Please build vignette for pdb structure manipulation

[Former user]

Please consider making a vignette that illustrates use of various PDB structure manipulation functions in Bio3d in one place (e.g., trim.pdb, align.pdb, atom.select, combine.select, etc.). Use multi-chain systems as an example if that is what Bio3d is capable of handling. Currently user has to go dig in every function individually and find examples or the code itself to understand how to best use them. Thank you.

[Lars Skjærven]

We can certainly consider some small code snippets on the web-site for this, or even a PDB vignette as you suggest. The examples provided in the documentation should already be a good start for a new user, but there is always room for improvements. Thanks for the comment !

[Barry Grant]

I agree, a focused vignette would be good. "Anonymous": We are always happy to take contributions if you would like to make a start on this, which we can then chime in on ;-)

[Lars Skjærven]

A start is given with commit 64c474f

[Barry Grant]

I have added some more details for section 3.1 to 3.3. See: 0a1fcbd More required for other sections, including example of concatenating, trimming, splitting, converting, rotating, translating and superposing PDB files. And working with multiple PDB files more broadly. Overall that should probably do it though.

[Xinqiu Yao]

Hi,

Sorry, it seems I have missed this issue. Will check all these updates soon. Thanks!