Unless you are confident that twin exists you should not use twin refinement (Occam’s razor)
> On 5 Apr 2024, at 17:24, venkatareddy dadireddy <[email protected]> wrote: > > CAUTION: This email originated from outside of the LMB: > [email protected] <mailto:[email protected]>-. > Do not click links or open attachments unless you recognize the sender and > know the content is safe. > If you think this is a phishing email, please forward it to > [email protected] <mailto:[email protected]> > > -- > > Hi Kay and Garib, > > Thank you for your input. > It is actually the twin refinement that gave rise to resolution discrepancy. > For what reason I don't remember that I have turned the twin refinement ON > and the same job was cloned again and again. > With the twin refinement OFF, it gave rise to resolution present in the MTZ > (2.0 A). > From Xtriage: the correlation between > the intensities related by the twin law 1/2*h-3/2*k, -1/2*h-1/2*k,-l with an > estimated twin > fraction of 0.10 is most likely due to an NCS axis parallel to the twin axis. > The statistics independent of twin laws show no twinning (more close to > untwinned than perfect twin). > Please suggest to me on how I proceed with refinement (twin OFF or ON). > > Thank you, > Venkat > > > > > > > > On Fri, Apr 5, 2024 at 1:00 AM Garib Murshudov <[email protected] > <mailto:[email protected]>> wrote: > Did you use twin refinement (is it really twin if you used that). > If twin refinement was used then twin related intensities might have > different resolution, in case when your crystal are pseudomerohedral twinned. > > Regards > Garib > >> On 4 Apr 2024, at 18:40, venkatareddy dadireddy <[email protected] >> <mailto:[email protected]>> wrote: >> >> CAUTION: This email originated from outside of the LMB: >> [email protected] <mailto:[email protected]>-. >> Do not click links or open attachments unless you recognize the sender and >> know the content is safe. >> If you think this is a phishing email, please forward it to >> [email protected] <mailto:[email protected]> >> >> -- >> >> Hi Kay, >> >> Thank you very much for your insights. >> Following are the cell parameters from mtz and pdb header. >> MTZ: 117.8560 66.1700 70.9040 90.0000 91.4240 90.000 >> CRYST1 117.856 66.170 70.904 90.00 91.42 90.00 C 1 2 1 >> >> The only difference is in the 3rd decimal point. >> >> >> Thank you, >> Venkat >> >> >> >> On Tue, Apr 2, 2024 at 10:10 PM Kay Diederichs >> <[email protected] <mailto:[email protected]>> >> wrote: >> Hi Venkatareddy Dadireddy, >> >> do the unit cell parameters of your MTZ file and PDB file agree exactly ? >> >> Take for example a cell of (100,110,120,90,90,90) in the header of the MTZ >> file, >> and (97,110,120,90,90,90) in the CRYST1 line of the PDB file. >> >> In this example, the (50,0,0) reflection would be at 2.0A resolution if >> using the cell from the MTZ file, >> but it would be at 1.94A resolution if calculating the resolution based on >> the cell from the PDB file. >> >> So perhaps REFMAC5 takes the cell from the PDB file, and phenix.refine takes >> the cell from the MTZ? >> I didn't check but it may be worth finding out. >> >> HTH, >> Kay >> >> >> On Tue, 2 Apr 2024 21:16:57 +0530, venkatareddy dadireddy >> <[email protected] <mailto:[email protected]>> wrote: >> >> >Hi, >> > >> >The resolution range in my MTZ file is 70.88 - 2.0 A. When I refined my >> >structure using REFMAC5, the resolution that it gives is 70.88 - 1.94 A, >> >the difference of 0.04 A. I also used Phenix.refine which gives the >> >resolution output as it is in the MTZ file. Again, EDS (validation report) >> >gives the right resolution. What could be the possible reason for this >> >discrepancy? I have the structure deposited in the Protein Data Bank and it >> >is on hold. Thank you in advance for your help. >> > >> >Thank you, >> > >> > >> > >> > >> > >> > >> >*Venkatareddy Dadireddy,B1-10,Prof. S. Ramakumar's Lab,Dept. of >> >Physics,IISc, Banglore.Cell: 07259492227* >> > >> >######################################################################## >> > >> >To unsubscribe from the CCP4BB list, click the following link: >> >https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> ><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 >> ><http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by >> >www.jiscmail.ac.uk <http://www.jiscmail.ac.uk/>, terms & conditions are >> >available at https://www.jiscmail.ac.uk/policyandsecurity/ >> ><https://www.jiscmail.ac.uk/policyandsecurity/> >> > >> >> ######################################################################## >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> <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 >> <http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by >> www.jiscmail.ac.uk <http://www.jiscmail.ac.uk/>, terms & conditions are >> available at https://www.jiscmail.ac.uk/policyandsecurity/ >> <https://www.jiscmail.ac.uk/policyandsecurity/> >> >> >> -- >> Venkatareddy Dadireddy, >> B1-10, >> Prof. S. Ramakumar's Lab, >> Dept. of Physics, >> IISc, Banglore. >> Cell: 07259492227 >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> > > > -- > Venkatareddy Dadireddy, > B1-10, > Prof. S. Ramakumar's Lab, > Dept. of Physics, > IISc, Banglore. > Cell: 07259492227 > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > <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/
