I've done this sort of thing (but different) using the Clipper libraries in C++. I found it easier to write short programs to do specific tasks rather than try to write generic all-purpose tools Phil
On 14 Dec 2011, at 15:07, Tim Gruene wrote: > -----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-----
