XDSGUI: Difference between revisions

Jump to navigation Jump to search

XDSGUI (view source)

Revision as of 22:22, 1 December 2020

223 bytes added ,  1 December 2020
→‎Known bugs, problems and workarounds
(7 intermediate revisions by the same user not shown)
Line 22: Line 22:
* the simple editor operating in the XDS.INP, XDSCONV and XSCALE tabs understands ctrl-X (cut), ctrl-c (copy), ctrl-v (paste), ctrl-z (undo) and ctrl-Z (redo).  
* the simple editor operating in the XDS.INP, XDSCONV and XSCALE tabs understands ctrl-X (cut), ctrl-c (copy), ctrl-v (paste), ctrl-z (undo) and ctrl-Z (redo).  
* ctrl-+ (control-plus) and ctrl-- (control-minus) enlarge or decrease the font size of characters.
* ctrl-+ (control-plus) and ctrl-- (control-minus) enlarge or decrease the font size of characters.
* flexibility of operation: all commands in the TOOLS tab may be modified by the user, simply by modifying the (bash) code in the text field below the button. The user-changed command is automagically and permanently stored in ~/.xds-gui . The user may also change what is written on a button, by editing ~/.xds-gui.
* flexibility of operation: all commands in the ''tools'' tab may be modified by the user, simply by modifying the (bash) code in the text field below the button. The user-changed command is automagically and permanently stored in ~/.xds-gui . The user may also change what is written on a button, by editing ~/.xds-gui.
* Menu / Settings is used for setting "Paths" for binaries (xds_par, xscale_par, shelxc/d/e, ...), "Library" (typically /usr/local/lib64/dectris-neggia.so), and "Appearance" (font size and default plot height).
* Menu / Settings is used for setting "Paths" for binaries (xds_par, xscale_par, shelxc/d/e, ...), and "Appearance" (font size and default plot height). "generic Library" (typically /usr/local/lib64/dectris-neggia.so) should currently not be filled out, due to a bug.


== Tabs ==
== Tabs ==
Line 128: Line 128:
=== Dependencies ===
=== Dependencies ===


XDSGUI depends on [[generate_XDS.INP]], [[XDS-viewer]], and of course [[XDS]] (both the xds and xds_par binaries!), [[XDSCONV]], and [[2cbf]]. The ''statistics'' tab requires [[XDSSTAT]] and [[XDSCC12]]. As discussed in [[Generate_XDS.INP#Dependencies]], [[Eiger]] data processing requires the <code>h5dump</code> binary, and either the <code>H5ToXds</code> binary or the <code>dectris-neggia</code> library (available from Dectris) or the <code>durin-plugin</code> library (download from Diamond Light Source, DLS). The library should be put into a directory (e.g. /usr/local/lib64), and the full path to it (e.g. /usr/local/lib64/dectris-neggia.so) should be entered into the "generic frame library" entry, in Menu->Settings.
XDSGUI depends on [[generate_XDS.INP]], [[XDS-viewer]], and of course [[XDS]] (both the xds and xds_par binaries!), [[XDSCONV]], and [[2cbf]]. The ''statistics'' tab requires [[XDSSTAT]] and [[XDSCC12]]. For visualization of the raw data frames in the ''Frame'' tab, [[Eiger]] data processing requires either the [https://www.dectris.com/features/features-eiger-x/h5toxds/ <code>H5ToXds</code>] binary or the [https://www.globalphasing.com/autoproc/wiki/index.cgi?DataProcessingHdf5 <code>hdf2mini-cbf</code>] binary (needs autoPROC license). Only the latter works for the .h5 files produced at Diamond Light Source; if hdf2mini-cbf should be used, it needs to be symlinked under the name H5ToXds (because XDSGUI has the name H5ToXds hardwired). ([https://github.com/biochem-fan/eiger2cbf <code>eiger2cbf</code>] does not seem to work with Eiger2 .h5 files.)


One of the items in the <code>tools</code> tab calls a graphical file comparison program; if the default (xdiff) is not available, [http://furius.ca/xxdiff xxdiff] or [http://sourceforge.net/projects/tkdiff tkdiff] or [http://kdiff3.sourceforge.net/ kdiff3] or [http://meldmerge.org/ meld] may be used - please adjust the command line (below the button) accordingly.  
One of the items in the ''tools'' tab calls a graphical file comparison program; if the default (xdiff) is not available, [http://furius.ca/xxdiff xxdiff] or [http://sourceforge.net/projects/tkdiff tkdiff] or [http://kdiff3.sourceforge.net/ kdiff3] or [http://meldmerge.org/ meld] may be used - please adjust the command line (below the button) accordingly.  


The XDSCONV functionality requires a working CCP4 installation for conversion to MTZ files. Likewise, XDSSTAT (in the statistics tab) needs CCP4.
The XDSCONV functionality requires a working CCP4 installation for conversion to MTZ files. Likewise, XDSSTAT (in the ''statistics'' tab) needs CCP4.


Technically, the word "dependency" means that these scripts/programs should be in your $PATH - an 'alias' is often not good enough because the ''TOOLS'' commands use <code>bash</code> as a shell, and that shell does not inherit the aliases from e.g. (t)csh.
Technically, the word "dependency" means that these scripts/programs should be in your $PATH - an 'alias' is often not good enough because the commands in the ''tools'' tab use <code>bash</code> as a shell, and that shell does not inherit the aliases from e.g. (t)csh.


