Hi.
> Second, Say I would like to analyze the main difference between two > trajectories of the same protein using PCA. is it KOSHER to use the same > first frame which is identical between both runs as the reference strucutre > and then just append both runs into a single trajectory and then use g_covar > to analyse the subsequent conformations? if not, how would one go about > comparing the PC's of two different trajectories? other than dumping all the > frames in gro/pdb format and running the analysis in another program (such > as MATLAB) > > This questuion may be hard. You need rabbi's advice)) But there are some feature of the reference structure that makes it good or bad. It is mean deviation of the atomic coordinates of the fited structures from the reference, the best reference minimizes this measure. For a rigid structure it is acceptable choice to use first or any other frame, but for a flexible it can produce misfit and tangible distortion of the conformations' relations. Yuri.
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