Installation: Difference between revisions

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This article has information that should ease the installation of XDS and related programs like ([[XDS-viewer]], [[xdsstat]], [[XDSGUI|xdsgui]]). It is ~~assumed that~~ binaries (or links to binaries) ~~should~~ go to /usr/local/bin . This means that you should do this as the administrator (root), or have sudo rights (Mac, and some Linux distros).

This article has information that should ease the installation of XDS and related programs like ([[XDS-viewer]], [[xdsstat]], [[XDSGUI|xdsgui]]). Generally, it is easiest if binaries (or links to binaries) go to /usr/local/bin . This means that you should do this as the administrator (root), or have sudo rights (Mac, and some Linux distros). But it is mostly possible to install without administrative privileges - the exception is XDSGUI on Linux which may require installation of certain libraries by the administrator.

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=== [[XDS]] package ===

If you are an academic user, as root (on Ubuntu, use "sudo -i" to become root)

If you are an academic user, as root (on Ubuntu, use "sudo -i" as a separate command, to become root):

<pre>

cd /usr/local/bin

wget ~~--no-check-certificate~~ -O- https://xds.mr.mpg.de/XDS-gfortran_Linux_x86_64.tar.gz | tar xzvf -

wget -O- https://xds.mr.mpg.de/XDS-gfortran_Linux_x86_64.tar.gz | tar xzvf -

ln -sf XDS-gfortran_Linux_x86_64/* .

# until 2025-05-02 the XDS tarfile for Linux had a different name:

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# ln -sf XDS-INTEL64_Linux_x86_64/* .

</pre>

In case the above website is unavailable, there is a [https://{{SERVERNAME}}/pub/xds backup site].

If you don't have root rights, replace /usr/local/bin by $HOME/bin in the first line above, and make sure that $HOME/bin is in your $PATH (google "linux set path" or similar).

If you want to process data from the [[Eiger]] detector: see below for plugins that allow XDS to read the .h5 files. Similarly for gzip-ed CBF files as mostly collected at EMBL Hamburg.

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=== other programs: [[XDS-Viewer]], [[XDSSTAT]], [[XDSCC12]], [[XDSGUI]], [[XSCALE_ISOCLUSTER]], [[spot2pdb]], [[generate_XDS.INP]] ===

... can be downloaded from https://{{SERVERNAME}}/pub/linux_bin/ . A simple way to obtain them is to create an empty folder, "cd" to that folder and then

wget ~~--no-check-certificate~~ -N https://{{SERVERNAME}}/pub/linux_bin/get_folder.sh

wget -N https://{{SERVERNAME}}/pub/linux_bin/get_folder.sh

chmod +x get_folder.sh

./get_folder.sh

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As root, the script copies the programs into /usr/local/bin/linux_bin, and links them to /usr/local/bin. As a normal user, they are downloaded to $HOME/bin/linux_bin, and linked to your $HOME/bin. In the latter case, make sure that $HOME/bin is in your $PATH.

Although CCP4 is not required by XDS, XSCALE or XDSGUI, some of the programs (namely XDSSTAT, and MTZ file creation in XDSCONV) need its tools (F2MTZ, ...) or libraries, or run its programs (POINTLESS and COOT can be run from XDSGUI). Therefore, CCP4 should be installed.

=== tools and helper programs for [[generate_XDS.INP]] and [[XDSGUI]], and libraries ===

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* helper programs for [[XDSGUI]] are listed and discussed at [[XDSGUI#Dependencies]]. Nota bene: XDSGUI needs [[generate_XDS.INP]] unless you already have a working XDS.INP.

Since XDSGUI depends on graphics packages that may need to be installed, you can check the xdsgui binary with

Since XDSGUI depends on graphics packages that may need to be installed (by root), you can check the xdsgui binary with

ldd `which xdsgui` | grep found

and that should show you the libraries it didn't find. Your friendly system administrator knows the specific commands to install those libraries.

and that should show you the libraries it '''didn't''' find. Your friendly system administrator knows the specific commands to install those libraries.

