Hi folks I can’t help feeling that if there are data extending to 0.97Å and there are multiple conformations/multiple components occupying the same region of (real) space/non-unity occupancies, the problem is crying out for SHELXL…
Harry > On 27 Apr 2020, at 07:53, Schreuder, Herman /DE <[email protected]> > wrote: > > 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 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
