Hi Ameya, If you do sphere refinement in coot on the disulfide bridges and repeat the final refinement, it should be solved.
Cheers, Robbie Sent from my Windows 10 phone From: ameya benz<mailto:[email protected]> Sent: 10 September 2017 09:19 To: [email protected]<mailto:[email protected]> Subject: [ccp4bb] Issue with disulphide bond Hi, I had uploaded a structure in PDB. Before uploading the structure to PDB, I used PDB validation server to validate my structure. The validation report did not mention any major issues with the structure. But after upload, I was communicated following issue: 1. Atomic Clashes Section 5.2 (Close contacts) of the validation report includes at least one physically unrealistic interatomic distance. Please upload a new coordinate file that resolves any issues or send correspondence clarifying the situation. Chain Atom Res Seq Chain Atom Res Seq Symm_Code Distance B SG CYS 53 - B SG CYS 98 1_555 Dist = 0.59 A SG CYS 53 - A SG CYS 98 1_555 Dist = 0.66 The validation report that I got do not mention this issue. Could you please help me in the fixing this issue. I am attaching the map images before and after refmac (zero cycles). The structure that I uploaded was before refmac. regards, Ameya
