XDS.INP: Difference between revisions

XDS.INP (view source)

Revision as of 13:12, 14 November 2007

1,108 bytes added , 14 November 2007

no edit summary

Kay

Bureaucrats

2,655

edits

@@ Line 1: / Line 1: @@
-XDS.INP is a user-provided file that is read by [[XDS]].  Each line consists of one or more <keyword>=<parameter(s)> pairs.
+XDS.INP is a user-provided file that is read by [[XDS]].  Each line consists of one or more <keyword>=<parameter(s)> pairs. Anything after a "!" is a comment.
 Complete documentation is at http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html .
@@ Line 50: / Line 50: @@
 ;[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#SPACE_GROUP_NUMBER= SPACE_GROUP_NUMBER]
-:a mapping of space group names against their numbers is near the end of [[IDXREF.LP]].
+:If you don't know the space group, put a 0 or comment out the line. A mapping of space group names against their numbers is near the end of [[IDXREF.LP]].
 ;[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#UNIT_CELL_PARAMETERS= UNIT_CELL_PARAMETERS]
-:unit cell parameters need to respect the constraints of the Laue group, e.g. all angles must be exactly 90.0 for orthorhombic and tetragonal space groups, a and b must be equal for trigonal and tetragonal, and so on.
+:If you don't know the space group, put six 0s or comment out the line. Unit cell parameters need to respect the constraints of the Laue group, e.g. all angles must be exactly 90.0 for orthorhombic and tetragonal space groups, a and b must be equal for trigonal and tetragonal, and so on.
 * If you want to assign a space group and unit cell parameters to a crystal you most probably need this keyword as well:
 ;[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#REINDEX= REINDEX]
-:12 numbers, 9 of which are used as a re-indexing matrix. The other 3 are normally 0. These 12 numbers can be obtained from [[IDXREF.LP]].
+:12 numbers, 9 of which are used as a re-indexing matrix (the other 3 are normally 0). These 12 numbers can be obtained from [[IDXREF.LP]].
 The way how to determine a space group (and unit cell parameters) is described in [[space_group_determination|space group determination]].
@@ Line 86: / Line 86: @@
 == Keywords which affect whether indexing will succeed ==
-In addition to [[Obtaining ORGX ORGY]], I recommend to look at:
+Again, the most important parameters are ORGX ORGY. Often the software which writes the frames puts these numbers into the headers of the frames. However, these numbers are sometimes wrong, and furthermore, XDS does not read and interpret headers of frames. How to obtain estimates for ORGY ORGY from frames is described in [[Obtaining ORGX ORGY]].
+;[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#SPOT_RANGE= SPOT_RANGE]
+:If this line is omitted, the whole DATA_RANGE is used. This is usually a good way to proceed. If there is radiation damage, I would advise to use the first half of the DATA_RANGE as SPOT_RANGE. The SPOT_RANGE in principle may comprise a single frame.
+;[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#STRONG_PIXEL= STRONG_PIXEL]
+:the default is 3, but 6 is usually more appropriate.
-[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#STRONG_PIXEL= STRONG_PIXEL] - the default is 3, but 6 is usually more appropriate.
+== Keywords which affect the speed of data reduction ==
-== Keywords which affect the speed of data reduction ==
+;[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#MAXIMUM_NUMBER_OF_PROCESSORS= MAXIMUM_NUMBER_OF_PROCESSORS]
+:speeds up XDS by use of several (e.g. 2-4) CPUs within a single machine.
-[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#MAXIMUM_NUMBER_OF_PROCESSORS= MAXIMUM_NUMBER_OF_PROCESSORS] - speeds up XDS by use of several (e.g. 2-4) CPUs within a single machine.
+;[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#MAXIMUM_NUMBER_OF_JOBS= MAXIMUM_NUMBER_OF_JOBS]
+:speeds up XDS by chopping the DATA_RANGE into pieces, and feeding each piece to a new process. That process may run on the local machine, or a different one (but this needs to be configured by the system administrator). Unless specifically set up for a given computer environment (e.g., at a synchrotron site), usually don't set ''both'' MAXIMUM_NUMBER_OF_PROCESSORS ''and'' MAXIMUM_NUMBER_OF_JOBS to values >1 !
-[http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#MAXIMUM_NUMBER_OF_JOBS= MAXIMUM_NUMBER_OF_JOBS] - speeds up XDS by chopping the DATA_RANGE into pieces, and feeding each piece to a new process. That process may run on the local machine, or a different one (but this needs to be configured by the system administrator). Unless specifically set up for a given computer environment (e.g., at a synchrotron site), don't set ''both'' MAXIMUM_NUMBER_OF_PROCESSORS ''and'' MAXIMUM_NUMBER_OF_JOBS to values >1!
+Some amount of "overcommiting of resources" is OK, i.e. if you are the sole user of a Dual-core workstation, you may set both parameters to 2. Wolfgang Kabsch found that this utilizes the machine even a bit better than either MAXIMUM_NUMBER_OF_PROCESSORS=2 or MAXIMUM_NUMBER_OF_JOBS=2.
 == What can go wrong with this file? ==