On 22/06/2021 06:47, Jiang Xu wrote:
I have a problem building and refining an xtal structure. My protein has a N-glycosylation site and I want to add N-acetylglucosamine and manose to my protein structure. I used Coot's carbohydrate module and let Coot automatically build the sugar chain to the electron density. It worked pretty well, but I noticed that the bond between the amine group of asparagine and the C1 of N-acetylglucosamine is depicted as a dashed line, rather than a solid line in Coot.
Coot draws solid lines for bonds between neighbouring monomers in a polymer. The bond between NAG and ASN is not such a bond - it is a link. Links are drawn as dashed lines in Coot.
After refinement of the structure using Phenix.refine, I found the bond just disappeared, and the amine group still has two hydrogen atoms, which should contain one hydrogen atom.
If there is no link for a ASN, then there should be two hydrogen atoms add to the ND2. I find it fascinating that these programs work so well together that it didn't even occur to you to examine the conduit through which structral information is passed. Paul. ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
