MOLMOL – Quick Reference

Li Liu, 02/19/07

Item Relationships. 1

Command list 1

1. Input/Output 1

2. Modify Molecules. 1

Item Relationships

command list

1. Input/Output

ReadAng ReadListAng ReadDg

ReadListDg ReadPdb ReadListPdb

ReadSybyl ReadXyz ReadSeq

ReadDump ReadLol ReadUpl

ReadAco ReadShift ReadOmap

ReadPot ReplaceDg ReplaceListDg

ReplacePdb ReplaceListPdb ReadLib

WriteAng WriteDg WriteSeq

WriteDump WriteLol WriteUpl

WriteLib WriteTransform WriteSecondary

ReadPdb /prg/molmol/data/1pit.pdb

ReadListPdb / prg/molmol/data/list1.nam

2. Modify Molecules

NewMol MeanMol NameMol

FirstMol RemoveMol AddRes

ChangeRes RemoveRes AddAtom

AddPseudo FlipAtom RemoveAtom

AddBond RemoveBond AddDist

AddHbond AddLol AddUpr

RemoveDist AddAngle RotateAngle

SetAngle RemoveAngle AddAco

RemoveAco

NewMol "Mol num1"

MeanMol "mean_1" avg_bfactor mean_only

AddRes last "ALA"

ChangeRes angles "ARG"

AddAtom "HB2" "CB" "CA" "HB1" 120 120 1.5

AddPseudo "QD"

3. Primitives

AddTitle AddText EditText

SizeText AddDrawobj MoveDrawobj

StyleDrawobj SetNeigh AddRibbon

SplitRibbon TypeRibbon StyleRibbon

SizeRibbon PaintRibbon AddPlates

SizePlate AddSurface TrimSurface

PaintSurface AddIsosurface AddTrajec

StyleTrajec AddCircles AddCylinder

AddDipole StyleCylinder AddSheet

AddSolid StyleMap ColorPrim

TintPrim LinePrim ShadePrim

RadiusPrim NearPrim MovePrim

LengthPrim RemovePrim

AddTitle 0.5 0.3 0.15 "Label"

AddText 0.15 "Label"

EditText "C_\a a^{2 * x}"

SizeText abs 0.15

AddDrawobj rect 2D

MoveDrawObj 0 0.3 0.1 0.2

StyleDrawobj cylinder

StyleRibbon rounded sharp arrow

SizeRibbon 3.0 0.5

PaintRibbon one_color

AddSurface vdw contact 1.4 dots 0

TrimSurface 1.0

AddCylinder spacing

StyleCylinder arrow

MovePrim 0.3 0.1 0.2

LinePrim solid 3

ColorPrim 1.0 0.0 0.0

4. Display

ZoomAbs ZoomRel Fullscreen

DrawSize Stereo StartRock

StopRock StartAnim StopAnim

BondMode BackColor Projection

ClipPos ClipSize ViewAngle

Light Fog Rendering

DrawDelay DrawPrec

ZoomAbs 0.2

DrawSize set 1000 750

DrawSize restore

StartRock cycle 50 0 10 0 18 0 -10 0 18

StartAnim cycle 50

Projection orthogonal

ClipPos 8.0

ClipSize 5.0

ViewAngle 0.5

Light point 0 5 5

Fog linear 0.1 7.0 13.0

Rendering 0 0 0 1 1 0 1 0

BackColor 1.0 0.2 0.7

DrawPrec 4 2

5. Movement

Center Fit MoveInit

MoveX MoveY MoveZ

RotateInit RotateX RotateY

RotateZ AutoScale

MoveX 10

RotateX 90

6. User Interface

UserInterface DialSelect DialMol

DialColor DialStyle DialMeasure

7. Selection

SelectMol SelectRes SelectAtom

SelectBond SelectAngle SelectDist

SelectPrim DefPropMol DefPropRes

DefPropAtom DefPropBond DefPropAngle

DefPropDist DefPropPrim ListSelectedMol

ListSelectedRes ListSelectedAtom ListSelectedBond

ListSelectedAngle ListSelectedDist ListPropMol

ListPropRes ListPropAtom ListPropBond

ListPropAngle ListPropDist ListPropPrim

SetRef UndefProp

SelectAtom 'name = "C*"'

SelectAtom 'name = "CA" & res.num < 10 & bfactor > 2.0'

SelectAtom 'res.num = 10 & name = "CA"'

SetRef

SelectAtom 'd < 5.0'

SelectBond 'atom1.name = "CA" & atom2.name = "CB"'

SelectAngle 'name = "OMEGA" & (val < 170 | val > 190)'

SelectDist 'res1.num = 7 | res2.num = 7'

DefPropDist 'hnd' 'atom1.name = "HN" | atom2.name = "HN"'

side

SelectDist 'hnd & viol > 1.5'

SelectDist '! hnd & viol > 2.0'

SelectPrim 'mol.num = 2'

DefPropRes 'helix' 'mol.name = "bpti*" & res.num = 47..56'

SelectAtom 'name = "CA" & res.helixres'

SelectAtom '#1-5:10-20,25-30@N,CA,C'

SelectAtom ':7@HN :12@HA'

SelectRes 'name = "ASP" & ! exists atom(name = "HD2")'

DefPropRes 'well_def' '! exists atom(heavy & bfactor > 1.0)'

