Re: [ccp4bb] Resolution discrepancy between MTZ file and Refinement

Hi Thank you Pavel for your input. Venkat On Wed, Apr 10, 2024 at 1:44 AM Pavel Afonine 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

Re: [ccp4bb] Resolution discrepancy between MTZ file and Refinement

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 differe

Re: [ccp4bb] Resolution discrepancy between MTZ file and Refinement

Thank you very much Garib. Venkat On Sat, Apr 6, 2024 at 1:12 AM Garib Murshudov 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 > wrote: > > CAUTION: This email originated from outs

Re: [ccp4bb] Resolution discrepancy between MTZ file and Refinement

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 wrote: > > CAUTION: This email originated from outside of the LMB: > .-owner-ccp...@jiscmail.ac.uk -. > Do not cli

Re: [ccp4bb] Resolution discrepancy between MTZ file and Refinement

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

Re: [ccp4bb] Resolution discrepancy between MTZ file and Refinement

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 wrote: > > CAUT

Re: [ccp4bb] Resolution discrepancy between MTZ file and Refinement

Hi Venkat, so what I suggested is not the real problem. To get to the bottom of this, I suggest you show the logfiles from REFMAC5 and phenix.refine, and the output of the following command: mtzdmp experimental_data.mtz >& mtzdmp.log run on the command line. Please upload the files to some clou

Re: [ccp4bb] Resolution discrepancy between MTZ file and Refinement

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. 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

Re: [ccp4bb] Resolution discrepancy between MTZ file and Refinement

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

[ccp4bb] Resolution discrepancy between MTZ file and Refinement

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