Hi Mitch, When i checked carefully again log files. I came to know that, when i used xdsconv then only the total completeness have been changed from 95% to 100%.
Before xdsconv all log-files have original 95%. Now what should i do?? thanks, yusuf Quoting "Miller, Mitchell D." <[EMAIL PROTECTED]>: > 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/ > ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/