SelectAtom 'res.well_def & (ca | heavysc)'

DefPropRes 'helix' 'num >= 47 & num <= 56'

DefPropAtom 'helixCA' 'name = "CA" & res.helix'

8. Attributes

ColorAtom ColorBond ColorDist

ColorInit TintDist TintInit

LabelAtom LabelDist LabelInit

LineAtom LineBond LineDist

LineInit RadiusAtom RadiusBond

RadiusDist RadiusInit MaterialAtom

MaterialBond MaterialDist MaterialPrim

MaterialInit TextureAtom TextureBond

TextureDist TexturePrim TextureInit

ShadeAtom ShadeBond ShadeDist

StyleAtom StyleBond StyleDist

StyleInit AttrAtom AttrBond

AttrDist AttrPrim AttrInit

ColorAtom 1.0 0.0 0.0

ColorAtom 0.5*bfactor 1.0-0.5*bfactor 0.0

LabelAtom "R N"

RadiusAtom 1.0

RadiusAtom 0.5+bfactor

RadiusBond 0.5

MaterialAtom 0.3 0.7 0.4 30 0.0 1.0 1.0

TextureAtom 'Blood_Marble' 0.5 0.0 1.0

9. Plotting

PlotUnit PlotPar PlotPs

PlotFm3 PlotFm4 PlotMeta

PlotTiff PlotJpeg PlotPng

PlotBmp PlotPov PlotMpov

PlotRib PlotVrml1 PlotVrml2

PlotPar 29.7 42 0 26 1500 0 1 1 1 4 0.5 90

PlotJpeg /tmp/MyPlot.jpg

PlotTiff /home/joe/MyPlot.tif

10. Calculations

CalcSecondary CalcRmsd CalcMatch

CalcCluster CalcSurface CalcPot

CalcShift CalcAtom CalcBond

CalcHbond CalcVdw CalcDist

CalcAngle CalcHelix CalcAxis

CheckBond CheckUpl CheckLol

CheckAco

CalcRmsd fit_pairs '5..32,37..55' 'bb' 'heavy' '' 'bb heavy heavysc' '' 'bb heavy'

CalcMatch 50 0.7

CalcCluster 5 0.02 1

CalcSurface 1.4 2

CalcPot vdw charge 2.0 80.0 1.4 0.3 2.0 10.0 zero foo.pot

CalcShift 1 0 Heigh-Mallion 0.5 5.0

CalcBond 5 1 0

CalcHbond 2.4 35 10 0 1 0 1

CalcVdw 0.3 1 0 1 0

CalcAtom "H*"

11. Figures

FigRamach FigAngles FigCircles

FigDist FigContact FigLimit

FigOff

FigRamach 'PHI' 'PSI' 'GLY' normal dot plus 1 0

FigAngles 'PHI PSI' 45

FigCircles 4 0.3

FigDist 4 3.0 7.0 0 1

FigContact 'selected' 'selected' 'bb' 'all' 3.0 5.0

FigLimit 'selected' 'selected' 5 1 0.7

12. Miscellaneous

Group LengthBond HelpViewer

HelpApropos HelpCmd HelpMouse

HelpButton HelpProp HelpManual

HelpTutorial HelpIndex HelpTip

HelpAbout SetUndo Undo

XMacStand XMacUser RecordMac

PathNames InitAll System

Group 2

LengthBond -0.5 1

SetUndo 3

XMacUser /temp/my_favorite.mac

InitAll yes

Short notation used for selecting atoms:

@CA

all atoms named CA

:10-20

all atoms in residues number 10 to 20

#1-3,5:10-20,25,LYS@N,CA,C

all atoms named N, CA or C in residues number 10 to 20 and 25, and residues named LYS, in molecules number 1 to 3 and 5

:10@HN :17@HA

atom named HN in residue number 10 and atom HA in residue number 17

Giving an empty string as selection expression selects all items. The expression '0' (a string with the digit zero as the only character) will deselect everything.

Values

The following table lists the values that can be referenced for each kind of data item.

item	value	type	explanation
`mol`	num	integer	molecule number
`res`	num	integer	residue number
`prim`	num	integer	primitive number
`mol`	name	string	molecule name
`res`	name	string	residue name
`atom`	name	string	atom name
`angle`	name	string	angle name
`atom`	shift	float	chemical shift of atom
`atom`	bfactor	float	B factor of atom
`atom`	vdw	float	van der Waals radius of atom
`atom`	charge	float	partial charge of atom
`atom`	heavycharge	float	charges on heavy atoms
`atom`	avgcharge	float	averaged charges on heavy atoms
`atom`	simplecharge	float	simple charges from setup file
`atom`	d	float	distance from reference atom(s)
`bond`	len	float	bond length
`angle`	val	float	angle
`dist`	val	float	distance
`dist`	limit	float	limit of constraint
`dist`	viol	float	violation of constraint
`dist`	upl	bool	true if distance is upper limit
`dist`	lol	bool	true if distance is lower limit
`dist`	hbond	bool	true if distance is H-bond
`atom`	attr	integer	graphics attribute index
`bond`	attr	integer	graphics attribute index
`dist`	attr	integer	graphics attribute index
`prim`	attr	integer	graphics attribute index

You can access values of related data items by using the corresponding prefix, e. g. in an expression for atoms, you can refer to the residue number by res.num.