Problems: Difference between revisions

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This is a collection of problems and their solutions.

== XDS does not start ==

XDS must be installed in the PATH, i.e. in one of those directories in the filesystem where the shell looks for binaries. On both Linux and macOS, there is a default set of such directories; these typically should have those binaries that the distribution provides. Additional software and its binaries can be installed by the user/admin in different (additional) directories. On macOS, these typically go into /Applications if they come with an installer, but /usr/local/bin could also be used e.g. for single binaries. On Linux, typically large packages have their own directory, often under /opt if they are for all users, or under $HOME for a single user.

The downloading and installation of the XDS package is documented at https://xds.mr.mpg.de/html_doc/downloading.html , and also in [[Installation]].

The important point is that after unpacking the XDS distribution, the resulting directory should be put into your PATH variable, as explained in the URL above. Failing to do so results in an error message, and a non-functional XDS installation.

For example, if you get the error message (e.g. in the terminal where you started XDSGUI)

/bin/bash: xds_par: command not found

then this means that either the XDS package was not installed at all, or the PATH variable does not point to its directory.

== XDS crashes ==

XDS should never crash (if it terminates with an error message, this does not count as crash). If it does, it is either a bug in the program which should be brought to the attention of Wolfgang Kabsch or Kay Diederichs, and will be fixed, or it is a problem with your computer, or (rarely) it is due to improper inputs ([[Problems#INTEGRATE_cell_and.2For_distance_run_away.3B_xds_crashes_or_has_to_be_killed|this]] is the only example I know of).

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== Indexing failures ==

In case of IDXREF problems, you should definitively inspect, using [[XDS-viewer]] or [[adxv]], the ~~FRAME~~.cbf file which is written by COLSPOT. This file shows the first frame of the SPOT_RANGE, together with strong pixels that COLSPOT found on this frame, marked with white pixels. IDXREF will use those spot positions which have at least as many strong pixels as MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT specifies.

In case of IDXREF problems, you should definitively inspect, using [[XDS-viewer]] or [[adxv]], the [https://xds.mr.mpg.de/html_doc/xds_files.html#SHOW_SPOT.cbf SHOW_SPOT.cbf] file which is written by COLSPOT. This file shows the first frame (can be changed by [https://xds.mr.mpg.de/html_doc/xds_parameters.html#SHOW_IMAGE_NUMBER= SHOW_IMAGE_NUMBER=]) of the [https://xds.mr.mpg.de/html_doc/xds_parameters.html#SPOT_RANGE= SPOT_RANGE], together with strong pixels that COLSPOT found on this frame, marked with white pixels. IDXREF will use those spot positions which have at least as many strong pixels as [https://xds.mr.mpg.de/html_doc/xds_parameters.html#MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT= MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT] specifies.

You will only be able to look at this file if you prevent XDS from running INTEGRATE. This can be achieved e.g. by

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=== INTEGRATE stops with error message ===

When using [[XDSGUI]], also inspect XDS.LP (to the right of the "Run XDS" button)!

If INTEGRATE stops after e.g.

******************************************************************************

@@ Line 1: / Line 1: @@
 This is a collection of problems and their solutions.
+== XDS does not start ==
+XDS must be installed in the PATH, i.e. in one of those directories in the filesystem where the shell looks for binaries. On both Linux and macOS, there is a default set of such directories; these typically should have those binaries that the distribution provides. Additional software and its binaries can be installed by the user/admin in different (additional) directories. On macOS, these typically go into /Applications if they come with an installer, but /usr/local/bin could also be used e.g. for single binaries. On Linux, typically large packages have their own directory, often under /opt if they are for all users, or under $HOME for a single user.
+The downloading and installation of the XDS package is documented at https://xds.mr.mpg.de/html_doc/downloading.html , and also in [[Installation]].
+The important point is that after unpacking the XDS distribution, the resulting directory should be put into your PATH variable, as explained in the URL above. Failing to do so results in an error message, and a non-functional XDS installation.
+For example, if you get the error message (e.g. in the terminal where you started XDSGUI)
+ /bin/bash: xds_par: command not found
+then this means that either the XDS package was not installed at all, or the PATH variable does not point to its directory.
 == XDS crashes ==
 XDS should never crash (if it terminates with an error message, this does not count as crash). If it does, it is either a bug in the program which should be brought to the attention of Wolfgang Kabsch or Kay Diederichs, and will be fixed, or it is a problem with your computer, or (rarely) it is due to improper inputs ([[Problems#INTEGRATE_cell_and.2For_distance_run_away.3B_xds_crashes_or_has_to_be_killed|this]] is the only example I know of).
@@ Line 68: / Line 78: @@
 == Indexing failures ==
-In case of IDXREF problems, you should definitively inspect, using [[XDS-viewer]] or [[adxv]], the FRAME.cbf file which is written by COLSPOT. This file shows the first frame of the SPOT_RANGE, together with strong pixels that COLSPOT found on this frame, marked with white pixels. IDXREF will use those spot positions which have at least as many strong pixels as MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT specifies.
+In case of IDXREF problems, you should definitively inspect, using [[XDS-viewer]] or [[adxv]], the [https://xds.mr.mpg.de/html_doc/xds_files.html#SHOW_SPOT.cbf SHOW_SPOT.cbf] file which is written by COLSPOT. This file shows the first frame (can be changed by [https://xds.mr.mpg.de/html_doc/xds_parameters.html#SHOW_IMAGE_NUMBER= SHOW_IMAGE_NUMBER=]) of the [https://xds.mr.mpg.de/html_doc/xds_parameters.html#SPOT_RANGE= SPOT_RANGE], together with strong pixels that COLSPOT found on this frame, marked with white pixels. IDXREF will use those spot positions which have at least as many strong pixels as [https://xds.mr.mpg.de/html_doc/xds_parameters.html#MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT= MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT] specifies.
 You will only be able to look at this file if you prevent XDS from running INTEGRATE. This can be achieved e.g. by
@@ Line 271: / Line 281: @@
 === INTEGRATE stops with error message ===
+When using [[XDSGUI]], also inspect XDS.LP (to the right of the "Run XDS" button)!
 If INTEGRATE stops after e.g.
   ******************************************************************************