How to Read in a Structure from a File and Save Results
Read in the Protein 4dfr.pdb
- Set the current default directory of your shell where you have
your structure files, and where you have write permission.
- To follow the present example, have a copy of the protein structure
file 4dfr.pdb in this directory.
- Start Moloc by typing 'mx'
(or whatever your alias may be).
- Select the menu item '...'. You will be thrown
into the general input, output, display menu, which
can also be reached from most other menus by clicking '.'.
- Select g (get entry from file).
- Select file type p (.pdb files). A string-requestor
appears that proposes to show you all files (*) with extension .pdb in
the current directory.
- Click the RIGHT-hand mouse button or press 'Enter' to answer this
requestor. Before, you may modify the specification (directory path,
file name, extension).
- In the list of files, select the one(s) you want to open by clicking
the corresponding red 'n' (for 'no') with the RIGHT-hand
mouse button to change it to 'y' (for 'yes').
An additional click brings it back to 'n'.
- Click 'x' to end your selection.
- If 4dfr.pdb was your selection, Moloc will show an index of that file:
- HOH 428 428(H2 O1)
- CA B 3 1 CALCIUM ION
- CL B 2 1 CHLORINE ION
- MTX B 1 33 METHOTREXATE
- CL A 2 1 CHLORINE ION
- MTX A 1 33 METHOTREXATE
- CHN B 159 chain
- CHN A 159 chain
Each item is preceded by a square containing the number 0 to indicates
that this item is not selected.
- Click into the squares of your choice to make your selection.
All items carrying the same number (1 to 8, caused by multiple clicking,
clicking with the middle mouse button reduces the count)
will be lumped together into a single Moloc entry.
Choose e.g. CHN A as entry 1, MTX A as entry 2, and HOH as entry 3.
(Alternatively choose all to have everything in a
single entry.)
- For each entry Moloc will present you with a color selector.
(For the 'all'-choice the color choice is a separate menu with centering
option 'z', followed by a string requestor to name
the entry.)
- Click 'x' to exit the 'get' menu and to return to
the display menu.
- Here click 'z' to move the structures in the
center of the display volume (actually, to move the display volume
around the visible structures).
Adjust Silent Hydrogen Counts for Methotrexate
The topology of methotrexate as a small molecule is
insufficiently specified in a .pdb file. Moloc tries to find out its true
topology from its geometry (bond distances, bond angles, planarity).
For inaccurate geometry this may not be successful.
Thus, for heterogens the user has to check whether
the topology was properly assigned.
To this end an entry has to be in the active status,
which can be set in the display menu '.' in which
you should still find yourself.
- Click 'a' to get the list of 3 entries, all labeled
V for visible, and p for polymer.
- Click twice into the V square of the chain and
water entries to make them disappear. Keep methotrexate active
'A' by just clicking once. The A-status
also elects an entry for participation in force field calculations.
- You may want to adjust the view here by
zooming in.
From its origin from a .pdb file, methotrexate is considered a polymer.
To have it considered as a simple small molecule take the following
steps see also:
- Click 'e' (change entry settings).
The list of entries appears again.
- Choose methotrexate from this list (alternatively by
picking the molecule).
The entry settings menu appears
with the entry name as header.
- Click 'o' to remove the (here trivial) monomer
information.
- Click 'l' to display the atom labels. (If the entry
was still a polymer only a single heterogen label would show up now.)
- Exit twice to return to the main menu.
Now, adjust the silent hydrogen counts of the heavy atoms:
- Choose dTp to enter the
builder menu (topology changer).
- Click 'h' (check modify silent H's) to enter the
'hyd' menu. The atom labels have now been replaced by
hydrogen counts (in white). You will recognize that the H-counts of atoms
NA2, NA4, N, CD, OE1, and OE2 are not correct.
The header of the 'hyd' menu is highlighted to indicate that
picking is required to modify the H-counts:
- Pick atoms NA2, NA4, and N with the LEFT-hand
mouse button to increase their H-count (by one for each pick).
- Pick atoms CD, OE1, and OE2 with the MIDDLE
mouse button to decrease their H-count.
- Exit if the H-counts are correct.
- Exit 'dTp'.
Store Methotrexate onto Disk File
Although it's structure is still the same as in
the .pdb file the topology of methotrexate has changed
through the modified H-counts. In order to save these changes the
molecule has to be stored in a file format that is able to preserve
the H-counts:
- Enter the display menu (this could have been done directly from
within the dTp menu!)
- Click 's' (store entries on file) to enter the
'sto' menu which presents a list of available file
formats.
- Choose e.g. 'm' (mab-file) to have the structure
stored in the Moloc-specific file format (.mab). A selector with the
entries currently held by Moloc will appear.
- Choose the structure to be stored ('n' -> 'y', see above).
- Exit from the selector 'x'.
- Moloc now asks for a file name (default: entry name).
(If you chose several structures, Moloc may ask you whether you want
them on a single file, if the file format allows for that.)
- Return the filename (say 'mtx') by a LEFT-hand mouse click
or by pressing 'Enter'.
- The program will issue the message
File written: mtx.mab.
Moloc writes all messages to the text port, i.e. the shell from where
it was started.
Project Startup by Means of Input List Files (.ils): my_project.ils
You may want to have the 3 entries (chain, water, methotrexate)
always available in Moloc, when you start the program without
having to repeat the above file reading procedure. This can be
arranged by the following steps:
- Store all all entries on separate files. You are still in
the 'sto' menu, thus:
- Store the chain as a .pdb file with the result
File written: 4dfr_A.pdb.
- Store water molecules as a .cif file:
File written: 4dfr_A_HOH.cif.
The .cif format is the only file type read by Moloc,
that also carries display parameter values such as entry coloring,
visibility, actual view.
- Start the editor to write a file 'my_project.ils'
containing the three lines:
mtx.mab yellow
4dfr_A.pdb cyan
4dfr_A_HOH.cif
- Start Moloc with an argument: mx my_project.ils
- A second Moloc window will start up with the three entries
in memory. The view will be the same that was actual when the .cif
file was stored. (The water entry may be set to invisible.)
- Of course the .ils file may contain full file paths to gather
project files from different directories.
- The file extensions in the .ils file must be indicative of the
format in which a file is written.
- Other Moloc objects may also be entered via the list file mechanism:
- Electron density maps (with contour indication), example:
map.pg 1.0 blue 2.0 red
This will read map in paginated format and calculate contours
at levels 1 (blue) and 2 (red).
- Positioned comments
- Surfaces