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MolArch+ - Syntax

This list gives an overview and short description on the syntax of commands accepted by MolArch+. These descriptions are listed also in the $MOLARCH/molarch+.syn file of your MolArch+ installation. A more detailed description is contained in the help file $MOLARCH/molarch+.hlp or may be obtained via the links below. This list applies to the latest version of MolArch+ (V7.35 09.MAY.2003) - please check the Updates and Bug Fixes section.

You may also use the frames version of this documentation.

Click the commands below to go directly to the corresponding detailed help page:

Top of Page MolArch+ - Introductory Remarks
From within MolArch+ all syntax and help information on specific can be commands may be obtained (printed to the console) by typing 'syntax <command> <options>' or 'help <command> <options>'. The command 'apropos <keyword1> <keyword2> ...' will list all commands and their options matching a given list of keywords (maximum 3). Each keyword and command may be abbreviated on the command line by the first three letters only; however this does not apply to filenames, numbers, and values.

All commands, options, and keywords are case-sensitive, sometimes lowercase and uppercase keywords may lead to different results (as for example 'save pdb ...' and 'save PDB ...').

On this page, the syntax of commands is described in the following format: 

	<command> <options> ...
where

  • '{ ... }' indicates lists of options of which one must be used,
  • '[ ... ]' indicates single options or lists of options of which one may be used, but which may also be omitted altogether,
  • '< ... >' indicates that a filename, number, or value is expected as stated (these parameter cannot not be omitted),
  • '<atomnum>', '<molnum>', '<surfacenum>', ... indicate atom-, molecule-, or surface numbers to be specified here.

For example, the command 'rotate {x, y, z} <value>' may be used as 'rotate x 50.0' or 'rotate z -30.0', but not as 'rotate y' (without the <value>).

Some commands require atom-, molecule-, or surface numbers, these are generally listed as last arguments to the commands, after all other keywords have been specified; some commands expect a fixed number of e.g. atom numbers, other commands accept even multiple or varying amounts of such numbers. Many commands acting on atoms, molecules, and surfaces may offer the possibility to select objects via mouse click if these numbers are omitted.

For example, the command 'distance [<atomnum1> <atomnum2>]' may be used as 'distance 5 7' (printing the distance between the atoms 5 and 7), or as 'distance' (letting atoms to be picked via mouse click), but not as 'distance 5' (missing second atom number). Additional keywords must be placed before the atom numbers as for example in 'distance search nosubstituents 5 7'.

Numbers separated by a single dash and white spaces such as '<num1> - <num2>' are expanded; e.g. the command 'view 1 - 6 9 - 12' is synonymous to 'view 1 2 3 4 5 6 9 10 11 12'.

Some keywords and options are mutually exclusive, MolArch+ may ignore them silently, or options specified latter may supersede former keywords. Misuse of options may lead to short warning messages and the command may be ignored entirely, sometimes nothing happens and no warnings are issued at all. In any case, you may read the console output carefully.

Some keywords and options are synonymous and will affect the same internal settings. For example the 'vrml', 'wrl', and 'povray' keywords in the 'set {vrml, wrl, povray} ...' commands are synonymous and will affect both the VRML and POVRAY settings. In addition, some commands are identical (e.g. 'sldload' and 'surface' are equivalent, this is included for convenience only), while lowercase and uppercase commands (e.g. 'scale' and 'SCALE') may have different effects.

The table below lists all commands (in the first column) and their options (second column); in some cases different commands (in one table cell) may all take equivalent options (listed in the same row). Bulleted lists indicate that the commands on the left may be used in different ways (see e.g. the commands 'rotate').

In any case, for more specific informations on any command use 'help <command> <option> ...' from the command line of MolArch+!

Top of Page MolArch+ - General Commands
help
manual
syntax
apropos
  • [command] [keywords]
history
previous
last
  • [<n>] [keywords]
stop
quit
exit
bye
 
sleep
  • <seconds>
escape
  • <number> <command>
wait
  • {key, mouse, event, <count>}
Top of Page MolArch+ - Loading Files (Import)
pdbload
outload
macload
macromodel
dg
dgload
p88load
ampload
rdfload
  • <filename> [<molnum1>] [<molnum2>]
PDBLOAD
hinload
hyperchem
xyzload
psfload
crdload
espload
pimmload
einload
optload
sldload
surface
contour
sub-structure-load
topology
rc
rcload
sprload
source
script
g94load
gaussian
fcheck-load
fragment
parload
parameter
ellipsoids
  • <filename>
datload
DATLOAD
cpimmload
  • <filename> [set <configuration>] [single] [center, nocenter] [shift, noshift] [all, asymmetric-units, original] <xcells> <ycells> <zcells>
cifload
  • <filename> [single] [center, nocenter] [shift, noshift] [all, asymmetric-units, original] [probability <value>] [ellipsoids] [type <n>] <xcells> <ycells> <zcells>
logload
  • <filename> [mulliken-charges, natural-charges]
spartan-load
  • <filename> [esp-charges, mulliken-charges, npa-charges]
addsurface
  • <filename1> <filename2> ...
dhxload
dcdload
rstload
DHXLOAD
DHXLOAD
celload
<dhx-file> [<configuration>]
<dhx-file> [<configuration>]
<rst-file> [<mode>]
<pdb-file> <dhx-file> [<configuration>]
<pdb-file> <dhx-file> sequence <pdb-output-file>
<filename> [nocenter]
cubload
  • <filename>
  • <filename> [multiple options]
  • calculate [multiple options] [additional options]
[multiple options] can be:

