Online Help, Pathfinder, and a Small Exercise in Matching
Sources of Help in Moloc
- Clicking '?' ('???') presents a short caption
of the menu items on the display screen. The flag for toggled help
(which can be modified in '.../:/h') governs toggled or flashed
appearance.
- Clicking a menu item with the Ctrl-key pressed
presents a more extended description of the menu item in the text
port window. Thus, 'Ctrl'-clicking
'h' (help and other toggles) from within menu
'.../:' will explain the difference between toggled and flashed
help, mentioned above.
- The text-port help is equipped with a search utility that
enables string searches within the help text of the current menu.
It is activated by clicking '?' with pressed
Ctrl-key and asks the user to type the expression to search for.
- Finally, the Moloc home page provides a source of help.
Searches with the web browser can help to find particular topics.
Searching the update pages will inform about new implementations.
Pathfinder
In Moloc's main (3-letter) menu the user can search the menu headers
and the corresponding help text for all of Moloc's menus.
This utility can help the user to find out where a specific task can be
performed.
- Choose any of the menu items (except '???') with the shift key
pressed. Choosing 'exi' searches the whole menu tree, otherwise only the
chosen subtree (e.g. 'mch') is searched.
- The program asks for a search expression (e.g. pharmacoph').
- It then asks for the amount of output required.
- Then all paths, where the corresponding expression was found, will
be presented on the text port. For 'parmacoph', 39 hits are reported when
choosing 'exi', 14 hits when choosing 'mch'.
- Paths are given in the form mch/d/h, meaning that one has to digress
through menus 'mch' and 'd' to find the corresponding text (and function)
under menu item 'h'.
- Entering more then one expression retrieves only menus in
which all of them can be found (logical AND).
- Using several synonyms or related expressions may enhance the success!
Matching the B-chain of '4dfr' onto the A-chain, an exercise
- Read in 'CHN A' and 'CHN B' as two separate Moloc entries from
the file 4dfr.pdb (see 'files').
- Generate the corresponding C-alpha structures:
- Go to menu 'pca' (peptide modeling)
- Click 'k' with the Ctrl-key pressed.
This will give you a description of the concept of C-alpha (Calf)
structures as relevant for Moloc.
- Click 'k' without Ctrl-key and pick the two
entries '4dfr_A' and '4dfr_B' to obtain two new entries '4dfr_A_ca'
and '4dfr_B_ca'. The original all-atom structures are set to
invisible.
- Exit to return to the main menu.
- Click '???' with the Ctrl-key pressed to obtain
a requester for the term you are looking for. Enter 'match' and
answer the requester (Enter-key or RIGHT-hand mouse click).
- On the text window the program will tell you that the 'mch'
menu is the place to go for matching functionality (all occurrences
of 'match' will be highlighted by upper case printing). Thus click
'mch' (match utilities).
- Click '?' with the Ctrl-key pressed, but
answer the requester just with a question mark '?'.
Now Moloc will print all menu items with their extended help texts
(where available) to the text port.
- Choose 'm' (pair-wise matching). Other options
(e.g. i, j) work with more than two entries (multi-match) and do
not return a resulting transformation.
- The extended help to menu item 'm' advises you to first pick
the structure to be moved (4dfr_B_ca), then the target (4dfr_A_ca).
Upon doing so you enter the menu for
pair-wise match (pmch):
- Here, options 's', 'n', and 'h' are specific to
Calf structures as you can find out by reading the corresponding
extended help texts.
- Click 's' (sequence-wise specifications)
whereupon you are thrown into the set menu. For simplicity, just
specify both entries (option 'e' and pick them).
- Exit the set menu, to be asked whether the assignment is meant
to be backwards (which it isn't). The program will now draw dotted
lines connecting corresponding Calf's, with an indication of the
actual distance.
- Click 'r' (do rigid-body match) to perform
a rigid-body superimposition. Almost all distances will now be in
the range of a few tens of picometers (fractions of an Angstrom).
A rmsd of 0.6838 Angstrom should result.
- The extended help of
'i' (iterative rigid body match) will tell you
that you have the possibility to emphasize regions of good overlap.
- Click 'i' to obtain a weighted rmsd of 0.3633
Angstrom after three iterations.
- Exit the pair-wise match menu to return to the match menu.
- Moloc will tell you that it has kept the overall transformation
(called mch1), and that this transformation is now the current one.
The two Calf structures are now superimposed. However, in order to
achieve the same for the full (all-atom) structures:
- Click 'r' (relocate entry with current transformation)
to obtain a selector of entries that ought to be moved with the same
(current) transformation.
- Select '4dfr_B' to have this structure moved on top of its
corresponding Calf structure '4dfr_B_ca'.
- By making '4dfr_A' and '4dfr_B' visible you will recognize a close
atom-wise correspondence except for peripheral side chains, and a few
loop regions.
The menu item 't' (handling of transformations)
leads to a separate menu where various operations with transformations
can be performed, most importantly storing them onto disk, and reading
them back again. Exploring details of this menu is left to your
inquisitiveness.