If you use the <code>get_folder.sh</code> script as explained in [[Installation]], most of these dependencies are checked, and binaries are downloaded.
If you use the <code>get_folder.sh</code> script as explained in [[Installation]], most of these dependencies are checked, and binaries are downloaded.
Line 171: Line 171:
# ''Problem description: On the Mac, after loading frames, by clicking “generate XDS.INP”, the program gives some strange symbol “” in XDS.INP. And the more you click “save” button, the more “” appeared. This looks like <br>SPACE_GROUP_NUMBER=0  ! 0 if unknown <br>UNIT_CELL_CONSTANTS= 70 80 90 90 90 90  .''<br> The problem is due to the “Rich text” format in TextEdit when saving "generate_XDS.INP". It is solved by re-downloading the script, and changing format to Plain - everything is working now.
# ''Problem description: On the Mac, after loading frames, by clicking “generate XDS.INP”, the program gives some strange symbol “” in XDS.INP. And the more you click “save” button, the more “” appeared. This looks like <br>SPACE_GROUP_NUMBER=0  ! 0 if unknown <br>UNIT_CELL_CONSTANTS= 70 80 90 90 90 90  .''<br> The problem is due to the “Rich text” format in TextEdit when saving "generate_XDS.INP". It is solved by re-downloading the script, and changing format to Plain - everything is working now.
# on a Mac, you may find a stream of the following error messages in the console window: <code>Jan 31 14:35:17  xdsgui[20939] <Error>: Error: this application, or a library it uses, has passed an invalid numeric value (NaN, or not-a-number) to CoreGraphics API and this value is being ignored. Please fix this problem. Jan 31 14:35:17  xdsgui[20939] <Error>: If you want to see the backtrace, please set CG_NUMERICS_SHOW_BACKTRACE environmental variable.</code> This sounds terrible, but is actually harmless. Since it is a message from Qt (which XDSGUI uses for graphics), ''it does not compromise the XDS data processing in any way''. If it bothers you, just suppress the printout of these messages, by <code>xdsgui 2>&1 | egrep -v 'CoreGraphics|CG_NUMERICS'</code>
# on a Mac, you may find a stream of the following error messages in the console window: <code>Jan 31 14:35:17  xdsgui[20939] <Error>: Error: this application, or a library it uses, has passed an invalid numeric value (NaN, or not-a-number) to CoreGraphics API and this value is being ignored. Please fix this problem. Jan 31 14:35:17  xdsgui[20939] <Error>: If you want to see the backtrace, please set CG_NUMERICS_SHOW_BACKTRACE environmental variable.</code> This sounds terrible, but is actually harmless. Since it is a message from Qt (which XDSGUI uses for graphics), ''it does not compromise the XDS data processing in any way''. If it bothers you, just suppress the printout of these messages, by <code>xdsgui 2>&1 | egrep -v 'CoreGraphics|CG_NUMERICS'</code>
# there is a bug in the Jan-2017 version of XDSGUI that prevents it from displaying non-CBF files. The symptom is that the frames appear to be blank. The workaround is: go to (upper left) "Menu"->"Settings"->remove the string "/usr/local/lib64/dectris-neggia.so". The fix is in the Oct-2017 version (thanks Wolfgang!).
# there is a bug in XDSGUI that prevents it from displaying .h5 files. The symptom is that the frames appear to be blank. The workaround is: go to (upper left) "Menu"->"Settings"->remove the string "/usr/local/lib64/dectris-neggia.so" from "generic library", and install <code>H5ToXds</code> or <code>hdf2mini-cbf</code> as explained above.
# in the COLSPOT tab, one sometimes has to jiggle a bit the border in the middle of the page, between the log output and the two plots, to trigger showing the plots.
# XDSGUI sometimes hangs (and must be killed with Ctrl-C) when running <pre>grep _E INTEGRATE.LP | tail -2 >x; sed -e 's/ BEAM_DIVERGENCE=/! BEAM_DIVERGENCE=/' -e 's/ REFLECTING_RANGE=/! REFLECTING_RANGE=/' XDS.INP >>x; mv x XDS.INP</pre> in the tools tab. A potential workaround is given [[XDSGUI#tools|above]] - pls try!


If you find a bug, please send email to Kay dot Diederichs at uni-konstanz dot de , with enough information/data to reproduce the bug.
If you find a bug, please send email to Kay dot Diederichs at uni-konstanz dot de , with enough information/data to reproduce the bug.
Line 182: Line 180:
* The display of large frames in the FRAME tab may be slow over the network.
* The display of large frames in the FRAME tab may be slow over the network.
* The green INCLUDE_RESOLUTION and red semi-transparent EXCLUDE_RESOLUTION_RANGE circles in the Frame tab as well as all resolution values in the Frame and IDXREF tabs are calculated from values in XDS.INP (rather than from the refined values in XPARM.XDS, which XDS uses). For the (curved) Pilatus 12M, the calculations in XDSGUI do not give the correct results.
* The green INCLUDE_RESOLUTION and red semi-transparent EXCLUDE_RESOLUTION_RANGE circles in the Frame tab as well as all resolution values in the Frame and IDXREF tabs are calculated from values in XDS.INP (rather than from the refined values in XPARM.XDS, which XDS uses). For the (curved) Pilatus 12M, the calculations in XDSGUI do not give the correct results.
* The path (e.g. /usr/local/lib64/dectris-neggia.so) to the <code>dectris-neggia</code> library (available from Dectris) or the <code>durin-plugin</code> library (download from Diamond Light Source, DLS) should be entered into the "generic frame library" entry, in Menu->Settings, to enable visualization of raw data from Eiger detectors, but this mechanism currently does not work properly. Therefore, <code>H5ToXds</code> or <code>hdf2mini-cbf</code> should be installed as explained above.


== News ==
== News ==
Kay
Bureaucrats
2,651

edits

Retrieved from "https://wiki.uni-konstanz.de/xds/index.php/Special:MobileDiff/4202...4219"
Cookies help us deliver our services. By using our services, you agree to our use of cookies.
More information

Navigation menu