Re: [ccp4bb] refining low resolution structures
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
Re: [ccp4bb] refining low resolution structures
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. The above is a very important point! Having now said that, restraining alpha-helices hydrogen bonding, and beta-sheet cross-strand hydrogen bonds, can be done in REFMAC, Phenix and CNS (its documented for all of them). This seems to be easier to do and helpful, but has to be done with care - like everything in low resolution refinement. A. 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