[grid <n>]
[cmap {esp, mep, mlp, gry, red, green, yellow, blue, magenta, pink, cyan, white, <colornum>}]
[contours <n>] [align-grid]
[crop-grid <value>] [xcrop-grid <value>] [ycrop-grid <value>] [zcrop-grid <value>]
[skip-points <n>] [default <value>] [minimum <value>] [maximum <value>]
[exclude-surface] [area-min <value>]
[combine-contours <n>] [transparency <value> <value> <value>]
[color-scale <value>] [red <value> [value]] [green <value> [value]] [blue <value> [value]]

[additional options] are:

[mode {esp, mep}] [molecule <molnum>]
[points <n>] [xpoints <n>] [ypoints <n>] [zpoints <n>]
[step <value>] [xstep <value>] [ystep <value>] [zstep <value>]
[size <value>] [xsize <value>] [ysize <value>] [zsize <value>]
[offset <value>] [xoffset <value>] [yoffset <value>] [zoffset <value>]
field-load or
field
  • <filename> [multiple options]
  • calculate [multiple options] [additional options]
[multiple options] can be:

[cmap {esp, mep, mlp, gry, red, green, yellow, blue, magenta, pink, cyan, white, <colornum>}]
[contours <n>] [align-grid]
[crop-grid <value>] [xcrop-grid <value>] [ycrop-grid <value>] [zcrop-grid <value>]
[skip-points <n>] [default <value>] [minimum <value>] [maximum <value>]
[exclude-surface] [area-min <value>]
[combine-contours <n>] [transparency <value> <value> <value>]
[color-scale <value>] [red <value> [value]] [green <value> [value]] [blue <value> [value]]

[additional options] are:

[mode {esp, mep}] [molecule <molnum>]
[points <n>] [xpoints <n>] [ypoints <n>] [zpoints <n>]
[step <value>] [xstep <value>] [ystep <value>] [zstep <value>]
[size <value>] [xsize <value>] [ysize <value>] [zsize <value>]
[offset <value>] [xoffset <value>] [yoffset <value>] [zoffset <value>]
next-structure
NEXT-STRUCTURE
 
Top of Page MolArch+ - Saving Files (Export)
save
  • {pdb, PDB, new, NEW, mac, MAC, esp} <filename> [<molnum1>] [<molnum2>]
  • {rc, spr, source, script, ein, EIN, pimm, amp, AMP, PIMM, g94, G94, gaussian, dat, cpimm} <filename>
  • {fragment, parameter, sub-structure, topology, ellipsoids} <filename>
  • {sld, SLD, surface, SURFACE, contour} <filename> [<surfacenum>]
  • {cube, field} <filename>
  • {art-file, ART-file} <filename>
  • {povray, POVRAY} <filename> [wire-model, capped-stick, ball-and-stick, cpk-model, CPK-model] [transparency <value>] [filter <value>] [aspect-ratio <value>]
  • {povray, POVRAY} <filename> {wire-model, capped-stick, ball-and-stick, cpk-model, CPK-model} <transparency-value> <filter-value> <aspect-ratio>
  • {wrl-file, WRL-file, vrml-file, VRML-file} <filename> [wire-model, capped-stick, ball-and-stick, cpk-model, CPK-model] [transparency <value>]
  • {wrl-file, WRL-file, vrml-file, VRML-file} <filename> {wire-model, capped-stick, ball-and-stick, cpk-model, CPK-model} <transparency-value>
  • {map-definition, cmap-definition, color-definition} <filename> {std-colors, esp-colors, mep-colors, mlp-colors, gry-colors} {color-file}
  • {object, vogle-object} <filename>
write
  • all-objects off
  • all-objects <file base name> {wrl, WRL, vrml, VRML, povray, POVRAY, pdb, PDB, new, NEW, amp, AMP, object, vogle} [wire, capped-stick, ball-and-stick, cpk, CPK] [transparency <value>] [filter <value>] [aspect-ratio <value>]
  • all-objects <file base name> {wrl, WRL, vrml, VRML, povray, POVRAY, pdb, PDB, new, NEW, amp, AMP, object, vogle} {wire, capped-stick, ball-and-stick, cpk, CPK} <transparency-value> <filter-value> <aspect-ratio>
Top of Page MolArch+ - Viewing
rotate
  • {x, y, z} <value>
  • xyz <xvalue> <yvalue> <zvalue>
  • <xvalue> <yvalue> <zvalue>
roll
  • {x, y, z} <total> <step>
  • xyz <xtotal> <ytotal> <ztotal> <xstep> <ystep> <zstep>
  • <xtotal> <ytotal> <ztotal> <xstep> <ystep> <zstep>
move
  • {x, y, z, a, b, c} <total> <step> [multiple options]
  • {xyz, abc} <xtotal> <ytotal> <ztotal> <xstep> <ystep> <zstep> [multiple options]
  • <xtotal> <ytotal> <ztotal> <xstep> <ystep> <zstep> [multiple options]
[multiple options] can be:

