New command listing:

New molauto options:

"-colsec" color based on secondary structure

New Molscript selection commands:

LOC id

only selects atoms at the alternate location "id". Useful if the pdb contains alternate confomers, and only one is desired.

PROTRINGS residue_selection
NUCLEORINGS residue_selection

fills in the ring portions of either
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.

Commands relevant to PovRay output:


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)

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: using the following color schemes for each type: 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.

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.

CONTOUR id AT cont_level [COVERING atom_selection]

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.

READSURF id1 filename [USING property] [LAMBDA number]

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).

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).

DRAWSURF id [COVERING atom_selection]
DRAWSURF id [NOTCOVERING atom_selection]

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.

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.


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)


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 MAPSTYLE is 0 - i.e. lines).


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.


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).


controls map rendering style. Currently supported values: 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).


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: 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.


turns vertex normal smoothing on/off. The default is on, resulting in smoothed surface renderings. Doesn't apply for MAPTYPE 0 mode.

Commands that are relevant to B factors:

SET BAXES number

sets the bfactor rendering setup - currently supported values: SET AXESRAD number

sets the radius of cylindrical axes in "baxes 1" output mode (POVRay, OpenGL only) (default: 0.02)

SET BSURF number

sets the bfactor rendering setup - currently supported values: 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.*


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.


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).

"hidden" features (i.e. don't use them unless necessary):


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;

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