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 <ga...@mrc-lmb.cam.ac.uk> 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 <venkatda...@gmail.com> > wrote: > > CAUTION: This email originated from outside of the LMB: > *.-owner-ccp...@jiscmail.ac.uk <owner-ccp...@jiscmail.ac.uk>-.* > 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 > phish...@mrc-lmb.cam.ac.uk > > > -- > 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 < > kay.diederi...@uni-konstanz.de> 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 < >> venkatda...@gmail.com> 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 >> > >> >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/ >> > >> >> ######################################################################## >> >> 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/ >> > > > -- > > > > > > > *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 > > > -- *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 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/
