Re: [ccp4bb] Co crystalization with less soluble ligand.

2021-06-22 Thread Steven Herron
Dear Gourab, Sorry for the delayed response, I missed your message earlier. Can you grow the protein crystals easily (do you have lots of them)? Is your ligand soluble in PEG, MPD, or Solutol? Often, you can exchange the crystal solution without destroying the crystal.  But, you have to

Re: [ccp4bb] missing covalent bond between asparagine and N-acetylglucosamine using coot carbohydrate module and phenix.refine

2021-06-22 Thread Paul Emsley
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

Re: [ccp4bb] missing covalent bond between asparagine and N-acetylglucosamine using coot carbohydrate module and phenix.refine

2021-06-22 Thread David Briggs
Hi Jiang Xu, (Phenixbb added as I suspect this is Phenix not coot that has caused your issue) Did you check the "add hydrogens" button in Phenix.refine? Sometimes this can erroneously add a second H to the ND of glycosylated Asn residues. (I assume this is because bond distances in the input