This menu contains a set of general purpose utilities.
Most options concern display settings, settings of entries,
or interfacing to the disk. Many of the parameters one can
influence here can be initialized by writing a file, called
.Moloc in the login or current directory.
In this menu various display features attached to single
entries can be modified.
Upon entering this menu for the first time, the program
asks for a identification signature. This signature appears
on the pictures and in the names of the documentation files.
These files (.doc) are generated upon leaving the option.
Also, a command, 'SLIDOC file-name\q, is issued. The user can
define a environment variable SLIDOC (e.g. an editor or
database start-up) to modify the documentation material,
which by default contains view parameters, color and status
of displayed entries as well as signature and date.
This is the interface for reading disk-files of structures
into the program memory. After an entry is read in, the user
is asked to give it a color and a name.
This is the interface for storing single or multiple (if
file type permits) entries onto disk-file. Most file-types
are described in the get-file menu.
This is a general utilities to deal mainly with entries as
ensembles.
This menu can appear in two different forms. The actual
form is determined upon entering the menu. At that instance
the user is asked, wether he wants to restrict browsing to
one or several entry sets. If not, browsing goes over all
entries loaded into Moloc. Then the menu provides tools for
an easy comparison of experimental structures with force
field results. Entries are displayed one at a time and can be
cycled through backwards and forwards. Various checks and
manipulations can be performed:
The following options are accessible after choosing the
":" from the .-menu. They constitute the less frequently
used options and have been transferred to a follow-up menu
for clarity.
Display and Input-Output Tool [. :]
a: entry activity stati
Entries have three possible stati. They are invisible,
visible or active (also visible). Active entries take
part in actions like repositioning in match or energy
evaluation. Hitting the provided fields cycles the sta
tus of an entry.
m: map-contour and surface visibilities
Contours of maps generated in the map menu and surface
entries generated in the surface menu are toggled from
visible to invisible. The visibility mode of maps is
set in the map menu.
e: change entry settings
Various display features attached to single entries can
be modified.
z: center visible entries
The center of the display will be placed at the centroid
of all visible entries.
c: center a picked atom
t: center a typed atom (residue)
For polymers the sequence number is requested. Center
ing is done for Calfa (proteins) or C1' (DNA). If a
water molecule is requested, its number has to be pre
ceded by a = character. Other heterogens are identified
by bracketing the heterogen identifier []. For small
molecules the user ought to apply the same nomenclature
as used in the atom labelling. The entry must be picked
first!
b: protein backbone-representation toggle
Of the currently visible proteins non-backbone bonds
are switched to not visible and back to visible when
operating this toggle switch.
f: photo-sized display
To take pictures from the screen this option may be cho
sen. If you enter it for the first time, you will be
asked for a identification signature. This signature
appears on the pictures and in the names of the documen
tation files. These files (.doc) are generated when you
leave the option. Also, a command, SLIDOC filename, is
issued. You can define a environment variable SLIDOC
(e.g. an editor or database start-up) to modify the
documentation material, which by default contains view
parameters, color and status of displayed entries as
well as signature and date.
g: get entry from file
Whole entries are read in from specified disk files.
s: store entries on files
Generates disk files of entries. Some file formats
allow to store multiple entries on a single files, oth
ers are single entry formats.
p: PostScript file
Makes an Encapsulated PostScript file (.eps) of the
current view to be sent to a printer.
v: stereoscopic view mode
A selector with the available view options pops up from
which the desired mode can be chosen. Alternatively,
the view mode can be changed in any menu by entering one
of the following keyboard key-combinations: 'Alt m\q for
mono, 'Alt s\q for side-by-side stereo, \qAlt f\q for full
screen stereo, and 'Alt w\q for stereo in a window. Full
screen stereo or stereo in a window may not be available
on certain machines.Stereo in a window may require
reduction of monitor resolution prior to login on cer
tain machines.
n: entry handling
Various activities to deal with entries and sets of
entries are possible here, e.g. browsing, deleting,
entry set handling, etc.
:: extras
Seldom needed options, such as changing display parame
ters, setting various toggles which influence the mode
of interactivity, etc.
