今天有客户反映说他做完分子对接后，用Pymol打开，发现两个没有共价键形成的残基之间以共价键连接了在一起。收到客户发过来的文件后，用Disconvery Studio Viusalizer打开后，这两个残基确实没有形成共价键。

那么肯定就是Pymol的问题了。搜索一番后找到了解决问题的方法，解决方法如下：

PyMOL sometimes displays bonds which are not correct and can be confusing. To remove a bond between to atoms, first set the selection argument to "Atoms", then select the first atom involved in the bond and rename its selection identifier to, e.g., "atm1". Unselect the atom, select the second atom of the bond, rename the selection identifier to "atm2".

Then enter the following at the PyMOL prompt:

cmd.unbond("(atm1)", "(atm2)")

Be sure to include all parentheses and quotation marks.

简而言之，就是选中其中一个残基，然后右键，actions->rename selection，将该残基命名为atm1。

同样的操作，将另外一个残基命名为atm2，然后在Pymol命令窗口中输入cmd.unbond("(atm1)", "(atm2)")即可。