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 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/