[molecules {box, BOX, all}] [molecules] [molecules <molnum1> <molnum2> ...] [all-molecules, box, BOX]
[surfaces {box, BOX, all}] [surfaces] [surfaces <surfacenum1> <surfacenum2> ...] [all-surfaces, box, BOX]
[slds {box, BOX, all}] [slds] [slds <surfacenum1> <surfacenum2> ...] [all-slds, box, BOX]
scale
SCALE
  • <final> <step>
center
  • [all-atoms, non-hydrogens, mass-weighted]
view
  • [<atomnum1> <atomnum2> ...]
VIEW
  • <h> <k> <l>
  • {a, b, c}
label
  • {on, no, off, all-atoms, non-hydrogens, special-atoms, fragments, units, sub-structures, multiple-bonds, <atomic symbol>, <atomic periodic number>, <mode>}
  • {symbols, names, numbers}
  • hydrogen-atoms
  • {atoms, bonds, distances, angles, torsions, dihedrals, geometry} {on, no, off, all-atoms, non-hydrogens, special-atoms, fragments, units, sub-structures, multiple-bonds, <atomic symbol>, <atomic periodic number>, <mode>}
  • {bonds, distances, angles, torsions, dihedrals, geometry} precision <n>
  • bonds MULTIPLICITY
hbonds
HBONDS
  • [<max-distance> <min-angle> <d1> <a1> <nbonds>] [off]
Top of Page MolArch+ - Manipulation of Structures
relabel
  • <atom-sort> [{atom(s), all-atoms}] [<atomnum1>] [-] [<atomnum2>] ...
  • <atom-sort> [molecule(s) <molnum1> <molnum2> ...]
  • water
RELABEL
  • <atom-name> [{atom(s), all-atoms}] [<atomnum1>] [-] [<atomnum2>] ...
  • <atom-name> [molecule(s) <molnum1> <molnum2> ...]
  • water
mirror
  • {x, y, z}
delete
  • {single-atoms, water, h2o}
  • double-atoms [<distance>]
  • {atoms, names, charges, unknown-atoms} [box, BOX] [<atomnum1>] [<atomnum2>] ...
  • {atoms, names, charges, unknown-atoms} all
  • bonds [box, BOX] [<atomnum1> <atomnum2>] [<atomnum3> <atomnum4>] ...
  • bonds all
  • BONDS <atomsort1> <atomsort2> <min-distance>
  • {molecules, pdb, hydrogens} [box, BOX] [<molnum1>] [-] [<molnum2>] ...
  • {molecules, pdb, hydrogens} all
  • {slds, surfaces} [box, BOX] [<surfacenum1>] [-] [<surfacenum2>] ...
  • {slds, surfaces} all
create
  • bonds [<atomnum1> <atomnum2>] [<atomnum3> <atomnum4>] ...
  • BONDS <atomsort1> <atomsort2> <max-distance>
reset
  • {all, ALL, bonds, multiple-bonds, mplacements, angles, torsions, dihedrals, delta-torsions, dlta-torsions, molecules, order-of-atoms, isotopes, atom-parameters, pimm-types, zmatrix, fragments, special-parameters}
  • {orientation, colors, quality, symmetry}
clear
  • {short-bonds, long-bonds} {<factor>}
  • {atoms, bonds, molecules, multiple-bonds, mplacements, fragments, special-parameters, unknown-atoms, grid, field}
hydrogens
  • [single-bonds] [double-bonds] [{rch, dch} <r(C-H)>] [{rxh, dxh} <r(X-H)>] [{nearest, closest} <closest>] [atoms [{all-atoms, <atomnum1> <atomnum2> ...}]] [molecules [{all-molecules, <molnum1> <molnum2> ...}]]
sort
  • {molecules, oz, bonds, hydrogens, chhydrogens, all-atoms}
  • {fragment, sub-structure} {all, [fragment-number]}
  • energy <filename1> <filename2>
check-geometry
  • [minimum-angle <value>] [maximum-angle <value>] [distance-minimum <value>] [vdwdistance-min <value>] [bond-maximum <value>] [noangle-check] [nocontact-check] [nobond-check] [all-molecules] [<molnum1>] [-] [<molnum2>] ...
compare-geometry
  • [out-of-plane-deviation <max-angle>] [torsion-deviation <max-angle>] [angle-minimum <min-angle>] [<molnum1>] [<molnum2>]
grep-structures
  • <filename> [multiple options]
  • multiple-files <filename1> <filename2> ... end-of-list [multiple options]
[multiple options] can be:

