New command listing:
(Thanks to David Cooper for page improvements/suggestions!)
New Molauto Options
PDB secondary structure settings
New residue/atom draw commands
New residue/atom selection commands
POVRay specific commands
Miscellaneous new commands/settings
map commands
Temperature factor visualization commands
New Commands
New Settings
New molauto options:
"-colsec" color based on secondary structure
"-ecutoff <number>" energy cutoff for ss_hb prediction
New Molscript PDB options:
SET SS_HB ON/OFF
SET COIL_MODE ON/OFF
SET ENERGYCUTOFF number
sets up how molscript will assign secondary structure upon reading in PDB
files (and therefore must be defined BEFORE reading in the file). SS_HB
tells molscript to use a DSSP-like criteria using the ENERGYCUTOFF value
(default: -0.5) for H-bond energies. COIL_MODE is similar to molauto's
"-turns" option.
New Molscript residue/atom draw commands:
AUTO residue_selection
sort of like a built-in "molauto" - it simply makes molscript figure out
how to draw a chunk of residues on its own (using helices, strands, coil,
etc). Currently, this only works with peptide chains.
PROTRINGS residue_selection
NUCLEORINGS residue_selection
fills in the ring portions of either
HIS/TYR/PHE/TRP in the case of PROTRINGS
A/T/U/C/G in the case of NUCLEORINGS
but does NOT draw the atoms/bonds in *ANY* way - so be sure to also
supply a bonds/ball-and-stick command if so desired. Color for the
rings is derived from the linecolor variable.
New Molscript residue/atom selection commands:
LOC id
only selects atoms at the alternate location "id". Useful if the pdb
contains alternate confomers, and only one is desired.
Commands relevant to PovRay output:
SET BLOBVIEW ON/OFF
only applies for CPK output in povray mode - connects all the
generated blobs in a cpk command into a mathematical isosurface,
rather than individual spheres. Off by default. (see the GRASP/rings/blobview page for an example)
SET INTERIORCOLOUR colour
sets the interior colour of a surface (see the gensurf examples page for an example). However,
this requires the map is read in without applying any vertex colours
(i.e. map property type "none" - this is due to current limitations in
POVRay)
Misc. commands/settings:
SET PEPTIDE_DISTANCE number
SET NUCLEOTIDE_DISTANCE number
sets the distance cutoff for determining if a residue is part of the
current chain. The larger the number, the longer the distance allowed
between C-alphas while still being part of the same chain. Default:
peptide_distance 4.2, nucleotide_distance 10.0.
SET FRONTSLAB number
SET BACKSLAB number
the SLAB setting is now a "set" parameter rather than a heading command,
which makes it convenient and easy to slab one object relative to
another. So one could do:
auto in molecule mol1;
set frontslab 0.0;
drawsurf surf covering in molecule mol1;
and the entire mol1 molecule will be drawn, but the surface held in "surf"
will be cut away at everything having a z value greater than 0.0.
In addition, the front and back slab values can be set
independently, so objects can be unequally sliced. For an example of
this, see the gensurf examples page.
Commands that are relevant to drawing maps:
Map properties:
All surface files (electron density maps, GRASP maps, etc) can employ
the following properties for use as the vertex color:
- none (default) - linecolour variable
- potential - poisson-boltzmann potential (GRASP) or amino acid type
(all other)
- curvature - curvature of the surface
- distance - distances (GRASP) or atom color/residue color of nearest
atom (all other surface types) (atom color used if colourparts is off)
- property1 - property1 (GRASP) or hydrophobicity of nearest residue
(all other)
- property2 - property2 (GRASP) or hydrogen bond donor/acceptor of
nearest residue(all other)
- discretecolours - discretecolours (GRASP only) - can be used in
conjunction with the coldef option under readsurf to read in user-defined
discrete colour values from GRASP.
- scalars <mapid> - map scalars from mapid onto the surface (used
for mapping APBS electrostatics onto generated surfaces, for example - see
here for more information)
using the following color schemes for each type:
- none: linecolour is used to determine map color (default)
- potential: positively charged aa's use the "mapramp from" color,
negative residues use the "to" color
- curvature: negative curvature (valleys) uses the "mapramp from"
color, positive curvature (peaks) uses the "to" color
- distance: color based on either the nearest residue color (if
colourparts is on) or atom color (if colourparts is off)
- property1: hydrophilic aa's use the "mapramp from" color,
hydrophobic aa's use the "to" color as based on the Kyte-Doolittle
scheme
- property2: H-bond donors use the "from" color, H-bond acceptors
use the "to" color
Finally, all maps can be smoothed using the "lambda" variable. This
defines the amount of smoothing performed on a surface using a
Laplacian/Gaussian filter. Typically, 0.5-0.6 works reasonably well.
However, this shouldn't typically be used with electron density maps,
since it may smooth out the inherent function thats being visualized.