Single-Entry Display Settings [entry's name]
z: center entry
Puts the center of the visibility volume in the entry's
centroid.
a: atom types on/off
The following color code is used: blue for N, red for O,
magenta for P, yellow for S, green for halogens, white
for alkali metals and group IIA elements, cyan for all
the others except for C and H, which are not colored.
User-defined colors can be set in the .Moloc file.
l: atom labels on/off
Toggles an entry flag to display atom labels. For the
case of polymers, only monomer specific labelling is
invoked (e.g. on C-alfa's). For the case of polymers &
Calf structure there are 3 states: No labels, labels
for all monomers, labels for every 5th monomer. Indi
vidually set flags are not affected, i.e. such atoms
keep their labels until the individual flag is cleared.
Individual flags are changed by picking (left button
on, middle button off), and have several states of
labelling complexity.
s: clear single atom labels and types
Clears all single atom labels, but leaves the entry
label flag unchanged.
t: entry label on/off
This switch toggles the visibility of the entry label
on and off. This label is positioned at the centroid of
the entry.
Toggles entry label
c: color entry
A palette of available colors appears from which the
color of the entry may be chosen. Partial coloring
remains.
p: partial coloring
Here, you are dropped into the set menu to define the
set of atoms on which a new color should be set. Upon
leaving the set menu all bonds for which both atoms
belong to the specified set get the new color.
r: reset color
All partial coloring is reset to the entry color.
h: half bonds
This option displays the bonds in two halves each of
which carries the color of the adjacent atom type. This
option is reset with the r-option.
k: crystallographic equivalents
If crystallographic equivalents have been generated,
they can be made visible or invisible with this toggle
switch.
b: ball stick representation
The program presents two sliders by which the atom
radii (in fractions of the v.d.W. radii) and the bond
radii can be chosen. Zero values correspond to conven
tional line drawings.
n: change atom name
For a picked atom a text box pops up containing the cur
rent name of the atom. Any changes in this box will turn
up in the display and in disk files upon storage of the
entry.
m: change monomer parameters
e: change entry name
g: arrange or relabel atoms
A new menu is entered which allows to rearrange the
sequence of atoms. The new arrangement will show up in
disk files.
f: print molecular formula
The molecular formula is printed to the text port. For
proteins the amino-acid sequence is also printed.
y: yank atom-data into T-factor field
i: change chain id
Select the chain identifiers you want to change.
d: delete entry
Photo Display [foto]
t: take documentation (and show photo-display)
The full-screen display entered with this option is
manipulated with the mouse keys. Pressing the left-
hand, right-hand or middle mouse button switches to
left, right stereo or mono (average) displays respec
tively. In this last case no cross appears on the dis
play. Exit from the full screen display occurs upon
pressing the ESC key. Hitting the space bar writes a
.rgb file from the current display. If the full screen-
display appears with the window managers border: change
the X resources in the .Xdefauls file by setting
'4Dwm*limitResize: false\q.
u: set user signature
The currently held user signature can be changed.
s: set session label
The currently held session label can be changed.
n: set numbering
The numbering can be altered here.
l: letter sizes
Separate letter sizes for the title and the atom labels
can be set.
d,f: foto and documentation
If this switch is set to 'd\q the program only writes a
documentation file when the t-option is chosen. The
setting 'f\q causes the program to enter also the full
size screen.
Get Structures from Files [get]
o: set options
A table of IO options is presented. Get help from that
table.
j: jkl-file
An editable ASCII file type. If written by Moloc it will
contain H-counts, but from other origin not necessar
ily.
f: frc-file
An ASCII file type in the Cambridge format. It contains
usually crystal information, but no H-counts.
s: shx-file
An ASCII file type produced by the SHELLX program pack
age for X-ray refinement. It contains crystal informa
tion but no H-counts. If alternatives are present
(keyword PART), Moloc expects identical atom sequences
in each of the equivalent parts!
r: rtp-file
An ASCII file type of ORTEP format. Three files need be
concatenated: the annotation file, the cell file, and
the coordinate file.
p: pdb-file
An ASCII file type, hopefully written in the Brookhaven
standard format for proteins and nucleic acids. While
H-counts for standard residues will be correctly
assigned (ATOM records) heterogens (HETATM records)
often produce erroneous H-counts, mostly due to the
limited resolution achievable in the measurement of
large structures. If the file contains a directory of
items, they can be read in as separate Moloc entries. Up
to seven entries can be specified.
q: pdb-file and automatic conversion to Calf structure
m: mab-file
An ASCII file type, produced, when a batch job for
energy minimization is launched out of a Moloc session.