[sub-structure <filename>] [sequence-of-structures <filename>]
[quiet-display] [renumber-fragments] [fragment-informations] [exclude-structures]
[{pdb-format, macromodel-format, dhx-charmm-format, dcd-charmm-format, dat-files, ccdf-files, spartan-files, rdf-files, amp-files, dg-files}]
[skip <structures>] [auto-skip] [tcoctahedron, boxsize <value>]
Top of Page MolArch+ - Crystal Structures
ellipsoids
  • <filename>
  • {on, off}
unit-cell
  • {on, off, all}
  • {a, b, c} <value1> <value2>
  • <valuea1> <valueb1> <valuec1> <valuea2> <valueb2> <valuec2>
Top of Page MolArch+ - Fragments and Sub-structures
search
  • [all, exact]
  • ring <value>
  • free-torsions
  • special {distance, bond, angle, torsion, dihedral, delta-torsion, dlta-torsion, c5q, c5p , c6q, c6p, c6t, j3h, jhh, j3c, jch, nbonds} <min> <max> [<atomnum1> <atomnum2> ...]
  • special {distance, bond, angle, torsion, dihedral, delta-torsion, dlta-torsion, c5q, c5p , c6q, c6p, c6t, j3h, jhh, j3c, jch, nbonds} automatic [<atomnum1> <atomnum2> ...]
  • special {angle, torsion, dihedral, delta-torsion, dlta-torsion} automatic all
  • search special name <min> <max> [<atomnum1>]
  • search special ring <min> <max> [<atomnum1> <atomnum2> atomnum3> ...]
fragment
parload
parameter
  • <filename>
select
  • [multiple options] [<atomnum1> <atomnum2> ...]

[multiple options] can be:

[search {all, non-hydrogens, alpha-only, nosubstituents, exact}] [structure] [sub-structure] [previous-search]
[fragment-informations]
save
  • {fragment, parameter, sub-structure, topology} <filename>
Top of Page MolArch+ - Atom Property Mapping
property
  • [multiple options]
[multiple options] can be:

[{charges, sigma-charges, pi-charges}] [{bond-energy, angle-energy, torsion-energy, bend-energy, coulomb-energy, vdw-energy}]
[color-map {esp, mep, mlp, gry}] [{esp, mep, mlp, gry}]
[range <value> <value>] [min <value>] [max <value>] [natural-range]
[{on, off}] [list] [all-atom-list] [information]
Top of Page MolArch+ - Geometry Analysis and Manipulation
distance
angle
torsion
dltatorsion
flip
puckering
plane-distance
tilt-angle
[multiple options] [<atomnum1> <atomnum2>]
[multiple options] [<atomnum1> <atomnum2> <atomnum3>]
[multiple options] [<atomnum1> ... <atomnum4>]
[multiple options] [<atomnum1> ... <atomnum4>]
[multiple options] [<atomnum1> ... <atomnum5>]
[multiple options] [<atomnum1> <atomnum2> ...]
[multiple options] [<atomnum1> <atomnum2> ... / <atomnumA> ...]
[multiple options] [<atomnum1> <atomnum2> ... / <atomnumA> ..]

[multiple options] can be:

[search {all, non-hydrogens, alpha-only, nosubstituents, exact}] [sub-structure] [previous-search]
[sequence <filename>] [multiple-files <filename1> <filename2> ... end-of-list]
[equal-weights] [energy-weighted] [temperature <value>]
[bond-recalculation, original-bonds] [check-geometry] [wait]
[fragment-informations] [quiet-display]
[{distributions, DISTRIBUTIONS} <filename> <steps> <min> <max>] [plotfile <filename>]
[set <value>] [change-to <value> <steps>]
[{pdb-format, macromodel-format, dhx-charmm-format, dcd-charmm-format, dat-files, ccdf-files, spartan-files, rdf-files, amp-files, dg-files]
[skip <structures>] [auto-skip] [tcoctahedron, boxsize <value>]
vangle
dlines
cp5
cp6
jhh
jch
hbridge
gyration-radius
[multiple options] [<atomnum1> ... <atomnum4>]
[multiple options] [<atomnum1> ... <atomnum4>]
[multiple options] [<atomnum1> ... <atomnum5>]
[multiple options] [<atomnum1> ... <atomnum6>]
[multiple options] [<atomnum1> ... <atomnum4>]
[multiple options] [<atomnum1> ... <atomnum4>]
[multiple options] [<atomnum1> <atomnum2> <atomnum3>]
[multiple options] [<atomnum>]

[multiple options] can be:

[search {all, non-hydrogens, alpha-only, nosubstituents, exact}] [sub-structure] [previous-search]
[sequence <filename>] [multiple-files <filename1> <filename2> ... end-of-list]
[equal-weights] [energy-weighted] [temperature <value>]
[bond-recalculation, original-bonds] [check-geometry] [wait]
[fragment-informations] [quiet-display]
[{distributions, DISTRIBUTIONS} <filename> <steps> <min> <max>] [plotfile <filename>]
[{pdb-format, macromodel-format, dhx-charmm-format, dcd-charmm-format, dat-files, ccdf-files, spartan-files, rdf-files, amp-files, dg-files}]
[skip <structures>] [auto-skip] [tcoctahedron, boxsize <value>]
multiplicity
aromaticity
[multiple options] [<atomnum1> <atomnum2>]
[multiple options] [<atomnum1> <atomnum2> <atomnum3> ...]

