VMD如何修改CPK、line等representations默认的键长？

若A和B之间出现了不想要的键，可以分别选择A和B，建立两个单独的Reps。

这是最取巧的办法了。

否则需要写tcl scripts，见问题：

http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/6470.html

At present, VMD doesn't calculate the bond order, it either gets this information from a loaded file which contains bond order information (such as Biograf, MOL2, etc...) or it sets the bond order to a default value of 1.0 if VMD's automatic bond determination code ends up being invoked.

You can set the bond orders yourself using atom selections if you have a way of calculating them. The automatic bond calculation code in VMD is just a relatively simple heuristic which can potentially be tricked by unusual atom names, bad VDW radii, or other bad parameters, so if you really need accurate bond information, the best thing to do is to provide it to VMD in the structure files you load. That said however, you can change the bond information in VMD on the fly as you wish, either by manually correcting any incorrect bonds with the mouse, or by writing scripts.