This file type may contain several entries, which are
then all read in automatically and given the names as
written in the file and default colors.
w: cor-file
A file type produced by the NMR structure determining
programs DISMAN and DIANA.
c: mca-file (Calf structures)
An ASCII file type, produced, when a batch job for
energy minimization is launched out of a Moloc session.
This file type may contain several entries, which are
then all read in automatically and given the names as
written in the file and default colors.
n: mol-file (also sd)
A structure file as produced by the MACCS database
software. If this file contains several structures (sd-
file) they appear as separate entries.
y: mol2-file
A file format produced by the SYBYL modelling package
l: smiles-file
By default DAYLIGHT data files (.tdt) are assumed, in
which 2- or 3-d coordinates are assumed to be present.
If simple smiles-files are meant, the corresponding
extension (.smi) has to be explicitly typed in the file
specification. If the file contains no 3-d coordinates
a force-field calculation is automatically invoked for
each structure, in order to produce a reasonable 3-d
conformation. If the file contains many structures this
last step may be quite time consuming!
d: gms-file GROMOS dynamics
A structure file as produced by the GROMOS program
package
i: cif file
Crystallographic Information File (CIF). An editable
ASCII file type of IUCr (International Union of Crys
tallography). Due to the generality of the format, the
file may contain much information, such as e.g. display
features.
h: php file
Pharmacophor ASCII file format of Moloc. This file for
mat may be used to set up database searches within the
BIOCAD software. An auxiliary program, Mbcd, provides
access to this possibility.
k: conformation libraries
Submenu to provide access to various multiconformer
format files which are then kept as conformational
libraries in Moloc.
u: user list of files
The user can compose a list names of files (each on a
separate record) which are read consecutively. The pro
gram expects file formats in accord with the file
extensions. If, in addition, a color is specified on
the record, the entry will be correspondingly colored.
This file may also contain electron density map files.
In this case the color has to be preceded by a contour
level. Several levels may be specified.
If the file type is chosen a file-name requester appears
with the default *. This default string will present a
selector with all files in the current directory. Then, the
program reads in all specified files, one after the other. In
interactive mode the user decides for each file whether to
keep it (by specifying color and name) or not. If the
returned string starts with a % (shell prompt), the
following part of the string is passed on to the shell. In
particular, the current directory can be changed by that
token.
Store Entries as Disk Files [sto]
o: IO options
j: jkl-file
s: shx-file
Crystallographic file to be read by the SHELX package.
When writing such a file, Moloc asks for an input file
name. From this file refinement information, not kept
within Moloc, is transferred to the output file. If no
file name is given, such information will be missing.
p: pdb-file
n: mol-file
y: mol2-file
m: mab-file
c: mca-file
d: dat-file (input for MOPAC)
This option produces a file that conforms with the for
mat of an input file for the semiempirical quantum
mechanical program package MOPAC.
l: smiles-file (.tdt)
A Thor data tree file (.tdt) compatible with the Day
light database software
h: php file
A file type to store pharmacophors from Moloc. These
files can be fed to the program Mbcd to issue a BIOCAD
query.
i: cif file
Crystallographic Information File (CIF). An editable
ASCII file type of IUCr (International Union of Crys
tallography). Select all entry with `E'. If you want to
store the library as whole, select it with `L'.
k: conformation libraries
Entry Handling
b: browse entries
The entries currently kept in memory can be looked at
one by one. There are two possible modes which lead to
different menus. If the user defines a entry set to
browse through the visibility of all entries not
belonging to the set remain unchanged, while entries
belonging to the set are set active one by one. If no
set is specified, the all entries in the memory are tog
gled through.
c: copy structure
Generates a new entry, identical with the one picked.