[multiple options] can be:

[search {all, non-hydrogens, alpha-only, nosubstituents, exact}] [structure] [sub-structure] [previous-search] [fragment-informations]
[set <value>]
chirality
zmatrix-definition
symmetry-relation
exchange
define
swap-atoms
name-atoms
renumber
circularity
CIRCULARITY
asphericity
ASPHERICITY
radius
RADIUS
[multiple options] [<atomnum1> ... <atomnum4>]
[multiple options] [<atomnum1>]
[multiple options] [<atomnum1> <atomnum2>]
new <atom-sort> [multiple options] [<atomnum1>]
new <atom-sort> <distance> <angle> <torsion> [multiple options] [<atomnum1> <atomnum2> <atomnum3>]
[multiple options] [<atomnum1> <atomnum2>]
new <atom-name> [multiple options] [<atomnum1> <atomnum2> ...]
[multiple options] [<atomnum1> <atomnum2> ...]
[multiple options] [<atomnum1> <atomnum2> ...]
[multiple options] [<atomnum1> <atomnum2> ...]
[multiple options] [mass-weighted, uniform-weights] [square-root, sqrt]
[multiple options] [mass-weighted, uniform-weights] [square-root, sqrt]
[multiple options] [<atomnum1> <atomnum2> ...]
[multiple options] [<atomnum1> <atomnum2> ...]

[multiple options] can be:

[search {all, non-hydrogens, alpha-only, nosubstituents, exact}] [structure] [sub-structure] [previous-search]
[fragment-informations]
diffusion
tumbling
[multiple options] [<atomnum1> <atomnum2> ...]
[multiple options] [<atomnum1> <atomnum2> ...]

[multiple options] can be:

[sequence <filename>] [multiple-files <filename1> <filename2> ... end-of-list]
[bond-recalculation, original-bonds] [check-geometry] [wait]
[quiet-display] [series-file <filename>] [timestep <value>]
[{pdb-format, macromodel-format, dhx-charmm-format, dcd-charmm-format, dat-files, ccdf-files, spartan-files, rdf-files, amp-files, dg-files}]
[skip <structures>] [auto-skip] [tcoctahedron, boxsize <value>]
mci
  • {0chi, 1chi, 2chi, 3chiC, 3chiP, 4chiC, 4chiPC, 4chiP} [<molnum>]
  • {0chiV, 1chiV, 2chiV, 3chiCV, 3chiPV, 4chiCV, 4chiPCV, 4chiPV} [<molnum>]
  • {type} [<molnum>]
Top of Page MolArch+ - Fitting and Animation
fitting
  • <filename> [multiple options] [atom/mol1, atom/mol2, ...]
  • multiple-files <filename1> <filename2> ... end-of-list [multiple options] [atom/mol1, atom/mol2, ...]
[multiple options] can be:

[structure, sub-structure, preloaded-sub-structure, old-fragment-definition, atom(s), molecule(s)]
[search] [fragment-informations] [include-hydrogens, exclude-hydrogens] [nosubstituents, alpha-substituents, beta-substituents, gamma-substituents, degree-of-substitution <n>] [best-sub-structure] [exact]
[all-atoms, non-hydrogens] [mass-weighted] [continuous-fitting]
[{use-current, current-orientation}]
[energy-weighted, equal-weights] [temperature <value>]
[bond-recalculation, recalculate-bonds] [original-bonds, write-bondlist]
[iterations <n>] [check-geometry] [wait-for-mouse] [quiet-display]
[sequence-of-all-structures <filename>] [save-all-molecules, only-sub-structures]
[individual-structures {<filename>, <filename(%e)>, <filename(%n)>}] [format {pdb, PDB, new, NEW, ein, EIN, amp, AMP}]
[units-of-sub-structures <filename>]
[mean-geometry-of-sub-structures <filename>]
[ellipsoids-of-atom-positions, ELLIPSOIDS <filename>]
[{pdb-format, macromodel-format, dhx-charmm-format, dcd-charmm-format, dat-files, ccdf-files, spartan-files, rdf-files, amp-files, dg-files}]
[skip <structures>] [auto-skip] [tcoctahedron, boxsize <value>]
film
  • <filename> [multiple options]
  • multiple-files <filename1> <filename2> ... end-of-list [multiple options]
[multiple options] can be:

[{fit, center} {all-atoms, non-hydrogens, mass, sub-structure}]
[wait <waitcount>] [check-geometry] [wait] [sequence-of-all-structures <filename>]
[individual-structures {<filename>, <filename(%e)>, <filename(%n)>}] [format {pdb, PDB, new, NEW, ein, EIN, amp, AMP}]
[interpolation <nsteps>] [{adjust-geometry, crude-geometry}] [offset <value>] [step <value>]
[mean-geometry <filename>] [ellipsoids <filename>]
[{pdb-format, macromodel-format, dhx-charmm-format, dcd-charmm-format, dat-files, ccdf-files, spartan-files, rdf-files, amp-files, dg-files}]
[skip <structures>] [auto-skip] [tcoctahedron, boxsize <value>]
[{povray-files, POVRAY-files} <filename> {wire-model, capped-stick, ball-and-stick, cpk-model, CPK-model}] [movie]
Top of Page MolArch+ - 3D Contouring and Surface Generation
calculate-contour
[multiple options]

