Difference between revisions of "Bruker data"

From XDSwiki
Jump to navigationJump to search
(Replaced content with "CCD detectors: XDS only reads "unwarped" Bruker "sfrm" format frames; unwarping can be done within the Bruker software called Proteum2. See also ccp4com:Bruker_data|Bruk...")
Tag: Replaced
 
(4 intermediate revisions by one other user not shown)
Line 1: Line 1:
CCD detectors: XDS only reads "unwarped" Bruker "sfrm" format frames; unwarping can be done within the Bruker software called Proteum2. See also [[ccp4com:Bruker_data|Bruker data]].
 
  
PHOTON detectors: XDS natively reads their .cbf files, and [[generate_XDS.INP]] generates XDS.INP for PHOTON II.
+
== SFRM files ==
  
Tim Grüne provides a program <code>sfrmtools</code> at [https://homepage.univie.ac.at/tim.gruene/research/programs/conv/sfrmtools/] that extracts parameters relevant for data processing with XDS from headers of .sfrm files. See [https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=CCP4BB;ce43e97e.1907] .
+
Bruker instruments save frames in SFRM file format.
 +
XDS correctly reads these files. Data from CCD detectors, however, need to be "unwarped"; unwarping can be done within the Bruker software called Proteum2. See also [[ccp4com:Bruker_software|Bruker software]]. Data from more recent detectors, in particular all Photon detectors, do not need to unwarped and can be processed directly with XDS.
 +
 
 +
For such files, [https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=CCP4BB;ce43e97e.1907 Tim Grüne] provides the program <code>sfrmtools</code> at [https://homepage.univie.ac.at/tim.gruene/research/programs/conv/sfrmtools/]. It extracts parameters relevant for data processing with XDS from the header. The output should be saved in a file - only three more keyword/parameter lines are required for a minimal XDS.INP, namely e.g.
 +
NAME_TEMPLATE_OF_DATA_FRAMES=/my/data/name_????.sfrm
 +
OVERLOAD=1000000
 +
INCIDENT_BEAM_DIRECTION=0 0 1
 +
Additional ones can of course be used to modify the operation of XDS, e.g.
 +
JOB= XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT
 +
INCLUDE_RESOLUTION_RANGE=50 1
 +
TRUSTED_REGION=0 1.4142
 +
! UNTRUSTED_QUADRILATERAL= <8 numbers, easily specified using XDSGUI>
 +
...
 +
 
 +
 
 +
== CBF files ==
 +
 
 +
New detector types (optionally?) write CBF files, which XDS natively reads. [[generate_XDS.INP]] generates XDS.INP for CBF data written by the PHOTON II detector.

Latest revision as of 08:53, 29 January 2020

SFRM files

Bruker instruments save frames in SFRM file format. XDS correctly reads these files. Data from CCD detectors, however, need to be "unwarped"; unwarping can be done within the Bruker software called Proteum2. See also Bruker software. Data from more recent detectors, in particular all Photon detectors, do not need to unwarped and can be processed directly with XDS.

For such files, Tim Grüne provides the program sfrmtools at [1]. It extracts parameters relevant for data processing with XDS from the header. The output should be saved in a file - only three more keyword/parameter lines are required for a minimal XDS.INP, namely e.g.

NAME_TEMPLATE_OF_DATA_FRAMES=/my/data/name_????.sfrm
OVERLOAD=1000000 
INCIDENT_BEAM_DIRECTION=0 0 1

Additional ones can of course be used to modify the operation of XDS, e.g.

JOB= XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT
INCLUDE_RESOLUTION_RANGE=50 1
TRUSTED_REGION=0 1.4142
! UNTRUSTED_QUADRILATERAL= <8 numbers, easily specified using XDSGUI>
...


CBF files

New detector types (optionally?) write CBF files, which XDS natively reads. generate_XDS.INP generates XDS.INP for CBF data written by the PHOTON II detector.