[ccp4bb] Idealizing helix
I am looking at a protein model (no electron density) that has a highly distorted helix. I would like to idealize this helix in the context of the protein, e.g. do least squares idealization with restrains on the backbone torsion angles, with the smallest possible divergence from the initial structure. Could someone point me to program that can do it? Mirek
Re: [ccp4bb] Idealizing helix
Refmac should be able to do this without moving stuff too much. CNS (no simulated annealing) also can do this kind of thing. If it becomes problematic, you can restrain the backbone. You can also do this via coot (which uses refmac I am pretty sure). William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/ On Jul 30, 2008, at 1:51 PM, Mirek Cygler wrote: I am looking at a protein model (no electron density) that has a highly distorted helix. I would like to idealize this helix in the context of the protein, e.g. do least squares idealization with restrains on the backbone torsion angles, with the smallest possible divergence from the initial structure. Could someone point me to program that can do it? Mirek
Re: [ccp4bb] Idealizing helix
Can try HELANAL Thanks and Regards -- ARNAB BHATTACHARJEE Dept. of Bacteriology and Immunology SERO Group, Haartman Institute Haartmaninkatu 3 University of Helsinki FIN-00014 HELSINKI Tel. +358-9-191 26385 Fax. +358-9-191 26382 Structural Biology and Biophysics Macromolecular X-ray Crystallography Group Institute of Biotechnology. Biocenter: 3, Viikinkari 1 University of Helsinki FIN-00790 HELSINKI Tel. +358-9-191 58922 Fax +358-9-191 59940 On 30 Jul 2008, at 23:51, Mirek Cygler wrote: I am looking at a protein model (no electron density) that has a highly distorted helix. I would like to idealize this helix in the context of the protein, e.g. do least squares idealization with restrains on the backbone torsion angles, with the smallest possible divergence from the initial structure. Could someone point me to program that can do it? Mirek