[multiple options] can be:

[connolly-surface, cpk-surface, CPK-surface, solvent-access-surface, vdw-interaction, electrostatic-interactions, crystal-surface, hirshfeld-surface]
[existing,pre-calculated <filename>, density-contour]
[offset <value>] [step-size <value>] [regression-steps <value>] [accuracy-of-dots <value>]
[radius-of-probe <value>] [charge-of-probe-sphere <value>] [sort-of-probe {<pimm-type>, <atomic symbol>}]
[coulomb-law] [ohno-klopman-relation] [dot-density <value>] [keep-files] [quiet]
[molecule <molnum>] [cnt-parameter <value>] [fast-parameter <value>] [parameter <value>]
[absolute-contours, relative-contours] [contours <number> <contour-value1> <contour-value2> ...] [both-values]
[grid <n>] [gaussian]
Top of Page MolArch+ - Surface Manipulation and Settings
sldload
surface
  • <filename>
addsurface
  • <filename1> <filename2> ...
save
  • {sld, SLD, surface, SURFACE, contour} <filename> [<surfacenum>]
dots
triangles
normals
mesh
solid
  • [all] [<surfacenum1>] [-] [<surfacenum2>] ...
color
  • {on, <colornum>, <color>, esp, mep, mlp, gry} [all] [<surfacenum1>] [<surfacenum2>] ...
quality
  • {number, atom-colors, oz, light, color, esp, mep, mlp, gry, grd, crv, hbonds, acceptor, donor, sign, cube} [all] [<surfacenum1>] [<surfacenum2>] ...
qdelete
  • {number, light, esp, mep, mlp, gry, grd, crv, hbonds, acceptor, donor, sign} [all] [<surfacenum1>] [<surfacenum2>] ...
  • all [<surfacenum1>] [<surfacenum2>] ...
qadd
  • {light, esp, mep, gry, crv, coulomb-esp, ohno-klopman-esp, atom-colors, oz, sign, cube-data} [all] [<surfacenum1>] [<surfacenum2>] ...
qrange
  • {global, absolute, individual} [all] [<surfacenum1>] [<surfacenum2>] ...
  • <minvalue> <maxvalue> [all] [<surfacenum1>] [<surfacenum2>] ...
qmin
qmax
  • {global, absolute, individual, <minvalue>} [all] [<surfacenum1>] ...
zclip
slice
  • {on, off, center, global-center, <z-coordinate>} [all] [<surfacenum1>] [<surfacenum2>] ...
scut
  • {on, off} [all] [<surfacenum1>] [<surfacenum2>] ...
smin
smax
  • <minvalue> [all] [<surfacenum1>] [<surfacenum2>] ...
heal-surface
HEAL-surface
  • {dmin, distance <value>} [all] [<surfacenum1>] [<surfacenum2>] ...
invert-normals
INVERT-faces
  • [all] [<surfacenum1>] [<surfacenum2>] ...
shrink-surface
  • [factor <value>] [all] [<surfacenum1>] [<surfacenum2>] ...
interpolation
  • {sld, surface} <surfacenum1> <surfacenum2> <offset> <step> <alpha>
Top of Page MolArch+ - Display Settings
show
info
  • {parameters, properties, bond-list, length-of-bonds, fragment, sub-structure, pdb, sumformula, formula, title, esp, dipoles, mass}
  • {hbond-list, HBONDS, unit-cell-data, cell-data, symmetry}
  • {surface, sld, quality, geometry, settings, rotation, display, maximal, planes, sizes}
  • {vrml, VRML, wrl, WRL, povray, POVRAY}
  • atom [<atomnum1>] [-] [<atomnum2>] ...
  • plane [<atomnum1>] [-] [<atomnum2>] ...
  • plane {on, off}
  • molecule [<molnum1>] [-] [<molnum2>] ...
  • moment-of-inertia [all-molecule(s)] [<molnum1>] [-] [<molnum2>] ...
  • {bonds, angles, torsions, dihedrals deltas, dltas}
echo
  • {all-parameters, model-type, single-buffer, display-offset, labels}
  • {multiple-bonds, torsion-definitions, angle-definitions, planes, cells}
  • {axis, occupancy, symmetry-operations, charge, center, homogeneous-bonds}
  • {cut-ellipsoids, quiet, sld, surface, double-dots, iso-contour-lines}
  • {texture, triangle-scale, scale, out-messages, err-messages, system-messages}
  • {graphics, logo, syntax-check, exact-spelling, vrml-parameters}
  • {wrl-parameters, povray-parameters, line-precision, precision-of-circles}
  • {number-of-colors, bond-width, hidden-line, spheres, front-line, ellipsoids}
  • {hatching, unit-cells, dot-radius, normal-length}
set
  • {wire, ball-and-stick, color, bw, inverse-display}
  • background {black, red, green, yellow, blue, magenta, pink, cyan, white, <colornum>}
  • {display-offset, bond-width, hidden-line, spheres, ellipsoids, precision-of-circles, line-precision} <value>
  • {unit-cells, dot-radius, normal-length, front-line} <value>
  • hatching {off, <value>}
  • set {scale, triangle-scale} {on, off}
  • set {scale, triangle-scale} position [<xvalue> <yvalue>]
  • set {scale, triangle-scale} {xposition, yposition} <value>
  • set scale length <value>
  • {single-buffer, homogeneous-bonds, cone-type-bonds, cylinder-type-bonds, texture} {on, off}
  • {unit-cells, asymmetric-units, ellipsoids, cut-ellipsoids} {on, off}
  • {quiet, sld, surface, double-dots, center, dipoles} {on, off}
  • {grid, field} {on, off}
  • display {offset, size, dimension, width} <value>
  • display {center, freeze} {on, off}
  • multiple-bonds {raw, integer, smooth, float, gaussian, lorentzian, on, off}
  • iso-contour-lines {on, off, <value>}
  • {angle-definitions, torsion-definitions, dihedral-definitions, planes} {on, off}
  • {cells, axis, occupancy, symmetry-operations, charge} {on, off}
  • {periodic, cubic, orthorhombic, tetragonal, toctaeder} {on, off}
  • {out-messages, err-messages, system-messages, graphics, logo} {on, off}
  • {debug-messages} {on, off, all, <level>}
  • history off
  • {syntax-check, exact-spelling} {on, off}
  • highlight-help {on, off, red, green, yellow, blue, magenta, pink, cyan, white, <colornum>}
  • light {on, off}
  • light position <xvalue> <yvalue> <zvalue>
  • light {xposition, yposition, zposition} <value>
  • number-of-colors <value>
Top of Page MolArch+ - Color Settings
mapcolor
 