CONTOUR id AT cont_level [COVERING atom_selection] [OUTPUT "output.gts"]
CONTOUR id AT cont_level [NOTCOVERING atom_selection] [OUTPUT "output.gts"]
Contours map "id" at the contour level "cont_level". If the covering
atom selection is specified, the map will be drawn at the stored
mapradius around the atoms, otherwise the whole map is drawn. Be sure
to use the "covering" selection if a property type other than "none"
is used, since it is at the contour stage that the vertex colors are
assigned. The optional "output" argument can be used to save the
resulting surface to a gts file (the file format of which is described here.
DELETEMAP id
DELETESURF id
Deletes electron density/surface map "id" from memory. ONLY USE IF
THE PROGRAM REPORTS MEMORY PROBLEMS. May be necessary if your map is
enormous. e.g.:
read prot "prot.pdb";
readmap foo "friggin_huge.omap";
ball-and-stick in residue A50;
contour foo at 1.0 covering in residue A50;
deletemap foo;
readmap bar "bar.omap" covering in residue B50 plus 2;
ball-and-stick in residue B50;
contour bar at 1.0 covering in residue B50;
deletemap bar;
DRAWSURF id [COVERING atom_selection] [OUTPUT "output.gts"]
DRAWSURF id [NOTCOVERING atom_selection] [OUTPUT "output.gts"]
Draws the surface map using an atom selection, if specified. The map
will be drawn at the stored mapradius around the atoms, or the inverse
if the NOTCOVERING version of drawsurf is used (i.e. the surface
around the atom selection is *ignored*). Only maptypes 0 and 1 apply
for surface maps. However, "smoothmap" on/off does apply. Be sure
to use the "covering" selection if a property type other than "none"
is used, since it is at the drawsurf stage (at least for
MSMS/generated surfaces) that the vertex colors are assigned. The
optional "output" argument can be used to save the resulting
surface to a gts file (the file format of which is described here.
GENSURF id1 [COVERING atom_selection PLUS radius] [USING property]
[SAMPLING number] [LAMBDA number]
generates a water-accessible surface using the function:
density = (1.0 - (dist/rad)^2)^2
on a grid covering the atom selection. The distance is the distance
from the atom and radius is the van-der-waal radius plus the radius of
water. All points with values greater than zero (and where (dist/rad)
<= 1.0) are considered part of the surface. The "sampling" is defined
as the number of times 1Angstrom will be sampled - e.g. a value of 0.5
generates a surface sliced at 0.5A intervals (default 0.75).
READMAP id filename [COVERING atom_selection PLUS radius] [USING
property] [LAMBDA number]
Reads map "id" from the DSN6 or BRIX file "filename". If you specificy
the covering selection, molscript will still read in the whole file,
but will set the initial map extent appropriately. It isn't
necessary, but can cut down on extra "junk" floating around the map.
The "USING" option can be specified to color the map vertices
according to the properties listed in the "properties" section.
READSURF id1 filename [USING property] [LAMBDA
number] [COLDEF filename2]
Reads surface file "id1" from the file "filename" (either GRASP or
MSMS format - specify the entire filename for GRASP, and the basename
("foo" for foo.vert and foo.face) for MSMS files). Reads the entire
map plus the color property in "id2" (see "properties" section). For
GRASP surfaces colored using a user-defined discretecolours file, this can
be read in using the coldef option.
SET MAPCLIP ON/OFF
Only draws triangles/vertices with Z axis normals >= 0.0 - this is
useful for only displaying the "back" of a surface. (see the bottom of
the electron density page for an example)
SET MAPRADIUS number
Sets the mapradius for contouring. Defaults to 2.4.
The appearance of the map contours may be altered by "linecolour",
"linewidth", and "linedash" parameters (although the latter two only
apply when MAPTYPE is 0 - i.e. lines).
SET MAPRADIUS_PROPERTY ON/OFF
rather than using the distance to atoms/residues as the distance criteria
cutoff, the map property values are used - this is handy if reading in a
distance file from GRASP, and parts of the surface at a distance greater
than some desired value should not be drawn. e.g.:
readsurf surf1 "input.surf" using distance;
set mapradius_property on;
set mapradius 20.0;
set mapramp from red to blue through white;
drawsurf surf;
will only draw parts of the surface if the distance values as defined by
the GRASP file are below 20.0 Angstroms.
SET MAPTHRESH number
Sets the map threshold for vertex clustering. Defaults to 0.2
(expressed as a fraction, i.e. 20%), but can range anywhere from -1.0
to 1.0. The more negative the number, the more the surface is refined
(i.e. triangles are *added*). The more positive, the more triangles
are *destroyed*. Be forewarned that topological inconsistencies are
possible if this value is set very high (e.g. closed surfaces may be
destroyed).