N.B. this may list libpng15.so for the latest XDSGUI (compiled May 2023), but you can ignore that!

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sudo apt-file update

Versions of XDSGUI compiled before 2021: Ubuntu 20.04: If the Qt5 libraries are missing, use <code>sudo apt install libqt5gui5 libqt5printsupport5 libqt5opengl5</code>. On CentOS7, this would be <code>yum -y install qt5-qtbase-gui qt5-qtbase</code> .

On Ubuntu, XDSGUI may require <code>sudo apt install libxcb-xinerama0</code>

On Ubuntu, ~~latest~~ XDSGUI may require <code>sudo apt install libxcb-xinerama0</code>

<code>xxdiff</code> is likely available for your distribution - google for it, or try e.g.

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on RHEL6/CentOS6/SL6 systems, or

apt install xxdiff

on Ubuntu. If Ubuntu ~~20.04~~ doesn't find it, use the latest from http://archive.ubuntu.com/ubuntu/pool/universe/x/xxdiff/

on Ubuntu. If Ubuntu doesn't find it, use the latest from http://archive.ubuntu.com/ubuntu/pool/universe/x/xxdiff/

An <code>xxdiff</code> binary that runs on CentOS7 (RHEL7, SL7) is provided by the <code>get_folder.sh</code> script.

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sudo mkdir /usr/local/bin

As an alternative that does not require root for installation, one may create a directory $HOME/bin and use that for the programs and links. Also, this requires modification of the $PATH, by a one-time

'''As an alternative that does not require root for installation''', one may create a directory $HOME/bin and use that for the programs and links. Also, this requires modification of the $PATH, by a one-time

mkdir $HOME/bin

echo 'export PATH=$PATH:$HOME/bin' >> ~/.zprofile

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if [ ! -e /usr/local/bin ]; then mkdir /usr/local/bin; fi

cd /usr/local/bin

# if the next command produces an error message, use the --insecure option

curl -L -o - https://xds.mr.mpg.de/XDS-OSX_64.tar.gz | tar xzvf -

ln -sf XDS-OSX_64/* .

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now enter the password, and then

if [ ! -e /usr/local/bin ]; then mkdir /usr/local/bin; fi

cd /usr/local/bin;

cd /usr/local/bin

curl -L -o - https://xds.mr.mpg.de/XDS-Apple_M1.tar.gz | tar xzvf - ;

# if the next command produces an error message, use the --insecure option

ln -sf XDS-Apple_M1/* . ;

curl -L -o - https://xds.mr.mpg.de/XDS-Apple_M1.tar.gz | tar xzvf -

ln -sf XDS-Apple_M1/* .

exit

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[[generate_XDS.INP]] requires the [https://developer.apple.com/download/more/ Xcode command line tools] to be installed (free of charge): open a Terminal window, and enter <code>sudo xcode-select --install</code> (the download has a size of about 750MB; the downloader is much too pessimistic about the time it takes).

Although CCP4 is not required by XDS ~~itself~~, some of the programs (XDSSTAT, and MTZ file creation in XDSCONV, POINTLESS ~~and~~ COOT) ~~use CCP4 tools or libraries~~. Therefore, CCP4 should be installed. Open a Terminal and check the existence of the file .zprofile , and its content:<pre>

Although CCP4 is not required by XDS, XSCALE or XDSGUI, some of the programs (namely XDSSTAT, and MTZ file creation in XDSCONV) need its tools (F2MTZ, ...) or libraries, or run its programs (POINTLESS, COOT can be run from XDSGUI). Therefore, CCP4 should be installed. Open a Terminal and check the existence of the file .zprofile , and its content:<pre>

kay@Kays-MacBook-Air-2018 ~ % ls -l .zprofile

-rw-r--r-- 1 kay staff 107 7 Mär 09:41 .zprofile

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source $HOME/.profile

# Added by CCP4 package manager:

. '/Applications/ccp4-8.0/bin/ccp4.setup-sh'

source '/Applications/ccp4-8.0/bin/ccp4.setup-sh'