cmap
  • <filename> {std, esp, mep, mlp, gry} [<ncolors>] [<alpha>]
cinv
  • {std, esp, mep, mlp, gry, STD, ESP, MEP, MLP, GRY}
Top of Page MolArch+ - POVRAY and VRML Settings
set
  • {vrml, wrl, povray} {bond-radius, cbond-radius, hbond-radius, sphere-size, radius, box-radius, unit-cell-radius, line-width} <value>
  • {vrml, wrl, povray} {sphere-size, SPHERE-SIZE} <atomic-symbol> <value>
  • {vrml, wrl, povray} color-label <atomic-symbol> <color-label>
  • {vrml, wrl, povray} {quality, slice-width, transparency, scale, size, plane, width, height, dimension, x, y, xy} <value>
  • {vrml, wrl, povray} {dotted-line-spacing, special-line-radius, text-size} <value>
  • {vrml, wrl, povray} {wire-model, capped-stick, ball-and-stick, cpk-model, CPK-model}
  • {vrml, wrl, povray} {front-clip, back-clip, rear-clip} <value>
  • {vrml, wrl, povray} finish <label>
  • {vrml, wrl, povray} lights {on, off}
  • {vrml, wrl, povray} camera [auto] {on, off}
  • {vrml, wrl, povray} camera [type] {perspective, orthographic, ultra-wide, fisheye, omnimax, panoramic, <mode>}
  • {vrml, wrl, povray} camera {angle, distance, blur-samples, aperture} <value>
  • {vrml, wrl, povray} camera {position, focus} <xvalue> <yvalue> <zvalue>
  • {vrml, wrl, povray} camera {xposition, yposition, zposition, xfocus, yfocus, zfocus} <value>
  • {vrml, wrl, povray} camera sky [on, off, <min> <max>] [{minimum, maximum} <value>]
  • {vrml, wrl, povray} camera floor [on, off, <color-label>, <yvalue>]
  • {vrml, wrl, povray} sky [on, off, <min> <max>] [{minimum, maximum} <value>]
  • {vrml, wrl, povray} floor [on, off, <yvalue>]
  • {vrml, wrl, povray} tbonds {on, off}
  • {vrml, wrl, povray} tbonds {minimum, maximum, fc1, fc2} <value>
  • {vrml, wrl, povray} {mbonds, multiple-bonds} {on, off}
  • {vrml, wrl, povray} {mbonds, multiple-bonds} center {on, off}
  • {vrml, wrl, povray} {mbonds, multiple-bonds} {horizontal, align, vertical, perpendicular} {on, off}
  • {vrml, wrl, povray} {mbonds, multiple-bonds} {distance, double-bonds, triple-bonds, quadruple-bonds} <value>
  • {vrml, wrl, povray} {mbonds, multiple-bonds} {fc1, fc2} <value>
  • {vrml, wrl, povray} triple-bonds {on, off}
  • {vrml, wrl, povray} quadruple-bonds {on, off}
  • {vrml, wrl, povray} {mbonds, multiple-bonds} triple-bonds {on, off}
  • {vrml, wrl, povray} {mbonds, multiple-bonds} quadruple-bonds {on, off}
  • {vrml, wrl, povray} aromaticity {on, off}
  • {vrml, wrl, povray} aromaticity {min-ring-size, max-ring-size, ring-size} <n>
  • {vrml, wrl, povray} aromaticity {dmax, puckering} <value>
  • {vrml, wrl, povray} aromaticity {distance} <value>
  • {vrml, wrl, povray} {mbonds, multiple-bonds} aromaticity {on, off}
  • {vrml, wrl, povray} {mbonds, multiple-bonds} aromaticity {min-ring-size, max-ring-size, ring-size} <n>
  • {vrml, wrl, povray} {mbonds, multiple-bonds} aromaticity {dmax, puckering} <value>
  • {vrml, wrl, povray} {mbonds, multiple-bonds} aromaticity {distance} <value>
  • {vrml, wrl, povray} anti-aliasing {on, off}
  • {vrml, wrl, povray} nquality <nvalue>
  • {vrml, wrl, povray} {shadows, reflections, images} {on, off}
  • {vrml, wrl, povray} gamma-value <nvalue>
  • adjust-labels {atoms, bonds, angles, torsions, dihedrals, all-types, labels, geometry-parameters} {on, off}
  • color-labels {atoms, bonds, angles, torsions, dihedrals, all-types, labels, geometry-parameters, lines, dotted} [multiple options]
[multiple options] can be:

