Dear Abhishek, I did not follow the links given by Paul. However the way I proceeded in these cases was to first generate an alternative conformation for the problem residues, save the file and then do the mutation and save the mutated file. Then, using an editor, I would cut the alternative conformation from the original residue and paste in the alternate conformation (e.g. conformation B) from mutated residue.
It is not very elegant, but it works (if coot and refmac cooperate). Best, Herman -----Ursprüngliche Nachricht----- Von: CCP4 bulletin board <[email protected]> Im Auftrag von Abhishek Anan Gesendet: Sonntag, 26. April 2020 21:42 An: [email protected] Betreff: [EXTERNAL] Re: [ccp4bb] modelling MET (methionine) and SME (met-sulfoxide) EXTERNAL : Real sender is [email protected] Dear all, Thanks for the suggestions. It is synthetic peptide so the residue identity is unambiguous. I am not clear on how to model both MET and SME in coot, do a real space refinement and then save the file for refinement in phenix. I tried alternate conformation and then mutating one of them but that didn't work as both conformations were mutated. What I also just noticed is that the refinement of structure with just SME results in positive densities around all side chain carbons even with the SME.cif loaded into phenix. What could be wrong here? best wishes, Abhishek On 4/26/20, Paul Emsley <[email protected]> wrote: > > On 26/04/2020 16:21, Abhishek Anan wrote: >> Dear all, >> >> I have a peptide crystal structure at 0.97 Å that contains two >> surface exposed Methionine. The CE atoms of both MET have a >> suspiciously high b-factor >40 and a positive density. In addition, >> the sulfur atom SD has a large negative density (b-factor ~23). >> >> I initially suspected that the MET may have oxidized to MET-sulfoxide >> and tried to model only the MET-sulfoxide. This again resulted in >> negative density. >> >> I think that the peptides might be partly oxidized which brings me to >> my question. Is there a way to model both MET and MET-sulfoxide into >> the density much like alternate conformation with options to refine >> their respective occupancies. > > > Yes. This is called micro-heterogeneity > > And is documented here: > > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.wwpdb.org_doc > umentation_procedure&d=DwIFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5 > qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=CYQUM_mrfiCDADJ1 > onMNLQYYLwXD23pcMOTm7KnoNkM&s=A_ke05wSRD1nm9vQxFwLPCzpmUAWRTVlaVkVSTRw > z8M&e= > > That should "just work" if you then give the model to refmac. > > FWIW, Coot is, AFAIR, not 100% happy with such models. > > Paul. > > > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwIFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=CYQUM_mrfiCDADJ1onMNLQYYLwXD23pcMOTm7KnoNkM&s=6ogarHdS3ZYDDHIOFlsDYS2crwXpeNiaY2wIG_dXsEA&e= ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
