Re: [ccp4bb] autoBuster--Rfree_falg
Dear Jerry, On Tue, Aug 17, 2010 at 04:26:14PM -0700, Jerry McCully wrote: Dear All: I am currently using autoBuster to refine my structure. I notice that autobuster generates a new column in the MTZ data file with the label of FreeR_flag. Because my MTZ file has already had the FreeRflag, I am wondering whether autoBuster generated a new set of Rfreeflags of just renamed the existing FreeRflags. Can anyone give some comments? Yes, it created a new column because the existing one has a label different from the supported ones - see: http://www.globalphasing.com/buster/manual/autobuster/manual/appendix1.html#SetvarParameter_ColumnName_FreeR_flag_allowed What you could do is to add the following line to a ~/.autoBUSTER file: ColumnName_FreeR_flag_allowed= I FreeR_flag| I FREE| I FreeRflag Or use this on the command-line: % refine ColumnName_FreeR_flag_allowed= I FreeRflag \ -p some.pdb -m other.mtz ... Both should work. Alternatively you might want to use the more common (?) labels FREE or FreeR_flag when you create your MTZ file. Cheers Clemens PS: for BUSTER questions you can also use buster-deve...@globalphasing.com -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) ***
[ccp4bb] autoBuster--Rfree_falg
Dear All: I am currently using autoBuster to refine my structure. I notice that autobuster generates a new column in the MTZ data file with the label of FreeR_flag. Because my MTZ file has already had the FreeRflag, I am wondering whether autoBuster generated a new set of Rfreeflags of just renamed the existing FreeRflags. Can anyone give some comments? Thanks a lot, Jerry
Re: [ccp4bb] autoBuster--Rfree_falg
There are many ways to test if the two test sets are identical. For example (using CCP4i): Go to Reflection Data Utilities - SF file analysis and then perform data correlation between your two FreeFlag columns. If they are identical, the resulting R-factor should be 0 and correlation coefficient should be 1. Or you can use ConvertFromMTZ into your own defined format so that you get two columns with values. You can also use sftools to subtract the two columns and see if the maximum and minimum are both zeros. etc, etc On Tue, 2010-08-17 at 16:26 -0700, Jerry McCully wrote: Dear All: I am currently using autoBuster to refine my structure. I notice that autobuster generates a new column in the MTZ data file with the label of FreeR_flag. Because my MTZ file has already had the FreeRflag, I am wondering whether autoBuster generated a new set of Rfreeflags of just renamed the existing FreeRflags. Can anyone give some comments? Thanks a lot, Jerry