The old entry is set to invisible and the new one
receives a different color and is visible.
k: connect structure
If a structure has missing bonds they may be generated
here. After picking the structure a threshold distance
for bonding must be entered. A value of zero causes the
program to utilize a threshold derived from the sum of
van der Waals radii. If shift-option is selected, all
atoms are disconnected, i.e. all bonds are deleted.
g: generate entry set
The members of the set are chosen by a select box. A
prompt for the set name follows.
a: alter entry set
After selection of an entry set, a selector is pre
sented containing all entries. The ones belonging to
the set are marked with y (yes) the others with n. By
changing these selections the set can be altered.
r: remove entry set
The set is removed, but the entries remain present.
f: define set of multi-fragment entries
A entry set is generated, which contains all entries
that contain more than one fragment.
s: sort entries in a set
The entries in a specified set are arranged such that
their similarity values increase.
d: delete entries
In a selection you can choose which entries to delete.
t: delete entries belonging to a set
p: delete picked entries
j: get new entry coordinates from a .jkl-file
For an existing entry the coordinates are taken over
from the specified .jkl disk file. (useful for DIANA
structures)
m: get mac coord. of entry(ies)
To read in coordinates from a .mac file, the corre
sponding set of entries must already reside in the pro
gram memory. Precisely the set of entries for which
coordinates are given on the .mac file (usually gener
ated by an energy optimization running in batch mode)
must be set in the active state.
5.5.1 Browse Entries
n: next (shifted: previous) entry
Cycling through the entries proceeds by this choice. If
the shift key is pressed, reverse cycling occurs.
Alternatively cycling can be achieved with the mouse
pointer in the display area. For this to happen, the
shift key must be pressed. Picking (anywhere) with the
left mouse button cycles forward, while using the mid
dle button cycles backwards.
c: current entry
A list of entries is presented from which the one can be
selected which will be displayed next. Cycling then
proceeds from here on. if only active entries are
cycled through, the choice must be among those.
s: define command string
If the user desires to make the same examination on
every entry, he can define the examination process as a
string. Then, when proceeding to the next entry, the
program will automatically perform the actions indi
cated on the command string. For example, a string 'e/
h' will cause to execute the examine action and then
display the hydrogen bonds automatically.
g: geometry (written)
The geometry tool is entered in the write mode.
h: check modify silent H's
l: evaluate smiles code
If the entry carries a smiles code to start with, this
code is deleted and a new one is generated. If this gen
eration fails the entry carries no smiles code.
u: united atoms +/-
Explicit H's are removed and replaced by H-counts. If
the shift key is pressed the reverse process takes
place, i.e. explicit H's are added for silent ones.
k: keep only explicit hydrogens
If a structure contains explicit hydrogens, all silent
ones are removed. This is to eliminate possible errors
in the H-count generation algorithm in cases where the
H-count was deduced from geometrical data (e.g. for
.frc files).
b: bond entry
For every pair of non-bonded atoms at bonding distance
a bond is introduced.
m: keep largest (maximum) fragment
d: delete set of atoms
t: delete entry
The currently visible entry is deleted and the next one
is displayed.
f: forge and optimize
e: examine energies
o: optimize duplicate and compare
A duplicate is optimized within the MAB force field and
compared with the original structure. Before optimiza
tion the duplicate worried, if the randomization param
eter is greater than 0.1 pm. Upon leaving the option the
duplicate is deleted.
r: set randomization amplitude
The amplitude for worrying the entry coordinated in the
duplicate of option o can be set here.
In case that the user has specified one or several entry
sets upon entering the menu, browsing is restricted to
entries within this set. Remaining entries can be made
visible or active and keep this state in the browsing
process. This mode is useful e.g. to browse through
inhibitors either in an active site environment or against a
pharmacophor they were found to match. Correspondingly, in
any force field calculation all active entries are included,
in particular also the environment, if the user happens to
set it active. Several of the above items are not available,
while the following new ones appear:
m: mark entry
If an entry is marked an asterisk * is added to its
name. Upon leaving the menu, the marked entries are put
into a net entry set.
p: match to pharmacophor
The current entry is matched on top of a pharmacophor
(specified in option t). The method is as in the match
ing utility.
t: define target pharmacophor
The target pharmacophor for the matching option p is
defined here.
