Hi, every time you run phenix.refine it may exclude some reflections from refinement per Read 1999 (Acta Cryst. (1999). D55, 1759-1764). Usually the number of reflections omitted ranges from none to just a few, however, this may be just enough to make the resolution statistics look slightly different. Also, if you use Iobs as input data, internally they are converted into Fobs using F&W method, and some reflections may not "survive" this conversion. This may be another reason for discrepancies. Pavel
On Fri, Apr 5, 2024 at 9:45 PM venkatareddy dadireddy <[email protected]> wrote: > > Thank you very much Garib. > > Venkat > > On Sat, Apr 6, 2024 at 1:12 AM Garib Murshudov <[email protected]> > wrote: > >> 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] <[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] >> >> >> -- >> 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]> >> 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]> >>> wrote: >>> >>> CAUTION: This email originated from outside of the LMB: >>> *[email protected] <[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] >>> >>> >>> -- >>> 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]> 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]> 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 >> >> >> > > -- > > > > > > > *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 > ######################################################################## 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/
