Image recenter rms-fit

[Mihir Date]

Hi I have several trajectories that I want to analyses using Bio3D. The trajectories are written in dcd format. Before I do any analysis like, RMSF, RMSD or PCA, I'ed like to recenter solute protein, image back to primary unit cell and rms fit all frames to a reference frame. Are there any utilities/tools in Bio3D which can do it? Can you point me to a tutorial or examples to do this kind of processing?

[Xinqiu Yao]

Hi Mihir,

The task can be simply accomplished with the fit.xyz() function. See help(fit.xyz) or visit http://thegrantlab.org/bio3d/html/index.html to have the documention, vignettes, and demos. You can also run example(fit.xyz) or demo("md", package="bio3d") to show the examples for analyzing PDB structures and MD trajectories.

Btw, the Issues here are used for bug report and/or suggestion for package improvement. Please send us emails directly if you have questions. Thanks!

[Mihir Date]

Ohh thanks. did not know this is not a forum to discuss usage/examples etc. Thanks though.

[Xinqiu Yao]

No problem, Mihir:) Don't hesitate to shoot me email for questions or asking for helps: [e-mail]