Hi Mario
Maintaining the secondary structure of your protein when refining against weak
data can be really challenging.
There are some options, but in the end you might have to accept a fairly large
number of Ramachandran plot outliers.
Try phenix.refine with the keyword "discard_psi_phi=False". Then the psi and phi
dihedral angles should be restrained according to the CCP4 monomer library
definitions. There was a discussion of in in the phenixbb in juli 2007.
(http://www.phenix-online.org/pipermail/phenixbb/2007-July/000357.html)
If you are really desperate, another option could be to use harmonic restraints
in CNS to keep your backbone fairly fixed in parts of the map where you believe
the secondary structure is correct (most likely alpha-helices). You could also
fix main chain elements completely (in any refinement program), but it is
definitely preferable to leave some room for change in the xyz-positions, and
harmonic restrains are a nice way of doing exactly that.
Also see the discussion in the ccp4bb from december 2006.
(http://www.dl.ac.uk/list-archive-public/ccp4bb/msg19554.html)
Remember that phi-psi angels are excellent for validation purposes, but only
when they are unrestrained, so if you restrain them you lose this option.
Hope this helps.
-Bjørn
--
Bjørn Pañella Pedersen
Ph.D Student, MSc
Department of Molecular Biology Office: +45 89425021
University of Aarhus Lab: +45 89425010
Gustav Wieds Vej 10c Email: [EMAIL PROTECTED]
DK-8000 Aarhus C Lab WWW: http://www.bioxray.dk
Denmark
Mario Milani wrote:
Hi,
it could be really useful in refining low resolution structure (with
poor electron density map) to have a refinement program that can
restrain phi and psi angles to follow Ramachandran plot. Does anyone
know if such program exist?
Thank you,
mario
Mario Milani, PhD
University of Milan
Dep. of Biomol. Science and Biotech.
Via Celoria 26, 20133 Milan, Italy
T. +39 0250314892-4
F. +39 0250314895
http://digilander.libero.it/mario.milani/
http://users.unimi.it/biolstru/Home.html
