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Dear Paul & Bernhard, I've detected what went wrong here: Coot's mt rotamer has always Chi angles of (-65, 175)! But when I wanted to modifiy the Chi angles with "Edit Chi Angles", apparently, the Chi angles were wrongly displayed. I've cross-checked this with another graphics program, Moloc, and "both" mt rotamers with Chi angles (-65,51) and (-65,-60) had indeed Chi angles of (-65,175)! So, there is no rotamer problem in Coot, but a problem with the displayed Chi angles of the "Edit Chi Angles" function. Best regards, Dirk. Am 19.06.13 10:17, schrieb Dirk Kostrewa: > Dear Bernhard, > > I'm using Coot version 0.7 for Mac OS X (the one from Bill Scott). > > Best regards, > > Dirk. > > Am 19.06.13 10:13, schrieb Bernhard Lohkamp: >> 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----- >> > -- ******************************************************* Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax: +49-89-2180-76999 E-mail: [log in to unmask] WWW: www.genzentrum.lmu.de *******************************************************