Hi Liz, Thanks a lot for pointing out the solution: indeed, this seems to be the only angle that needs changing in the ****_mon_lib.cif file.
I tried that earlier and hoped that Coot magically could flip the bond by 180 degrees. This does not work and has to be done by hand, it seems. After that Coot regularizes the structure perfectly in cis. Thanks much for your help! Best, Oliv PS: Many thanks to the people refering to the PRODRG server. PRODRG handles cis bonds perfectly fine and the drawing inferface is also much better. The only reason why I stick with Sketcher is the freedom to provide my own atomnames. On Mon, Jun 15, 2009 at 3:33 AM, Liz Potterton <l...@ysbl.york.ac.uk> wrote: > Hi Oliv, > > I'm sorry, I think you will need to edit the output file from Sketcher > ****_mon_lib.cif - the torsions section ( _chem_comp_tor) will have > something like > > test CONST_1 C1 C2 C3 C4 180.0 0.0 0 > > the 180 needs changing to 0.0. > I think that is all you need to do - no doubt someone will correct me if > I'm wrong! > > Liz > > > On 15 Jun 2009, at 04:35, Oliv Eidam wrote: > > Hi, > > Could somebody explain how to sketch cis double bonds with Sketcher? > For example a cis-but-2-ene? > > No matter how I draw the the molecule: When I create a library description > I always get the trans double bond. > I hope there is way to this through the Sketcher GUI, because I prefer not > to edit the angles by hand... > > Many thanks, > > Oliv > > > -- > 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: eid...@blur.compbio.ucsf.edu > > >
