Chem-X Menüs

  1. Main
  2. System
  3. Action
  4. User
  5. Help
  6. Stop

MAIN

  1. Dismiss
  2. Read Data
  3. Write Data
  4. Databases
  5. Display
  6. Modify/Build
  7. Crystal Symmetry
  8. Geometry
  9. Energy
  10. Parameterisation
  11. Quantum Mechanics
  12. Maps
  13. Generate Conformations
  14. Study Conformations
  15. Surfaces (Punktwolken)
  16. Motion
  17. Fitting
  18. () QSAR (Quantitative Structure-Activity Relationship)
  19. () Peptides
  20. Polymers

SYSTEM

  1. Dismiss
  2. Enter Command (aus Chem-X)
  3. Replay Log File
  4. Goto System (?)
  5. Command Mode (zurück mit menu)
  6. Change Directory (relativ)
  7. Retrace Path
  8. Define Batch Job
  9. Environment
  10. Exit Chem-X

ACTION

  1. Dismiss
  2. Select Active Segment
  3. List Segment Information
  4. Read Structure
  5. Write Structure
  6. () Search Database
  7. Display
  8. Modify/Build
  9. Crystal Pack
  10. Calculate Energy
  11. Optimise Geometry
  12. Minimise VdW Energy
  13. Map
  14. Fit
  15. Generate Conformations
  16. Study Conformations
  17. Surface (Punktwolken)

USER

  1. Dismiss
  2. Display Quick
  3. Display Solid
  4. Display Stick
  5. Label

HELP

  1. Dismiss
  2. () About Menus
  3. Current Menu
  4. Worked Examples
  5. Support

Read Data

  1. Dismiss
  2. Offset Structure (neuer bzgl. alter)
  3. Segment Name From File
  4. () Use Secondary Structure
  5. 2D-3D Builder Options
  6. CSSR
  7. PDB (Brookhaven Protein Data Bank)
  8. Smiles
  9. Fragment Library (Chem-X)
  10. DBS Database
  11. Other Formats
    1. Dismiss
    2. Offset Structure
    3. Segment Name From File
    4. 2D-3D Builder Options
    5. Cambridge CSD (Cambridge Structure Database FDAT)
    6. Maccs (MOL von MDL)
    7. () Darc F1
    8. Chemlab-I
    9. Tribble (.CON)
    10. North
    11. Read Compound File
    12. Open Compound File
    13. Replace Structure
    14. Append Structure
    15. Merge Structure
  12. Read Fragment Library
  13. () Protein-Related Data
  14. Read Other Data
  15. () Read Compound File
  16. () Open Compound File
  17. Read Archive File
  18. Replace Structure
  19. Append Structure
  20. Merge Structure

2D-3D Builder Options

  1. Dismiss
  2. First Match Only
  3. Use Frameworks
  4. Keep Bonding Stereochemistry
  5. Random Stereochemistry
  6. Set Quality Criteria
  7. Set Isomer Limit
  8. Read Fragments

Read Fragment Library

  1. Dismiss
  2. Offset Structure
  3. Amino Acid
  4. Nucleic Acid
  5. Acyclic
  6. Sat Carbocyclic
  7. Unsat Carbocyclic
  8. Sat Heterocyclic
  9. Unsat Het'cyclic
  10. Inorganic
  11. () Monomers
  12. User-Defined
  13. Keyboard
  14. Replace Fragment
  15. Append Fragment
  16. Merge Fragment

Read Other Data

  1. Dismiss
  2. Read Parameter File
  3. Read Spacegroup File
  4. Read Surface File
  5. Read Map File
  6. Read Archive File
  7. () Read Conform File
  8. Read Fca File

Write Data

  1. Dismiss
  2. Only Displayed Atoms
  3. Include Dummy Atoms
  4. () Use Secondary Structure
  5. Dynamic Rootname
  6. CSSR
  7. PDB
  8. Other Formats
    1. Dismiss
    2. Maccs (MOL von MDL)
    3. Chemlab-I
    4. Tribble
  9. () Write DBS Database
  10. Geometry Values
  11. List Atomic Data
  12. Other Types of Data
  13. () Protein-Related Data
  14. Set File Rootname
  15. Write Archive File
  16. Write Cartesian
  17. Write Fractional

List Geometry

  1. Dismiss
  2. List to a File
  3. Coordinates
  4. Distances
  5. Bond Lengths
  6. Bond Angles
  7. Torsion Angles
  8. () Backbone Torsions
  9. () Side Chain Torsions
  10. all Geometry

List Atomic Data

  1. Dismiss
  2. List to Screen
  3. () List to Notebook
  4. List to File
  5. Atom Names
  6. Full Atom Description
  7. Entries
  8. Segments
  9. Coordinates
  10. Connectivity
  11. Atomic Charges
  12. Chirality

Other Types of Data

  1. Dismiss
  2. Write Spaceg'p File
  3. Write Archive File
  4. () Write Conform File
  5. Write Parameter File
  6. Write Surface File
  7. Write Map File

Databases

  1. Dismiss
  2. Open DBS Database
  3. Read DBS Database
    1. Dismiss
    2. Open DBS Database
    3. () List D'base Segments
    4. List Chem-X Segments
    5. Replace Structure
    6. () Append One Segment
    7. () Append all Segments
    8. () Read Answer Set
    9. () Review Answer Set
  4. () Write DBS Database
  5. () Search DBS Database
  6. () Search Pharmacophore
  7. () Field Definitions
  8. () Set Field Value
  9. () Missing Data
  10. () Read External Data
  11. () Examine Table
  12. () Review Answer Set
  13. () Display Answer Set
  14. () QSAR (Quantitative Structure-Activity Relationship)

