[Chimera-users] Covalent bond making and docking

Eric Pettersen pett at cgl.ucsf.edu
Fri May 14 16:52:29 PDT 2021

Hi Bixia,
	It's a little unclear to me exactly what went wrong.  No code in Chimera issues a message containing the phrase "poor connection".    Perhaps you could send me a session of your structure just after you make the serine/uracil bond and then I can run it myself through Dock Prep and get a better understanding of the problem.


	Eric Pettersen
	UCSF Computer Graphics Lab

> On May 13, 2021, at 9:38 PM, Zhang, Bixia <bixia.zhang at wsu.edu> wrote:
> Good evening,
> I was trying to make a man made side chain, which is serine plus uracil. I used the command “bond sel” to connect the oxygen and nitrogen. Then I was trying to do docking to see if this mutation changed the binding affinity. However, after I ran dock prep, the uracil was got rid of because of “poor connection”. I am wondering if this arbitrary bond is feasible in chimera and can I do docking with this artificial model?
> Thank you,
> Bixia
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