Hi Jon, Recently, I had the same problem: http://www.mail-archive.com/[email protected]/msg11138.html
I suspect that Sketcher will always give you the trans isomer. Therefore, you have to edit the torsion angle in ****_mon_lib.cif manually as indicated by Liz Potterton in the previous post. Then you load the pdb generated by sketcher (with trans bonds) into coot, model cis bonds manually and regularize. Coot will regularize cis bonds according to the edited cif file. Good luck, Oliv On Thu, Feb 25, 2010 at 9:52 PM, SUBSCRIBE CCP4BB Anonymous < [email protected]> wrote: > Hi, > > I'm using Sketcher to create the following: > > C=C C=C > / \ / \ > C C C > > The problem is that I can't figure out how to keep the carbons cis. I see > the "Add Row" button in Sketcher and I can specify the "Sign." There are > also spaces to fill in "B/3" F/4" "1/5" "2/6" which I assume assigns > priority. So how do I actually implement what I want to do? I've read the > manual, fiddled with settings, and found an old post on a similar subject > but I still cant get my bonds to hold after creating a library. > > Old Post: > Sketcher and stereochemistry - Mon, 19 Mar 2007 > > Thanks for any ideas! > -Jon > -- Oliv Eidam, Ph.D. Postdoctoral fellow University of California, San Francisco Dept. of Pharmaceutical Chemistry 1700 4th Street, Byers Hall North, Room 501 San Francisco, CA 94158 - Box 2550 Phone: 415-514-4253 Fax : 415-514-4260 Email: [email protected]
