Hi Thank you Pavel for your input.
Venkat On Wed, Apr 10, 2024 at 1:44 AM Pavel Afonine <pafon...@gmail.com> wrote: > 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 < > venkatda...@gmail.com> wrote: > >> >> Thank you very much Garib. >> >> Venkat >> >> On Sat, Apr 6, 2024 at 1:12 AM Garib Murshudov <ga...@mrc-lmb.cam.ac.uk> >> 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 <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 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 >>> >>> >>> >> >> -- >> >> >> >> >> >> >> *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/
