coot.md
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We are running `coot` from ccp4 version 7.1 and there are several other versions available.
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### Changing the application that provides coot - overriding default titles
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-SBGrid uses CCP4's `coot` by default, but that can be changed with an environmental variable. A default title can be specified for any duplicate executable with the `<_EXECUTABLE>` variable where `<EXECUTABLE>` is the **all-capital** name of the executable.
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-For example, since `coot` comes from CCP4 by default, we can change it to CCPEM by setting :
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+SBGrid uses CCP4's `coot` by default, but that can be changed with a configuration file in the ~/.sbgrid_capsules directory. A default title can be specified for any duplicate executable by creating a file with the **name of the executable** that contains a single line with the name of the application. For coot this would be:
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- export _COOT=coot
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+ mkdir -p ~/.sbgrid_capsule
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+ echo echo > ~/.sbgrid_capsule/coot
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-for bash, or
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-
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- setenv _COOT coot
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-
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-for tcsh users.
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-
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-`_COOT` is the executable name, `coot` is the name of the title that will provide the program when we run `coot`.
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-
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-If we do this, we can see (in bash)
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+If we do this, we can see:
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```
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-$ export _COOT=coot
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$ coot --sbwhich
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/programs/x86_64-linux/coot/0.9.1/bin/coot
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```
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@@ -90,7 +81,7 @@ Now `coot` comes from the applciation title **coot**. The default version there
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Let's switch to CCPEM as the provider of the `coot` program.
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To do that we just set the variable:
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```
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-$ export _COOT=ccpem
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+$ echo ccpem > ~/.sbgrid_capsule/coot
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$ coot --sbwhich
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/programs/x86_64-linux/ccpem/1.4.1/bin/coot
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@@ -131,7 +122,7 @@ To use coot from CCPEM version 1.3.0, we set the CCPEM_X variable to 1.3.0
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Set the title for the `coot` executable to "coot" to use Paul Emsley's builds for linux :
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```
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- $ export _COOT=coot
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+echo echo > ~/.sbgrid_capsule/coot
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$ coot --version
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0.9.1 (revision-count 10157)
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Now, let's change `coot` to come from CCP4 and check the version :
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```
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- $ export _COOT=ccp4
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+echo echo > ~/.sbgrid_capsule/ccp4
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$ coot --version
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0.9 (revision-count 9932)
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For more info, see [capsules](capsules), and [version manangement](overrides).
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-For questions or to report bugs, please email bugs@sbgrid.org
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+For questions or to report bugs, please email bugs@sbgrid.org