Hi Yusuf, You need to run the uniqueify script to expand the input file to include all possible reflections (observed and missing from your data set). I have not run xdsconv with the GENERATE_FRACTION_OF_TEST_REFLECTIONS=0.05 However, generally after running xdsconv without that command, it is necessary to run f2mtz, cad and uniqueify to prepare the input file for refmac.
You can do a quick test like mtzdump test.mtz if it reports that your Fobs are 100% complete, then you need to run uniqueify to expand the file to contain all possible reflections up to the highest resolution in your input file. Without this, then the statistics will not be reported correctly in refmac and many other programs. see http://www.ccp4.ac.uk/dist/html/refmac5/files/log.html#pobs "Percentage observed Fraction of the observed reflections in %. If uniqueify has been run before using REFMAC, this value will be calculated correctly. Otherwise it will be 100.0%. " If your free flag column label is FreeRflag, then you can run the uniqueify script from the command line like: uniqueify -p 0.05 -f FreeRflag test.mtz if your input file is test.mtz the output from the script will be test-unique.mtz. or you can use the ccp4i task "merge mtz files (CAD)" by inputting your existing .mtz file and checking the box to complete the reflection list and extend your input freeR set. Regards, Mitch -----Original Message----- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Yusuf Akhter Sent: Friday, August 08, 2008 2:20 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Refmac out-put file header information Dear Mitch, I did not run uniqueify but i have added free-R flags by running xdsconv with extra command line in in-put file GENERATE_FRACTION_OF_TEST_REFLECTIONS=0.05 Dear Leo, This 94.5% is total completeness of the data. I am pasting below the header information in that PDB file. REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.74 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 100.00 REMARK 3 NUMBER OF REFLECTIONS : 12072 Have anybody some suggestions?? Thanks, yusuf -- Yusuf Akhter EMBL Hamburg c/o DESY, Notkestraße 85, 22603 Hamburg, Germany Thank you very much to Artem, Lijun, Dale and Paul for giving me great suggestions regarding my earlier query on D to L amino acid residues. Now one more problem is in same 3 A structure refinement. For those who not remembered my case. I have processed a diffraction data-set at 3 A using XDS. I am using Refmac for refinement. My data is 95.4% of completeness at Signal/noise >=-3. I noticed that in the header of out-put PDB file from Refmac shows 100% completeness. Is it a bug?? May somebody tell me where the problem is? Thanks in advance. yusuf -- Yusuf Akhter EMBL Hamburg c/o DESY, Notkestraße 85, 22603 Hamburg, Germany Quoting Yusuf Akhter <[EMAIL PROTECTED]>: > Hi Everybody, > > I am refining structure of a protein at 3 Angstrom. I am doing model building > in > Coot. > After several rounds of refinement using Refmac when I tried to run PROCHECK > on > my partially build model I found that some of the residues are D-amino > acids. > > How to change these D-amino acids to L-amino acids?? > > Is there any option in Coot for that?? > > > Thanks in advance, > yusuf ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/