# or

. '/Applications/ccp4-9/bin/ccp4.setup-sh'

source '/Applications/ccp4-9/bin/ccp4.setup-sh'

</pre>If the file does not exist, create it - the easiest way is:

<pre>

echo . /Applications/ccp4-8.0/bin/ccp4.setup-sh >> $HOME/.zprofile

echo source /Applications/ccp4-8.0/bin/ccp4.setup-sh >> $HOME/.zprofile

# or

echo . /Applications/ccp4-9/bin/ccp4.setup-sh >> $HOME/.zprofile

echo source /Applications/ccp4-9/bin/ccp4.setup-sh >> $HOME/.zprofile

# depending on which CCP4 version you have installed

</pre>The <code>get_folder.sh</code> script (below) checks the CCP4 setup, and creates the necessary files if needed.

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mkdir -p /usr/local/bin/mac_bin

cd /usr/local/bin/mac_bin

# if the next command produces an error message, use the --insecure option

curl -O -R https://{{SERVERNAME}}/pub/mac_bin/get_folder.sh

chmod +x get_folder.sh

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mkdir -p /usr/local/bin/mac_bin

cd /usr/local/bin/mac_bin

# if the next command produces an error message, use the --insecure option

curl -O -R https://{{SERVERNAME}}/pub/mac_bin/get_folder_silicon.sh

chmod +x get_folder_silicon.sh

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In order to enable [[Eiger]] data processing, the <code>get_folder.sh</code> (or <code>get_folder_silicon.sh</code>) script

# copies Dectris' Neggia library and DLS's Durin library into <code>/usr/local/lib64</code> . NOTE that the names of the native libraries for the Apple Silicon Macs ends with *-Apple-arm64.so . On Silicon Macs you can either use the Intel binaries for XDSGUI and XDS, or the Silicon binaries - the latter are recommended. You could in principle mix them but then you have to be careful with what you enter in the LIB= line of XDS.INP; and what you enter in Menu/Preferences/Paths/generic library of XDSGUI.

# copies Dectris' Neggia library and DLS's Durin library into <code>/usr/local/lib64</code> . NOTE that the names of the native libraries for the Apple Silicon Macs ends with *-Apple-arm64.so .

# copies [https://www.globalphasing.com GlobalPhasing's] <code>hdf2mini-cbf</code> into <code>/usr/local/bin</code>, but under the name <code>H5ToXds</code> (consider getting a [https://www.globalphasing.com/autoproc/ autoPROC] license!)

# copies <code>h5dump</code> [https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.1/bin/unix/hdf5-1.12.1-Std-macos11_64-clang.tar.gz] into <code>/usr/local/bin</code>

A [https://{{SERVERNAME}}/pub/mac_bin/XDS-Viewer-macOS10.13.dmg 10.13] Qt5 version of XDS-viewer (compiled by T. Hauß) works on macOS Catalina, and is installed by <code>get_folder.sh</code>. Older Macs need [https://{{SERVERNAME}}/pub/mac_bin/XDS-Viewer-0.6.dmg this version]; newer macOS should install [https://{{SERVERNAME}}/pub/mac_bin/XDS-Viewer-macOS10.15.dmg 10.15].

For XDSGUI, you have a choice between the version for Intel Macs and that for Silicon Macs. Both do work on Silicon Macs, except for the plugin libraries - for these, the correct version (ending with -Apple-arm64.so) must be used together with xdsgui_mac_silicon.

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A quick way is also

which generate_XDS.INP xdsgui xds xds-viewer xdsstat ~~xdscc12~~

which generate_XDS.INP xdsgui xds xds-viewer xdsstat coot

and this should return a line for each of the programs asked for.

