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
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***************************************************
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]
