check:=0A=A0 =A0 =A0 http://www.ccl.net/spamm= ers.txt=0A=0A=0A= =0A=0A Explore and discover exciting holidays and getaways with Yahoo!= India Travel http://in.travel.yahoo.com/ --0-1428823028-1242294417=:66482 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Sten
=0A
 
=0A
Good morning
= =0A
 
=0A
I am a ccl subscribers. Regularly I check the m= ails.
=0A
 
=0A
As suggusted by use I am able to sel= ect the point group and then I saved the coordinates of the selected s= ymmetry of the molecule using "file/save strucutre in xyz format". =0A
 
=0A
To check symmetry of the the saved geom,&nbs= p;I used gaussview program, to my surprise it have given same initial symme= try of the molecule not the chemcraft saved symmetry molecule.
= =0A
 
=0A
Please suggest how to save the symmetry in chem= craft.
=0A
 
=0A
Thanks in advance
=0A
&nbs= p;
=0A
Dr. Joshi Laxmikanth Rao 
=0A
IICT, Hyderabad= . India
=0A

=0A
=0A
=0A= From: Sten Nilsson Lill ste= nil]*[chem.gu.se <owner-chemistry-*-ccl.net>
To: "Rao, J.laxmikanth " <lkjoshiji-*-yah= oo.com>
Sent: Wednesd= ay, 13 May, 2009 1:32:19 PM
Subject= : CCL: Generating symmetry from where it almost exists...


Sent to CCL by: "Sten Nilsson Lill" [stenil=3D-=3Dchem.gu.se]John,

> from my experience Chemcraft is very useful for symmetr= izing molecules.

You can download the program at http://www.chemcraftprog.com/ an= d it works
for Windows and Linux.

If you go to the Edit menu ther= e's an option called "Set Point Group". I
normally let the program sugge= st the symmetry by using the "Auto"
function. There you will get a few p= oint group options to select from. If
the program doesn't include your speci= fic symmetry you can directly define
it to set the point group you are s= earching for, just pick it in the menu.

Hope that helps,

Sten=




> Folks,
>
> I have a bunch of cartesian= geometries that have "almost" C2 symmetry.
> Graphical inspection sa= ys yhey should be C2 but the code I'm using won't
> generate C2, even= with large "out-of-symmetry" threshold values.  Can
> anyone> point me to a simple utility that could be used to clean these struct= ures
> up?
>
> Thanks!
>
> John McKelvey
&= gt;


Ph. D. Sten Nilsson Lill
Dep. of Chemistry
University = of Gothenburg
Kemig=E5rden 4
S-412 96 G=F6teborg, Sweden
Phone: +4= 6-31-772 2873
Fax: +46-31-772 3840
E-mail: stenil{}chem.gu.se
Alte= rnative e-mail: stenil{}physto.se



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