Installing Coot Interface¶
Coot¶
The coot script file “flynn.scm” is included in your FLYNN distribution in the “etc” directory. The following steps are required to integrate FLYNN with coot.
The current default version of COOT is 0.9.5, to install another version please look for the files with the appropriate extension.
Install coot (at least version 0.3.3)
Install flynn and writedict somewhere in your path. If you can’t run FLYNN from the command line, neither can Coot.
Place flynn.scm to the coot extensions directory. This is the directory where the files extensions.scm and coot.scm are located.
This directory may be one of the following:
/usr/local/coot/scheme /usr/local/xtal/coot64/share/coot/scheme/ /my_coot_installation/share/coot/scheme/ /ccp4-7.0/share/coot/scheme/ for the cpp4 installation
- on OSX the install for Coot 0.7/0.8 is most likely
/Library/Coot/share/coot/scheme/
Typing which coot may help locate these directories.
Copy flynn.scm to the extension list in coot.scm which is in the same directory as extensions.scm. Please use the appropriate file for your version of coot.
To accomplish this, change the following code in coot.scm for coot 0.7
(define load-all-scheme (lambda (use-gui?) (let ((pre-list (list "filter.scm" "coot-utils.scm")) (post-list (list "coot-lsq.scm" "shelx.scm"
to look like this:
(define load-all-scheme (lambda (use-gui?) (let ((pre-list (list "filter.scm" "coot-utils.scm")) (post-list (list "coot-lsq." "shelx.scm" "flynn.scm"
Finally, make the following changes to extensions.scm
For coot 0.3.3 to 0.5 near the top of the file, change:
(if (defined? 'coot-main-menubar) (let ((menu (coot-menubar-menu "Extensions")))
to become:
(if (defined? 'coot-main-menubar) (let ((menu (coot-menubar-menu "Extensions"))) (add-simple-coot-menu-menuitem menu "Flynn..." (lambda () (do-flynn-gui))) (add-simple-coot-menu-menuitem menu "Make Dictionary..." (lambda () (do-flynn-gendict-gui))) (add-simple-coot-menu-menuitem menu "Fit Sidechains..." (lambda () (do-flynn-fitsidechains-gui)))
For coot 0.6.x, near the top of the file, change:
(if (defined? 'coot-main-menubar) ;; --------------------------------------------- ;; extensions ;; --------------------------------------------- ;; (let ((menu (coot-menubar-menu "Extensions")))
to become:
(if (defined? 'coot-main-menubar) ;; --------------------------------------------- ;; extensions ;; --------------------------------------------- ;; (let ((menu (coot-menubar-menu "Extensions"))) (add-simple-coot-menu-menuitem menu "Flynn..." (lambda () (do-flynn-gui))) (add-simple-coot-menu-menuitem menu "Make Dictionary..." (lambda () (do-flynn-gendict-gui))) (add-simple-coot-menu-menuitem menu "Fit Sidechains..." (lambda () (do-flynn-fitsidechains-gui)))
For coot 0.8 you should make the change to the “Modules” section as shown below:
;; --------------------------------------------------------------------- ;; Modules ;; --------------------------------------------------------------------- (add-simple-coot-menu-menuitem submenu-modules "Fit Ligand..." (lambda () (do-flynn-gui))) (add-simple-coot-menu-menuitem submenu-modules "Make cif..." (lambda () (do-flynn-gendict-gui))) (add-simple-coot-menu-menuitem submenu-modules "Fit sidechains..." (lambda () (do-flynn-fitsidechains-gui)))
WinCoot 0.9.4.1+¶
WinCoot does not support writing extensions in GUILE. Extensions may be written in PYTHON, however.
The WinCoot scheme script file flynn.py is included in your FLYNN distribution in the Data/wincoot directory. The following steps are required to integrate FLYNN with WinCoot.
Install WinCoot (at least version 0.9.4.1)
Install flynn and writedict somewhere in your path. If you can’t run FLYNN from the command line, neither can WinCoot.
Place this file flynn.py in the coot extensions directory where extensions.py is located.
Typically, this directory is C:\WinCoot\lib\python-2.7\site-packages\coot.
Add flynn.py to the extension list in coot_load_modules.py. (same directory as above) before extensions.py
For example:
... "get_recent_pdbe.py", "flynn.py", "extensions.py", ...
Modify the file named enhanced_ligand.py
To add Flynn and MakeDict, find the last menu item in enhanced_ligand.py and add the following menu items below it:
add_simple_coot_menu_menuitem(menu, "Use Flynn to Fit Ligand...", lambda func: do_flynn_gui()) add_simple_coot_menu_menuitem(menu, "Use WriteDict to generate CIF...", lambda func: do_writedict_gui())For example, if “Display Ligand Distortions” is the last menu time, it would look like this:
add_simple_coot_menu_menuitem(menu, "Display Ligand Distortions", lambda func: display_ligand_distortions_func()) add_simple_coot_menu_menuitem(menu, "Use Flynn to Fit Ligand...", lambda func: do_flynn_gui()) add_simple_coot_menu_menuitem(menu, "Use WriteDict to generate CIF...", lambda func: do_writedict_gui())This results in the Ligand menu being updated to include Flynn’s functionality
WinCoot 0.3.3 to 0.8.9.2¶
WinCoot does not support writing extensions in GUILE. Extensions may be written in PYTHON, however.
The WinCoot scheme script file flynn.py is included in your FLYNN distribution in the utilities/flynn/wincoot directory. The following steps are required to integrate FLYNN with WinCoot.
Install WinCoot (at least version 0.3.3)
Install flynn and writedict somewhere in your path. If you can’t run FLYNN from the command line, neither can WinCoot.
Place this file flynn.py in the coot extensions directory where extensions.py is located.
Typically, this directory is C:WinCootsharecootscheme.
Add flynn.py to the extension list in coot_load_modules+gui.py. (same directory as extensions.py) before extensions.py
For example:
"coot-gui.py", "flynn.py", "extensions.py",
Add the following lines to the file named extensions.scm (this will be in your coot distribution)
The easiest place to put this right after the line
menu = coot_menubar_menu("Extensions")
here are the lines to add:
add_simple_coot_menu_menuitem(menu, "Fit Ligand...", do_flynn_gui) add_simple_coot_menu_menuitem(menu, "Make CIF...", do_writedict_gui) add_simple_coot_menu_menuitem(menu, "Fit Sidechains...", do_fitsidechains_gui)