Extras
i: label isolated atoms
Since atoms are not directly displayed, it is sometimes
difficult to realize the presence of isolated atoms.
This option facilitates finding them by making their
labels visible. The choices are no change (BLANK), atom
labels (l), atom markers (a), atom labels and markers
(*), or none (n).
q: label by set
Atom and monomer labels and atom markers can be switch
on and off by the set menu. A select box will prompt
you, which label you want to have them on or off
d: add dashed lines
Add a dashed line between 2 atoms by picking the two
atoms. To remove, click the same to atoms again
v: keep present view
The present view is kept in memory for later retrieval.
If a file name is specified, the view is also stored
onto disk.
w: restore view (e.g. from a file)
A view as defined on a file can be set in this option.
If you specify a view or documentation file, the pro
gram will take the view parameters stored there. Other
wise a view stored in memory can be chosen.
p: set view parameters
The stereo angle influences the impression of depth.
The larger the absolute value, the bigger the depth.
Positive values require to look at the left picture
with the right eye and vice versa. Slice/width varies
the position of the front and back clipping planes,
leaving the center. Hither and far move the front and
back clipping planes, resp. The center gets adjusted
correspondingly. Depth intensity determines the rela
tive intensity of drawing at the back clipping plane as
compared with the intensity at the front plane.
m: set map, line, and font parameters
The linewidth parameter influences the appearance of
lines; positive values lead to non-smoothed lines the
width of which in pixels is given by the linewidth
parameter; zero or negative values lead to smoothed
lines, the more negative the value, the brighter the
lines and the less effective the smoothing (-4 is rec
ommended). lines for maps can be independently speci
fied, though in color-map mode smoothing is always
identical. Map brightness is the brightness of a map
line relative to a bond line. It requires RGB mode.
o: surface dot size
Three dot sizes are available. Large and middle sized
dots use a different type of representation than small
dots. This may result in substantial performance loss,
in particular for machines with limited drawing speed.
For those small dots are recommended in interactive
work. However, for documentation small dots are often
too faint.
c: color editor
Select the color you want to edit. You can adjust your
color in RGB or HSB system. Notice: these systems are
not independent, i.e. moving the RGB sliders will
effect the HSB values and vice versa.
f: colormode
There are two color modes: color-map mode or RGB mode.
The advantages of RGB mode is mainly the blending, but
that requires blending ability. In RGB mode, antialias
ing requires blending ability, too. Depending on the
graphics the may or may not cost performance. Graphics-
dependent means RGB mode if blending does not slow down
the drawing, else color-map mode. Color map mode is not
implemented in the X-version Molox.
b: blending
Different modes off blending. Requires RGB mode and
blending ability of the hardware.
*: lightning of stick and ball representation
The position is determined by a azimuth angle that
fixes the x and y-coordinates of a source on a unit cir
cle and a z-coordinate. Ambient is the diffuse reflec
tion in the shade. It is given in relation to the object
color. Shininess defines the sharp reflex on the sur
face. It is always white.
h: help and other toggles
The visibility of the help list can, on the one hand, be
toggled on and off: The help list is written over the
display. Choice of options can also be made on the ver
tical letter bar, while the list is visible. On the
other hand, the help list only flashed i.e. visible
until the next action: in this case the remaining dis
play is cleared while the help table is visible. Sur
face pick determines whether surface points can be
picked or not.
t: change window title
Change the window and icon title.
l: lock
Locks the Moloc session. The session must be unlocked
with the user password.
k: set recover time
If this parameter is positive (say 10) Moloc writes a
recovery file called 'Moloc.rcv\q every 10 minutes in
the current directory. This file has .cif format and
contains all molecular entries present in core memory
at the time of writing. In the start-up file, .Moloc,
this parameter is called savetime. A value of zero
switches off recovery.
g: get parameter file
Sets the parameter according to the parameter file. A
text box prompts for the file name. Default extension
is .Moloc
s: store parameter file
Writes the current parameters on a file. A text box
prompts for the file name. Default extension is .Moloc
r: write RGB image file
The actual drawing area (without menu) bar is trans
ferred to a pixel image file of RGB format.