SET MAPTYPE number
controls map rendering style. Currently supported values:
- 0 - lines
- 1 - triangulated mesh (default)
- 2 - df3 file
type 2 outputs a df3 file rather than rendering the map. Each contour
command generates a file starting at "edmap.1.df3". DF3 can be read
in by PovRay, and the povray output mode (when specified) will
automatically read these files in, if the maptype is 2 and the povray
output mode is specified on the molscript commandline.
Additionally, it may be necessary to set ALL the lights in the PovRay
files to shadowless - so the bounding box of the df3 file isn't
rendered (click here for examples/details).
SET MAPRAMP FROM colour TO colour [ THROUGH colour ]
sets the colour ramp for map rendering. Defaults to: from blue to
red. If "through " is used, the midpoint color is set to the
given color; otherwise, the two ramp colors are mixed (in terms of
pigment).
SET MERGEMAP number
kludge that is only necessary when drawing multiple GRASP/df3 files
over the *same area* - i.e. when issuing the same drawsurf/contour
command twice, only with differing mapfiles/contour levels each time.
The result is that the GRASP/df3 files are merged so that common areas
aren't dominated by the last rendered map. Supported values:
- 0 - write all (default)
- 1 - write header + media
- 2 - write media only
- 3 - write media + closing declaration
e.g.: to draw a 2fo-fc map and a fo-fc map over the same residue, the
following would accomplish this:
read prot "prot.pdb";
ball-and-stick in residue A50;
readmap 2fofc "2fofc.omap" covering in residue A50 plus 5;
readmap fofc "fofc.omap" covering in residue A50 plus 5;
set maptype 2;
! setup the ramp for the 2fofc
set mapramp from black to red;
! starting a merge statement
set mergemap 1;
contour 2fofc at 1.0 covering in residue A50;
! change the ramp
set mapramp from black to green;
! next media component (and also the last, so we also write
! the closing declaration)
set mergemap 3;
contour fofc at 2.0 covering in residue A50;
or for a GRASP map, only mergemap values 0, 1 or 3 are necessary:
readsurf surf "surf.srf" potential;
set colourramp rgb, mapramp from red to blue through white;
set mergemap 1, transparency 0.0;
drawsurf surf covering in residue A100;
set mergemap 3, transparency 0.7;
drawsurf surf notcovering in residue A100;
so a solid surface is drawn around residue A100 while the rest of the
surface is drawn as a transparent object.
SET PROBE_RADIUS number
sets the probe radius (in Angstroms) with which surfaces are generated
- deafults to 1.4.
SET SMOOTHMAP ON/OFF
turns vertex normal smoothing on/off. The default is on, resulting in
smoothed surface renderings. Doesn't apply for MAPTYPE 0 mode.
SET SURFRANGE number number number
Sets the upper, mid and lower limits for scaling color values in GRASP
renderings and curvature renderings, in order to make color ramps more
dramatic (see the povscript+ output for the low and high values of the
GRASP map as it is read in). The order the numbers are put in is not
important - the lowest value is taken as the low, middle as the mid,
etc.
Commands that are relevant to B factors:
SET AXESRAD number
sets the radius of cylindrical axes in "baxes 1" output mode (POVRay,
OpenGL only) (default: 0.02)
SET BAXES number
sets the bfactor rendering setup - currently supported values:
- 0 - no axes drawn (default)
- 1 - principal axes rendered as lines
- 2 - principal axes rendered as ellipses
SET BSURF number
sets the bfactor rendering setup - currently supported values:
- 0 - old school molscript style (overrides baxes setting) (default)
- 1 - no atom surface (just principal axes, if desired)
- 2 - solid surface, rendered according to B factor
NOTE: versions prior to 2.02 had "bsurf"
default to 2 - so atoms were rendered at 30% transparency and according to
B factor BY DEFAULT - use "set bsurf 0" to fix this!
for both BAXES and BSURF, the "quality" of the rendering in OpenGL is
determined by the segments statement in Molscript. So if the
ellipsoids/principal axes look roughly drawn, try increasing the
segments to 5 or 10. For postscript and VRML output, as long as bsurf
is greater than 0, the atoms are drawn according to their principal
axes *only.*
SET BTRANSP number
sets the transparency of the ellipsoid *only*. Handy for "bsurf 2",
where the ellipsoid typically has a higher transparency than
the principal axes. In such case, the ellipsoid is drawn as a
different color in povray output mode, so it should be relatively
easy to redefine the ellipsoid vs. principal axis coloring/texture
settings. This number can range from 0.0 (solid) to 1.0 (fully
transparent) (default: 0.3).
SET PROB_LEVEL number
sets the probability level (given a B factor) with which ellipsoids
(or spheres as the case may be) are rendered - defaults to 0.5
(i.e. 50%). This number can range from 0.01 to 0.99 in steps of 0.01.
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