Can you clarify your reason for doing this? JPK
On Mon, Dec 12, 2011 at 3:36 PM, Fred <ccp4bb.l...@gmail.com> 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----- -- ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *******************************************
