Dear Fred, In this case, I would take one monomer and edit the CRYST1 card of the pdb to have a sufficiently large tetragonal unit cell. Next I would manually align the helix of one monomer with the fourfold axis, e.g. the Z-axis. If you display the unit cell, you will get e.g. the 0,Z,0 axis to guide you. Then I would manually translate the monomer such that it forms a nice tetramer with its symmetry mates and would write out these symmetry mates. Once you have one good tetramer, you can (or have somebody) write a script to superimpose all your other monomers onto this template.
My two cents,... Herman -----Original Message----- From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Fred Sent: Wednesday, December 14, 2011 3:13 PM To: [email protected] Subject: Re: [ccp4bb] artificial tetramer 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: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > 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 > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.10 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > > iD8DBQFO6G0aUxlJ7aRr7hoRAlMyAJ9ekKa8oatBgpiNsumGCzJtG1Gu9QCgq5Q7 > ZDe36RL5FfSU1usr2p7AZxw= > =QHqV > -----END PGP SIGNATURE-----
