I have calculated solution NMR structure of 45 residue membrane protein using cyana-3.97, but the backbone RMSD of 20 lowest target function conformers is about 3.5. Can someone suggest me what do I have to do so that I get backbone RMSD below 1.00?
You should first explain how did you calculate the RMSD. Usually, for calculation of RMSD with respect to a target structure, first the NMR ensemble of structures must be aligned with respect to the target structure, then calculate RMSD. You can use VMD software for calculation of RMSD (http://www.ks.uiuc.edu/Research/vmd/).
Next, you can also use molecular dynamics simulations of the system in explicit solvent (using the same conditions as NMR), to obtain an ensemble of structures, for which you can calculate RMSD.
Thank you Dr. Hiqmet for responding to my question. I calculate RMSD using molmol with respect to the first structure. On alining the other 19 structures with the first on the RMSD comes to be higher. Do you have any idea to decrease the RMSD of the structures so that I can get a tight structure?
Usually on calculation of the RMSD, first, the overall rotation and translational motions must be removed using, for example, least square minimization method. Another question that I have, how did you select these 20 conformers?
Dr. Hiqmet,
During the Structure calculation using cyana I set macro to get me 20 conformers with lowest target functions. I get the PDB file for the 20 conformers having least target functions.
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