@@ Line 1: / Line 1: @@
-This article has information that should ease the installation of XDS and related programs like ([[XDS-viewer]], [[xdsstat]], [[XDSGUI|xdsgui]]). It is assumed that binaries (or links to binaries) should go to /usr/local/bin . This means that you should do this as the administrator (root), or have sudo rights (Mac, and some Linux distros).
+This article has information that should ease the installation of XDS and related programs like ([[XDS-viewer]], [[xdsstat]], [[XDSGUI|xdsgui]]). Generally, it is easiest if binaries (or links to binaries) go to /usr/local/bin . This means that you should do this as the administrator (root), or have sudo rights (Mac, and some Linux distros). But it is mostly possible to install without administrative privileges - the exception is XDSGUI on Linux which may require installation of certain libraries by the administrator.
@@ Line 6: / Line 6: @@
 === [[XDS]] package ===
-If you are an academic user, as root (on Ubuntu, use "sudo -i" to become root)
+If you are an academic user, as root (on Ubuntu, use "sudo -i" as a separate command, to become root):
 <pre>
   cd /usr/local/bin
-  wget --no-check-certificate -O- https://xds.mr.mpg.de/XDS-gfortran_Linux_x86_64.tar.gz | tar xzvf -
+  wget -O- https://xds.mr.mpg.de/XDS-gfortran_Linux_x86_64.tar.gz | tar xzvf -
   ln -sf XDS-gfortran_Linux_x86_64/* .
 # until 2025-05-02 the XDS tarfile for Linux had a different name:
@@ Line 15: / Line 15: @@
 # ln -sf XDS-INTEL64_Linux_x86_64/* .
 </pre>
 In case the above website is unavailable, there is a [https://{{SERVERNAME}}/pub/xds backup site].
+If you don't have root rights, replace /usr/local/bin by $HOME/bin in the first line above, and make sure that $HOME/bin is in your $PATH (google "linux set path" or similar).
 If you want to process data from the [[Eiger]] detector: see below for plugins that allow XDS to read the .h5 files. Similarly for gzip-ed CBF files as mostly collected at EMBL Hamburg.
@@ Line 21: / Line 23: @@
 === other programs: [[XDS-Viewer]], [[XDSSTAT]], [[XDSCC12]], [[XDSGUI]], [[XSCALE_ISOCLUSTER]], [[spot2pdb]], [[generate_XDS.INP]]  ===
 ... can be downloaded from https://{{SERVERNAME}}/pub/linux_bin/ . A simple way to obtain them is to create an empty folder, "cd" to that folder and then
-  wget --no-check-certificate -N https://{{SERVERNAME}}/pub/linux_bin/get_folder.sh
+  wget -N https://{{SERVERNAME}}/pub/linux_bin/get_folder.sh
   chmod +x get_folder.sh
   ./get_folder.sh
@@ Line 27: / Line 29: @@
 As root, the script copies the programs into /usr/local/bin/linux_bin, and links them to /usr/local/bin. As a normal user, they are downloaded to $HOME/bin/linux_bin, and linked to your $HOME/bin. In the latter case, make sure that $HOME/bin is in your $PATH.
+Although CCP4 is not required by XDS, XSCALE or XDSGUI, some of the programs (namely XDSSTAT, and MTZ file creation in XDSCONV) need its tools (F2MTZ, ...) or libraries, or run its programs (POINTLESS and COOT can be run from XDSGUI). Therefore, CCP4 should be installed.
 === tools and helper programs for [[generate_XDS.INP]] and [[XDSGUI]], and libraries ===
@@ Line 32: / Line 36: @@
 * helper programs for [[XDSGUI]] are listed and discussed at [[XDSGUI#Dependencies]]. Nota bene: XDSGUI needs [[generate_XDS.INP]] unless you already have a working XDS.INP.
-Since XDSGUI depends on graphics packages that may need to be installed, you can check the xdsgui binary with
+Since XDSGUI depends on graphics packages that may need to be installed (by root), you can check the xdsgui binary with
   ldd `which xdsgui` | grep found
