Xdsconv: Difference between revisions
m (→how to obtain a MTZ file with DANO SIGDANO F(+) SIGF(+) F(-) SIGF(-): correction of text)
Revision as of 11:58, 17 March 2011
XDSCONV is the conversion program of the XDS suite.
Possible output formats are SHELX, CNS, CCP4 (for F SIGF DANO SIGDANO), CCP4_F (for F+ F- SIGF+ SIGF-) and CCP4_I (for I+ I- SIGI+ SIGI-).
XDSCONV does outlier rejection in some modes.
A typical input file XDSCONV.INP might look like
INPUT_FILE=XDS_ASCII.HKL INCLUDE_RESOLUTION_RANGE=50 1 ! optional OUTPUT_FILE=temp.hkl CCP4 ! Warning: do _not_ name this file "temp.mtz" ! FRIEDEL'S_LAW=FALSE ! default is FRIEDEL'S_LAW=TRUE
This produces the file temp.hkl which is then converted to a MTZ file XDS_ASCII.mtz with (these lines are also printed out by XDSCONV):
f2mtz HKLOUT temp.mtz<F2MTZ.INP cad HKLIN1 temp.mtz HKLOUT XDS_ASCII.mtz<<EOF LABIN FILE 1 ALL END EOF
This latter step is not necessary for CNS and SHELX output formats, which are written directly by XDSCONV. For the CNS output format, one could use MERGE=FALSE to keep observations separate. For the SHELX output format, MERGE=FALSE is the default (I guess because George Sheldrick suggests that his programs, in particular XPREP, should be fed unmerged data. However I sometimes found that I obtain better SHELXD results with merging inside XDSCONV, using MERGE=TRUE).
N.B. It is good practice to always use FRIEDEL'S_LAW=FALSE - see Tips and Tricks.
how to change column labels
To have control over the column labels, one might want to modify the simple example above as:
f2mtz HKLOUT temp.mtz<F2MTZ.INP cad HKLIN1 temp.mtz HKLOUT junk_xdsconv.mtz<<EOF LABIN FILE 1 E1=FP E2=SIGFP E3=DANO E4=SIGDANO E5=ISYM LABOUT FILE 1 E1=FP E2=SIGFP E3=DANO_sulf E4=SIGDANO_sulf E5=ISYM_sulf END EOF
ISYM column is important if you want to run SHARP afterwards.
In the case of a MTZ file that should be used for molecular replacement and refinement, the CAD step could be used to transfer the R_free flag from a different dataset to this new dataset. Alternatively, change of labels and transfer of columns can be done in the ccp4i GUI.
how to obtain a MTZ file with DANO SIGDANO F(+) SIGF(+) F(-) SIGF(-)
You have to run XDSCONV twice, and combine the output with cad. At the latter step you can also change the column labels:
#!/bin/csh -f # produce xds_allFinfo.mtz with FP SIGFP DANO SIGDANO F(+) SIGF(+) F(-) SIGF(-) # in the same way, the labels produced with CCP4_I could be included! # # first xdsconv run producing FP SIGFP DANO SIGDANO echo "INPUT_FILE= XDS_ASCII.HKL" > XDSCONV.INP echo "OUTPUT_FILE= temp.hkl CCP4" >> XDSCONV.INP echo "FRIEDEL'S_LAW= FALSE" >> XDSCONV.INP xdsconv f2mtz HKLOUT temp1.mtz<F2MTZ.INP # second xdsconv run producing F(+) SIGF(+) F(-) SIGF(-) echo "INPUT_FILE= XDS_ASCII.HKL" > XDSCONV.INP echo "OUTPUT_FILE= temp.hkl CCP4_F" >> XDSCONV.INP echo "FRIEDEL'S_LAW= FALSE" >> XDSCONV.INP xdsconv f2mtz HKLOUT temp2.mtz<F2MTZ.INP # for CAD, the 2 LABOUT cards are only required if the labels should be changed cad HKLIN1 temp1.mtz HKLIN2 temp2.mtz HKLOUT xds_allFinfo.mtz<<EOF LABIN FILE 1 E1=FP E2=SIGFP E3=DANO E4=SIGDANO LABIN FILE 2 E1=F(+) E2=SIGF(+) E3=F(-) E4=SIGF(-) LABOUT FILE 1 E1=FP_Hg E2=SIGFP_Hg E3=DANO_Hg E4=SIGDANO_Hg LABOUT FILE 2 E1=F(+)_Hg E2=SIGF(+)_Hg E3=F(-)_Hg E4=SIGF(-)_Hg END EOF
Hint for long-time XDSCONV users
The latest versions of the program do not require
because these are picked up from the header of the input reflection file. However, if you want to change the parameters of either keyword then you have to specify both! I.e. if you want to change the spacegroup then you also have to specify the unit cell parameters.