Modifying Display Features
- Startup Moloc with my_project
by issuing the shell command 'mx my_project.ils'. This will
load the protein DHFR and its inhibitor methotrexate into Moloc.
- Enter the display menu with a RIGHT mouse click onto the item
'...' in the main menu ('.' in a submenu).
- Press 'z' center visible entries to put the
visible molecules into the center of the display volume. (Some
structures are positioned so far off the origin, that they are
totally out of sight to start with). Alternatively, centering can
be achieved at startup by adding the switch -c when starting Moloc:
'mx -c my_project.ils'.
- If you are not happy with the side-by-side stereo mode, click
'v' stereoscopic view mode to get a selection of
possible viewing modes. Changes such as to 'mono' or 'window stereo'
can also be caused any time by typing 'Alt-m' or 'Alt-w' as indicated
on the selector panel.
- Furthermore, 'Alt-b' provides a toggle to switch between bitmap
display and a "drawn font" for lables of atoms etc. The drawn font
may be substantially faster for certain graphics board (optimized
for gaming).
Display Methotrexate in Ball and Stick Representation
This can be achieved as follows:
- Click menu item 'e' (change entry settings)
and select methotrexate from the selector or by picking the
structure.
This will throw you into a new menu in which the appearance of
the entry can be modified. All other entries are now invisible.
- Click 'b' ball stick representation to obtain
two sliders by which you can set bond- and atom radius.
The display will change upon accepting the selected slider values.
Experiment with the radii until they satisfy your expectations.
The appearance may still disappoint you because there is not yet
covering of objects drawn behind a surface. Before arranging that
you may experiment with some of the other options of the present
menu, such as:
- a: switching atom types (markers) on/off
- l: switching atom labels on/off
- c: change the color of the entry
- h: make half-bond representation
and several additional possibilities. Important are the two options
for resetting:
- s: clear single atom labels and types
- r: reset color. Here partial coloring and half-bond coloring are
removed in favor of the genuine bond color of the entry.
- Exit this menu to return to the general display menu.
Now, to achieve hiding of covered objects select
menu item:
':', Extras for Interface (GUI)
Here, various less frequently used options to modify display and
user-interface are collected in a separate menu.
- Click 'b' (blending) to obtain a choice of
three blending options, with 'overblend' as default.
- Chose 'cover' to achieve that bond cylinder parts that are within
atomic spheres become invisible behind the sphere.
You may still be dissatisfied with the 'polyhedral' appearance of
the atomic balls. In this case:
- Click 'm' (set map and line parameters) to be
confronted with numerous sliders of which the lowest 'ball pixels'
is here of relevance. Values 0 to 4 of this slider will show you the
various levels of sophistication of ball (and stick) representation.
Higher values will make this level dependent on the size of balls
and sticks as they appear on the screen. The higher the slider
value the less sophisticated will be the representation of a sphere
of given size. Correspondingly, the drawing speed will increase.
Of the numerous options of this menu we just mention a few of the
more important ones.
- *: lightning of stick and ball representation. Here you can play
with ambient light, position of the light source and with the way
spectral reflexes appear.
- p: set view parameters, for stereo angle and clipping planes.
- r: write RGB image file
- h: help and other toggles, governs the function of the '?' button.
For detailed description of the various functionalities and effects
use the extended on-line help facility!
'k', Handling Views, Camera Movies
This menu serves to take and restore views. Several views can be
combined to a 'camera' movie, i.e. they can be replayed with a
specified set of interpolating frames.
- v: keep present view. The current view is kept in memory and can,
optionally, stored in a file.
- Alt v: In addition, the current view can be transferred to memory
from any location in the program by pressing the key combination 'Alt v'.
Particularly, when taking views in option frg/m, where a set of atoms
is moved around, the corresponding movement transformation is
stored in addition to the view.
- w, s, g: Views can be restored, saved to and retrieved from file.
- m: Several views can be combined to a camera movie. When views
have been taken in option 'frg/m', the movie not only contains the
sequence of views but also the movement of atoms. In this case the
set of atoms has to be specified here again.
- i: A movie can be stored as a .cif file. This file contains all
visible structures as well as, in user set 'u0', the atomes specified
for movement. All other sets are removed. At the end of the file
the views (and transfomations) which specify the movie, are stored.
An example, 4dfr_mv.cif, is found in Moloc's data directory
(moloc/dat):
- Read in the file in .../g/i. The program anounces:
'Found movie with 4 views, starting with cif0.'
- Go to .../k. The program anounces: 'Movie installed!'
- Play the movie by selecting 'd' ('Shift d' for backwards playing).
The speed is governed by the number of interpolating frames between
views (option 'p').
- p: Parameters to play a movie are set here. In particular, it
is possible to write every frame of a movie to a bitmap file. This set
of (rather large) files serves to reproduce the movie with display
programs other then Moloc (see below).
- r: Rocking motion about an axis can be specified here. This is
the simplest form of a camera movie.
For more detailed option description consult the help texts (produced
by selecting options with the Ctrl key pressed).
Produce a Video File
- Moloc can produce a set of RGB-files (.bmp, .rgb, .tif) that are
consecutively numbered (options '.../k/d' or 'Dyn/v/w').
- From such consecutively numbered RGB-files one can produce a video file
with the help of 3rd-party programs (e.g. ffmpeg).
- As an example, the (Linux) command to produce a video file (mv.mpg) from
a set of consecutively numbered files (mv_xxx.tif) would read:
ffmpeg -pattern_type glob -i 'mv_*.tif' mv.mpg