Hello, You can also contact elNemo or NOMAD-Ref server developers about getting covariance/correlation matrices from normal mode analysis outputs to know the correctly coordinated mobile atoms. In this way you can compare with biological data also. In Shekhar's said paper K. Suhre (one of the developer of el-Nemo server) has done the same very correctly.
best wishes, Arpita On Tue, Oct 21, 2014 at 5:40 AM, Appu kumar <appu.kum...@gmail.com> wrote: > Dear CCP4 Users, > I seek your valuable advice and suggestion in carrying out the normal mode > structure refinement which manifest the dynamics of protein as linear > combination of harmonic modes, used to describe the motion of protein > structure in collective fashion. Studies suggest that it is highly useful > in refining the protein structure which harbors a considerable magnitude of > flexibility in atomic position owing to high thermal factors. > Therefor I want to know is there any software/script available to execute > the normal mode of refinement. Thanks a lot in advance for your imperative > suggestions > > Appu > -- Arpita -- Arpita Goswami Senior Research Fellow Structural Biology Laboratory Centre for DNA Fingerprinting and Diagnostics (CDFD) Tuljaguda (Opp MJ Market), Nampally, Hyderabad 500 001 INDIA Phone: +91- 40- 24749401/404 Mobile: 9390923667, 9502389184 Email: arp...@cdfd.org.in
