Hi Jon, There are placeholders for ASP/ASN and GLU/GLN ambiguities: ASX and GLX respectively. You can just use those. AFAICT there no such thing for VAL/THR ambiguities. You could look for the most likely canadidata based on multiple sequence alignments. Refinement of both alternatives can give hints in B-factors and if you are lucky in difference density. But if hydrogen bonding gives no hints, then the residues are also not in a place where the identity really matters. You can give your best guess with a CAVEAT record or use the name UNK to indicate that you do not know what the residue is. You would loose the knowledge that it is either VAL or THR in that case.
Cheers, Robbie > -----Original Message----- > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Jon > Cooper > Sent: Friday, July 29, 2022 12:14 > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Checking X-ray sequence (no more protein). > > Hello, I am looking for suggestions of ways to check a 1.7 Angstrom X-ray > sequence for a protein where it is impractical to do experimental sequencing, > protein or DNA. The structure refines to publishable R/R-free and the main > ambiguities seem to be Thr/Val, Asp/Asn and Glu/Gln where alternative H- > bonding networks are possible. Running alpha-fold seems an interesting > option? Any suggestions much appreciated. > > Cheers, Jon.C. > > Sent from ProtonMail mobile > > > > > ________________________________ > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## 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/
