Hej Bernhard, Thanks a lot! It works well to do it as below.
Best regards, Maria 9 Jan 2013 kl. 13:24 skrev Bernhard Lohkamp <[email protected]>: Hej Maria, Coot uses by default libcheck to generate the restraints from smiles strings. It appears that there is a bug in libcheck which does not give an ideally regularised structure (trapped in a local mninimum). The restraints seem to be correct however. Deleting the hydrogens and doing a refinement/regularization will result in an undistorted structure (so does moving of the distorted hydrogens in Coot). B > We have problems with generating structures in coot from smiley strings. > The small structures (even simple stuff like an aromatic ring - smiley string > c1ccccc1) > does not work. The structures that appear are distorted and are not possible > to regularize in a > proper way. > > We are using Coot version 0.7-pre. > > Any suggestions? > > Best regards, > > Maria > > > Maria Håkansson, phD, MAX-lab Crystallization Facility Manager > Senior Scientist > > SARomics Biostructures AB > Scheelevägen 22 > P.O. Box 724 > SE-220 07 Lund, Sweden > > Cellular: +46 768 585 706 > Direct: +46 46 222 4365 > Fax: +46 46 19 12 77 > -- *************************************************** Dr. Bernhard Lohkamp Assistant Professor Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: [email protected] > > > Maria Håkansson, PhD, MAX-lab Crystallization Facility Manager > Senior Scientist > > SARomics Biostructures AB > Medicon Village > SE-223 81 Lund, Sweden > > > Cellular: +46 768 585 706 > Direct: +46 46 222 4365 > Web: www.saromics.com >
