Coot can do this using the Rubik's Cube principle: transform to some state where the operation can be performed, perform the operation, then transform back.
So, in coot, I would (1) rotate the molecule to the appropriate orientation (2) move to the appropriate place in the unit cell (3) change the symmetry to P4 (3) apply P4 symmetry (4) change the symmetry back to whatever (5) move the tetramer back to the appropriate place in the unit cell (6) rotate the molecule back Then, your original molecule will be in the original place surrounded by it's symmetry mates. James On Dec 12, 2011, at 2:36 PM, Fred wrote: > Hi James, > In my first post "arbitrary orientation into the cell" only means not > parallel to any crystallographic axis, which would simplify things very much. > I want to apply the 4-fold axis to the protein coordinates. If I have a cell > and therefore an origin, I can take a point at any distance of the origin, > pass a vector/axis through it and take the 3 others molecules by symmetry. > That's trivial, given the point, the orientation and the property of the > rotation. Don't know which program to use. > Regards, > Fred > > > > Em 12-12-2011 19:18, James Stroud escreveu: >> This is not trivial. Assuming an arbitrary origin, the simplest 4-fold >> symmetry operation (4-fold rotation) has 5 free parameters (translation >> along the symmetry axis is irrelevant). The biggest problem is determining >> the values for these parameters. For example, once you apply the symmetry, >> your molecule may clash with its symmetry mates or not even contact them. >> And even if you solve this latter problem automatically (which is not >> trivial because of irregularity), that leaves a net of 3 parameters >> describing the orientation of the protomer. >> >> James >> >> >> >> On Dec 12, 2011, at 1:34 PM, Fred wrote: >> >>> Hi Tim, >>> Thanks for your message and sorry if I wasn't clear. I don't have neither >>> the axis orientation nor the rotation matrix. I would like to create them >>> but don't know how and which program to use. Theoretically a have to create >>> a axis (vector) at some distance of the molecule into the cell and give it >>> the 4-fold propriety. Quite simple, but don't which program to use. >>> Regards, >>> Fred >>> >>> >>> Em 12-12-2011 18:23, Tim Gruene escreveu: >>>> -----BEGIN PGP SIGNED MESSAGE----- >>>> Hash: SHA1 >>>> >>>> Hello Fred, >>>> >>>> if you know the rotation matrix, you can use pdbset with its 'rotate' >>>> keyword. >>>> It is not clear to me whether or not you have the rotation matrix or how >>>> you define rotation. >>>> >>>> Cheers, >>>> Tim >>>> >>>> On 12/12/2011 08:49 PM, Fred wrote: >>>>> Hi List, >>>>> I would like to build an artificial tetramer from a monomer PBD file. >>>>> All that I have is the coordinates it self with CRYST/CELL information >>>>> cards. The artificial 4-fold axis has an arbitrary orientation into the >>>>> cell. I mean, its not parallel to any crystallographic axis and have to >>>>> be at a certain distance of the molecule. This sounds conceptually >>>>> simple, but I would like to do that in batch mode for hundreds of PDB's. >>>>> Could someone, please, tell me the easiest way/program to do that? >>>>> Thanks in advance, >>>>> Fred >>>>> >>>> - -- - -- >>>> Dr Tim Gruene >>>> Institut fuer anorganische Chemie >>>> Tammannstr. 4 >>>> D-37077 Goettingen >>>> >>>> GPG Key ID = A46BEE1A >>>> >>>> -----BEGIN PGP SIGNATURE----- >>>> Version: GnuPG v1.4.10 (GNU/Linux) >>>> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ >>>> >>>> iD8DBQFO5mKwUxlJ7aRr7hoRAsyuAKDfnH50sG/EuKiFz7tCzgTUtnZrdQCg3zSn >>>> cqs8GHOu5M3JQahA/CofR1k= >>>> =tDUj >>>> -----END PGP SIGNATURE----- >
