Dear Dirk, I am not sure which program you are using ;-) , but Coot uses LEU mt Chi1 -65deg and Chi2 174deg and hence CD2 is not anywhere near N. Of course if you use chi2 angle of 51 the situation is different... I assume something else is going wrong here.
B > Dear Tim, > > the mt rotamer in Coot is simply wrong: I really need quite frequently > the correct mt rotamer from Richardson's penultimate rotamer library, > which Coot should be using, according to its documentation. The Coot mt > Chi angles -65, 51 lead to a close contact of CD2 with N of 2.9 A. > The correct mt rotamer with Chi-angles -65, 175 have no close contacts: > CD1-N: 3.7 A, CD2-N: 4.6 A. And it really "looks" correct. > > Best regards, > > Dirk. > > Am 18.06.13 22:52, schrieb Tim Gruene: >> -----BEGIN PGP SIGNED MESSAGE----- >> Hash: SHA1 >> >> Dear Dirk, >> >> it may simply be a different definition of the angles - when I set >> chi2 to 175 degree in the coot mt-rotamer, the CD1 atom is in eclipse >> position with the N atom, so this is probably not a rotamer! You may >> have a reason for flagging one setting wronger than another? >> >> Best, >> Tim >> >> On 06/18/2013 08:11 PM, Dirk Kostrewa wrote: >>> Dear Paul, >>> >>> the leucine "mt" rotamer in Coot 0.7 appears to be wrong: the >>> Richardson penultimate rotamer library says for leucine "mt" >>> Chi1=-65, Chi2=175, but if I choose the leucine "mt" rotamer in >>> Coot, the resulting Chi angles are Chi1=-65, Chi2=51. Could you >>> please check this? >>> >>> Best regards, >>> >>> Dirk. >>> >> - -- >> Dr Tim Gruene >> Institut fuer anorganische Chemie >> Tammannstr. 4 >> D-37077 Goettingen >> >> GPG Key ID = A46BEE1A >> -----BEGIN PGP SIGNATURE----- >> Version: GnuPG v1.4.12 (GNU/Linux) >> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ >> >> iD8DBQFRwMigUxlJ7aRr7hoRAhgAAJ9HkEUZE1NZwI2c8a5Mtwf28zr1xwCfdm9g >> XfIDotbnr8ZMP/s+hDlHxlE= >> =hGeD >> -----END PGP SIGNATURE----- > -- *************************************************** 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]
