Dear Allen, Sue,
we also have had some luck with ACORN, but as our peptide did not have
alpha-helical structure, the postdoc on the project used a 4-aa
beta-turn fragment instead. I can put you in contact with him for more
details. As I understand it, ACORN uses a mixed MR/direct methods
approach.
We had also tried extensive MR before, but without luck - it appears
peptides often are too different for it.
Mark
Quoting s...@email.arizona.edu:
Have you tried acorn in ccp4? I've had it work well at this resolution,
especially if the protein/peptide has some alpha helical content. We used
acorn to solve a small cro protein that we couldn't get molecular replacement
to work with by using a 5-residue ideal poly-ala helix as the starting model.
Sue
Quoting "Sickmier, Allen" <sickm...@amgen.com>:
I am trying to do molecular replacement on a small peptide (less
than 40 AA) and have not had any success using phaser. Are there
any tricks or better programs for really small peptides?
The data is great 1.1 A, ~35% solvent, and two molecules in the
ASU. I have tried all the standard stuff, changing resolution cut
off etc. I may move to sulfur phasing at this resolution but I
would like to get the MR to work.
Allen