-and that should show you the libraries it didn't find. Your friendly system administrator knows the specific commands to install those libraries.
+and that should show you the libraries it '''didn't''' find. Your friendly system administrator knows the specific commands to install those libraries.
 N.B. this may list libpng15.so for the latest XDSGUI (compiled May 2023), but you can ignore that!
@@ Line 48: / Line 52: @@
    sudo apt-file update
-Versions of XDSGUI compiled before 2021: Ubuntu 20.04: If the Qt5 libraries are missing, use <code>sudo apt install libqt5gui5 libqt5printsupport5 libqt5opengl5</code>. On CentOS7, this would be <code>yum -y install qt5-qtbase-gui qt5-qtbase</code> .
+On Ubuntu, XDSGUI may require <code>sudo apt install libxcb-xinerama0</code>
-On Ubuntu, latest XDSGUI may require <code>sudo apt install libxcb-xinerama0</code>
 <code>xxdiff</code> is likely available for your distribution - google for it, or try e.g.
@@ Line 56: / Line 58: @@
 on RHEL6/CentOS6/SL6 systems, or
   apt install xxdiff
-on Ubuntu. If Ubuntu 20.04 doesn't find it, use the latest from http://archive.ubuntu.com/ubuntu/pool/universe/x/xxdiff/
+on Ubuntu. If Ubuntu doesn't find it, use the latest from http://archive.ubuntu.com/ubuntu/pool/universe/x/xxdiff/
 An <code>xxdiff</code> binary that runs on CentOS7 (RHEL7, SL7) is provided by the <code>get_folder.sh</code> script.
@@ Line 73: / Line 75: @@
   sudo mkdir /usr/local/bin
-As an alternative that does not require root for installation, one may create a directory $HOME/bin and use that for the programs and links. Also, this requires modification of the $PATH, by a one-time
+'''As an alternative that does not require root for installation''', one may create a directory $HOME/bin and use that for the programs and links. Also, this requires modification of the $PATH, by a one-time
   mkdir $HOME/bin
   echo 'export PATH=$PATH:$HOME/bin' >> ~/.zprofile
@@ Line 84: / Line 86: @@
   if [ ! -e /usr/local/bin ]; then mkdir /usr/local/bin; fi
   cd /usr/local/bin
+ # if the next command produces an error message, use the --insecure option
   curl -L -o - https://xds.mr.mpg.de/XDS-OSX_64.tar.gz | tar xzvf -
   ln -sf XDS-OSX_64/* .
@@ Line 110: / Line 113: @@
 now enter the password, and then
   if [ ! -e /usr/local/bin ]; then mkdir /usr/local/bin; fi
-  cd /usr/local/bin;
+  cd /usr/local/bin
-  curl -L -o - https://xds.mr.mpg.de/XDS-Apple_M1.tar.gz | tar xzvf - ;
+ # if the next command produces an error message, use the --insecure option
-  ln -sf XDS-Apple_M1/* . ;
+  curl -L -o - https://xds.mr.mpg.de/XDS-Apple_M1.tar.gz | tar xzvf -
+  ln -sf XDS-Apple_M1/* .
   exit
@@ Line 128: / Line 132: @@
 [[generate_XDS.INP]] requires the [https://developer.apple.com/download/more/ Xcode command line tools] to be installed (free of charge): open a Terminal window, and enter <code>sudo xcode-select --install</code> (the download has a size of about 750MB; the downloader is much too pessimistic about the time it takes).
-Although CCP4 is not required by XDS itself, some of the programs (XDSSTAT, and MTZ file creation in XDSCONV, POINTLESS and COOT) use CCP4 tools or libraries. Therefore, CCP4 should be installed. Open a Terminal and check the existence of the file .zprofile , and its content:<pre>
+Although CCP4 is not required by XDS, XSCALE or XDSGUI, some of the programs (namely XDSSTAT, and MTZ file creation in XDSCONV) need its tools (F2MTZ, ...) or libraries, or run its programs (POINTLESS, COOT can be run from XDSGUI). Therefore, CCP4 should be installed. Open a Terminal and check the existence of the file .zprofile , and its content:<pre>
