-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hello Fred,
as far as I understand your problem I am not aware of existing programs to carry out the tasks. To automatise the process I would write a program myself which takes the PDB-file and the reside numbers which make that helix as input and: 1) determine the axis of that straight helix (probably by determining the moments of intertia, see e.g. Gruene, T. & Sheldrick, G. M. (2011). Acta Cryst. A67, 1-8, section 2.2.1 with x_o the centre of mass. 2) copy the monomer by 3 rotations of 90 degrees about this axis to get the tetramer. 3) move each of the four monomers stepwise perpendicularly to the rotation axis until no more clashes are there (mask the volume of one monomer and check each atom/atom volume whether it falls into that volume. Because of the 4-fold rotation axis you only need to mask one monomer and check against its next and its opposite neighbour). The tricky bit w.r.t automatisation would be to determine the helix axis, unless you already have a list of composing residues for each PDB-file. That's probably nothing I would finish in a week's time, though... Tim On 12/14/2011 03:13 PM, Fred wrote: > Hi Tim, > Thanks for your replay. All pdb monomers have the same primary sequence > and a perfect matching long helix, which I have used to superpose the > coordinates. Such helix is almost straight so that, the idea would be to > create a vector along the helix main axis, shift this axis to a some > distance (perhaps minimizing clashes) and apply 4-fold rotation. A > second step would be to take these into pdbset to make things in batch > mode. It sounds simple, but don't know the easiest way/programs to do > that. I can do just the basics in Coot. I remember that Xfit had some > options to trace vectors inside a cell and give it rotation properties. > However, Xfit seems to be frozen and integration with pdbset would be > painful. > Regards, > Fred > > Em 14-12-2011 07:32, Tim Gruene escreveu: > Hi Fred, > > this sentence of yours, "All pdb's are superposed by a common sequence > region, which also will be part of the tetramer interface." probably > hides the information which would be necessary for a reasonable answer > to your question. > > If you still are stuck, you might post again with a more detailed > description of what you mean. > > Cheers, Tim > > On 12/13/2011 07:28 PM, Fred wrote: >>>> Dear CCP4bb list, >>>> Thank you very much all of you who have answered my post. I'm really >>>> sorry if I was unclear. Such operation is so unusual that I could be >>>> able to express myself appropriately. From quick reading some replies >>>> (James Stroud and Guillaume Ponchel), it seems is possible do build >>>> artificial tetramers with Coot. Several problems have been raised like >>>> clashes, unusual interfaces and so on. A second step would be to take >>>> Coot's rotation and translation matrix and apply it to all pdb's in >>>> batch mode with pdbset. All pdb's are superposed by a common sequence >>>> region, which also will be part of the tetramer interface. I'll try to >>>> make things work. >>>> Once more, sorry for any inconvenience and thank you very much. >>>> Kind regards, >>>> Fred >>>> > -- - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > - -- - -- 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/ iD8DBQFO6LusUxlJ7aRr7hoRAk5QAJ0ewv3ZjLRSU9fF1c2xBDDypcLX6ACg5+2P X01grlPsYcSeWZbQWIVtXD0= =Fse5 -----END PGP SIGNATURE-----
