Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] modelling MET (methionine) and SME (met-sulfoxide)
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 > 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 Im Auftrag von Abhishek Anan > Gesendet: Sonntag, 26. April 2020 21:42 > An: CCP4BB@JISCMAIL.AC.UK > Betreff: [EXTERNAL] Re: [ccp4bb] modelling MET (methionine) and SME > (met-sulfoxide) > > EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk > > > > 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 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=DwIFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5 >> qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=CYQUM_mrfiCDADJ1 >> onMNLQYYLwXD23pcMOTm7KnoNkM=A_ke05wSRD1nm9vQxFwLPCzpmUAWRTVlaVkVSTRw >> z8M= >> >> 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=DwIFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=CYQUM_mrfiCDADJ1onMNLQYYLwXD23pcMOTm7KnoNkM=6ogarHdS3ZYDDHIOFlsDYS2crwXpeNiaY2wIG_dXsEA= > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] modelling MET (methionine) and SME (met-sulfoxide)
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 Im Auftrag von Abhishek Anan Gesendet: Sonntag, 26. April 2020 21:42 An: CCP4BB@JISCMAIL.AC.UK Betreff: [EXTERNAL] Re: [ccp4bb] modelling MET (methionine) and SME (met-sulfoxide) EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk 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 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=DwIFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5 > qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=CYQUM_mrfiCDADJ1 > onMNLQYYLwXD23pcMOTm7KnoNkM=A_ke05wSRD1nm9vQxFwLPCzpmUAWRTVlaVkVSTRw > z8M= > > 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=DwIFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=CYQUM_mrfiCDADJ1onMNLQYYLwXD23pcMOTm7KnoNkM=6ogarHdS3ZYDDHIOFlsDYS2crwXpeNiaY2wIG_dXsEA= To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] modelling MET (methionine) and SME (met-sulfoxide)
Occupancy. On Sunday, 26 April 2020, 20:41:49 BST, Abhishek Anan wrote: 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 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://www.wwpdb.org/documentation/procedure > > 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://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] modelling MET (methionine) and SME (met-sulfoxide)
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 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://www.wwpdb.org/documentation/procedure > > 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://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] modelling MET (methionine) and SME (met-sulfoxide)
> 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://www.wwpdb.org/documentation/procedure > > That should "just work" if you then give the model to refmac. > > FWIW, Coot is, AFAIR, not 100% happy with such models. Neither is Refmac ☹ Cheers, Robbie > > Paul. > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] modelling MET (methionine) and SME (met-sulfoxide)
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://www.wwpdb.org/documentation/procedure 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://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] modelling MET (methionine) and SME (met-sulfoxide)
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. best wishes, Abhishek To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