 kay@Kays-MacBook-Air-2018 ~ % ls -l .zprofile
 -rw-r--r--  1 kay   staff  107  7 Mär 09:41 .zprofile
@@ Line 134: / Line 138: @@
 source $HOME/.profile
 # Added by CCP4 package manager:
-. '/Applications/ccp4-8.0/bin/ccp4.setup-sh'
+source '/Applications/ccp4-8.0/bin/ccp4.setup-sh'
 # or
-. '/Applications/ccp4-9/bin/ccp4.setup-sh'
+source '/Applications/ccp4-9/bin/ccp4.setup-sh'
 </pre>If the file does not exist, create it - the easiest way is:
 <pre>
-echo . /Applications/ccp4-8.0/bin/ccp4.setup-sh >> $HOME/.zprofile
+echo source /Applications/ccp4-8.0/bin/ccp4.setup-sh >> $HOME/.zprofile
 # or
-echo . /Applications/ccp4-9/bin/ccp4.setup-sh >> $HOME/.zprofile
+echo source /Applications/ccp4-9/bin/ccp4.setup-sh >> $HOME/.zprofile
 # depending on which CCP4 version you have installed
 </pre>The <code>get_folder.sh</code> script (below) checks the CCP4 setup, and creates the necessary files if needed.
@@ Line 158: / Line 162: @@
   mkdir -p /usr/local/bin/mac_bin
   cd /usr/local/bin/mac_bin
+ # if the next command produces an error message, use the --insecure option
   curl -O -R https://{{SERVERNAME}}/pub/mac_bin/get_folder.sh
   chmod +x get_folder.sh
@@ Line 165: / Line 170: @@
   mkdir -p /usr/local/bin/mac_bin
   cd /usr/local/bin/mac_bin
+ # if the next command produces an error message, use the --insecure option
   curl -O -R https://{{SERVERNAME}}/pub/mac_bin/get_folder_silicon.sh
   chmod +x get_folder_silicon.sh
@@ Line 174: / Line 180: @@
 In order to enable [[Eiger]] data processing, the <code>get_folder.sh</code> (or <code>get_folder_silicon.sh</code>) script
-# copies Dectris' Neggia library and DLS's Durin library into <code>/usr/local/lib64</code> . NOTE that the names of the native libraries for the Apple Silicon Macs ends with *-Apple-arm64.so . On Silicon Macs you can either use the Intel binaries for XDSGUI and XDS, or the Silicon binaries - the latter are recommended. You could in principle mix them but then you have to be careful with what you enter in the LIB= line of XDS.INP; and what you enter in Menu/Preferences/Paths/generic library of XDSGUI.
+# copies Dectris' Neggia library and DLS's Durin library into <code>/usr/local/lib64</code> . NOTE that the names of the native libraries for the Apple Silicon Macs ends with *-Apple-arm64.so .
 # copies [https://www.globalphasing.com GlobalPhasing's] <code>hdf2mini-cbf</code> into <code>/usr/local/bin</code>, but under the name <code>H5ToXds</code> (consider getting a [https://www.globalphasing.com/autoproc/ autoPROC] license!)
 # copies <code>h5dump</code> [https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.1/bin/unix/hdf5-1.12.1-Std-macos11_64-clang.tar.gz] into <code>/usr/local/bin</code>
-A [https://{{SERVERNAME}}/pub/mac_bin/XDS-Viewer-macOS10.13.dmg 10.13] Qt5 version of XDS-viewer (compiled by T. Hauß) works on macOS Catalina, and is installed by <code>get_folder.sh</code>. Older Macs need [https://{{SERVERNAME}}/pub/mac_bin/XDS-Viewer-0.6.dmg this version]; newer macOS should install [https://{{SERVERNAME}}/pub/mac_bin/XDS-Viewer-macOS10.15.dmg 10.15].
 For XDSGUI, you have a choice between the version for Intel Macs and that for Silicon Macs. Both do work on Silicon Macs, except for the plugin libraries - for these, the correct version (ending with -Apple-arm64.so) must be used together with xdsgui_mac_silicon.
@@ Line 195: / Line 199: @@
 A quick way is also
-  which generate_XDS.INP xdsgui xds xds-viewer xdsstat xdscc12
+  which generate_XDS.INP xdsgui xds xds-viewer xdsstat coot
 and this should return a line for each of the programs asked for.