{on, off, natural, oz, atom-colors, black, red, green, yellow, blue, magenta, pink, cyan, white, <number-of-color>}
Top of Page MolArch+ - POVRAY and VRML Viewing
wrl-model
WRL-model
vrml-model
VRML-model
  • [{wire-model, capped-stick, ball-and-stick, cpk-model, CPK-model}] [{width, x} <value>] [{height, y} <value>] [{size, xy, dimension} <value>] [{small, very-small}] [transparency <value>]
povray-model
POVRAY-model
  • [{wire-model, capped-stick, ball-and-stick, cpk-model, CPK-model}] [{width, x} <value>] [{height, y} <value>] [{size, xy, dimension} <value>] [{small, very-small}] [transparency <value>] [filter <value>] [aspect-ratio <value>]
Top of Page MolArch+ - Special Objects (Surfaces, Ribbons, Orbitals, Pseudo Atoms, etc.)
make
  • polar <angle-step> <angle-tics> <amplitude> <tics-amplitude>
  • p3d <filename>
  • cell
  • single {molecules, sld, SLD, all}
  • solid {tetraeder, TETRAEDER, octaeder, OCTAEDER, toctaeder, cube, CUBE, dodecaeder, icosaeder, ticosaeder, prism, PRISM, trigonal-bipyramid, TRIGONAL-BIPYRAMID, pyramid, PYRAMID, square-pyramid, SQUARE-PYRAMID, pentagonal-pyramid, PENTAGONAL-PYRAMID, hexagonal-pyramid} [center <atom-sort>] [atoms <atom-sort1> <atom-sort2> <atom-sort3> ...] [heal-surface] [{nogeometry-check, nospecial-parameters}]
  • solid plane [x-dimension] [y-dimension] [z-dimension]
  • solid disc [nsteps] [x-radius] [y-radius] [z-dimension]
  • solid ring [radius-offset] [z-dimension] [<atomnum1> <atomnum2> ...]
  • solid RING [radius-offset] [z-dimension]
  • solid smoothring [nsteps] [radius-offset] [z-dimension] [<atomnum1> ...]
  • solid SMOOTHRING [nsteps] [radius-offset] [z-dimension]
  • solid sphere [radius] [dot-density] [x] [y] [z]
  • box <atom-sort> <a> <b> <c>
  • BOX <atom-sort> <x0> <y0> <z0> <a> <b> <c>
  • center [mass-weighted] [new <atomsort>] atoms [<atomnum1> <atomnum2> ...]
  • center [mass-weighted] [new <atomsort>] molecules [<molnum1> <molnum2> ...]
  • center [mass-weighted] [new <atomsort>] all-molecules
  • {contact, repulsion} {<na> <nb> <nc> <nd> <n1> <n2>}
  • orbital {px, py, pz, sp3} [density <n>] [{scale, x, y, z} <factor>] [<atomnum1> <atomnum2> ...]
  • {ribbon, RIBBON} [multiple options]
[multiple options] can be:

[{cyclic, non-cyclic}] [adjust-normals] [invert-chain] [band, cylinder]
[{chain-reference, normal-reference}] [width <value>] [height <value>]
[radius <value>] [rotate <value>] [precision <n>] [steps <n>] [molecule <n>] [skip-points <n1> <n2>]
[spiral <n>] [{correction, nocorrection}] [{include-hydrogens, exclude-hydrogens}] [{plane-definitions}, {moments-of-inertia}]
Top of Page MolArch+ - External (PIMM91)
pimm91
geoopt
  • {&, bg}
get
strain
 

© Copyright PD Dr. S. Immel