Display

  1. Dismiss
  2. Redraw Automatically
  3. Peptides
  4. Polymers
  5. Inorganic
  6. Small Molecules
  7. Atom Style
  8. Bond Style
  9. Label Style
  10. Visibility
  11. Picture Style
  12. Stereo & Perspective
  13. Bonds and Fragments
  14. Assign Dials
  15. Monitor Structure
  16. Set a View
  17. Titles

Atom Style (Small Mol Display)

  1. Dismiss
  2. Redraw Automatically
  3. Atoms Visible
  4. Atom Size, Shape
    1. Dismiss
    2. Redraw Automatically
    3. Very Small Radius
    4. Small Radius
    5. CPK Radius
    6. VdW Radius
    7. Other Radius
    8. Set Element Radius
    9. Set Atomtype Radius
    10. Set Atom Radius
    11. Reset Atom Radius
  5. Atom Colour
    1. Dismiss
    2. Set Element Colour
    3. Set Atomtype Colour
    4. Set Atom Colour
    5. Reset Atom Colour
  6. Carbon Atoms
  7. Heteroatoms
  8. Hydrogen Atoms
  9. Apply Style

Bond Style

  1. Dismiss
  2. Redraw Automatically
  3. Bonds Visible
  4. Kekule Aromatic Bonds
  5. Bond Size
  6. Use Split Bonds
  7. Use Multiple Bonds
  8. Colour By Entry
  9. Fixed Colour
  10. Colour By Order
  11. Show Polarity
  12. Show Potential
  13. Show Bond Strain
  14. Show Torsion Strain
  15. Apply Bond Style
  16. List Styles

Label Style (Small Mol Labels)

  1. Dismiss
  2. Atom Labels Visible
  3. Charge Lab's Visible
  4. Chiral'y Lab's Visible
  5. (-) QM Labels Visible (Vorsicht!)
  6. Label Colour, Etc
    1. Dismiss
    2. Atom Label Colour
    3. Charge Label Colour
    4. Chiral'y Label Colour
    5. QM Label Colour
    6. QM Label Options
    7. Set Atomtype Synonym
  7. Atom Name
  8. Atomtype
  9. Serial Number
  10. Group Number
  11. Sequence Number
  12. Symmetry Operator
  13. Residue Name
  14. Segment Name
  15. Carbon Atoms
  16. Heteroatoms
  17. Hydrogen Atoms
  18. Apply Labels (Untermenü)

Visibility

  1. Dismiss
  2. Atoms and Bonds
  3. Webs, Faces, Ribbons
  4. () Protein Schematics
  5. Dummy Atom Graphics
  6. Maps
  7. Surfaces
  8. Labels
  9. Set all Visible
  10. Set None Visible

Picture Style

  1. Dismiss
  2. Highlighting (inkl. depth-cueing, shading)
  3. Shading (inkl. depth-cueing)
  4. Depth-Cueing (Hinteres dunkler)
  5. No Lighting
  6. Auto Scale Picture
  7. Auto Window Picture
  8. Bonds Visible
  9. Atoms Visible

Stereo & Perspective

  1. Dismiss
  2. Crossed Stereo
  3. Relaxed Stereo
  4. Red-Green Stereo
  5. Orthogonal Pair
  6. Dynamic Stereo (Vorsicht. Abbruch: Alt-F9, Icon öffnen)
  7. Use Perspective
  8. Use Stereo
  9. Set Rotation Angle

Bonds and Fragments

  1. Dismiss
  2. Redraw Automatically
  3. 1-D Motion Only
  4. Origin On Atom
  5. Screen Centre Origin
  6. Bond 1 (für Rotation um Bindung)
  7. Bond 2
  8. Bond 3
  9. Bond 4
  10. Fragment 1
  11. Fragment 2
  12. Fragment 3
  13. Fragment 4
  14. List Setup
  15. Clear Setup

Assign Dials

  1. Dismiss
  2. Bond 1
  3. Bond 2
  4. Bond 3
  5. Bond 4
  6. all Bonds
  7. Fragment 1
  8. Fragment 2
  9. Fragment 3
  10. Fragment 4
  11. Global
  12. Define Bonds
  13. Define Fragments
  14. List Setup

Monitor Structure

  1. Dismiss
  2. VdW Energy
  3. MM Energy
  4. () ChemLib Energy
  5. Count VdW Contacts
  6. () Set ChemLib Routine
  7. Display Energy
  8. Display H-Bonds
  9. Draw VdW Contacts
  10. Display Key Search
  11. Distance (Messung, zwischen 2 Atomen)
  12. Angle (Messung, 3 Atome)
  13. Torsion Angle (Messung, 4 Atome)
  14. () Vector Magnitude
  15. () Angle Between Planes
  16. List Setup
  17. Clear Geometries
  18. Clear Setup

Set a View

  1. Dismiss
  2. Best Plane (Global)
  3. Best Plane (Select)
  4. () Onto Dummy Plane
  5. Along Two Atoms
  6. Along Dummy Vector
  7. Onto Crystal Face
  8. Reset Original View

Titles

  1. Dismiss
  2. Current File
  3. Header
  4. Systematic Name
  5. First File
  6. Compound Title
  7. Reference Code
  8. Root Name
  9. User Text 1
  10. User Text 2
  11. User Text 3
  12. Draw Automatically
  13. Set Position (Coord)
  14. Pick Position
  15. Set Colour
  16. Set Size
  17. Sub- & Superscripts
  18. Set Text
  19. List Title
  20. List all Title
  21. Draw Title

Modify/Build

  1. Dismiss
  2. Redraw Automatically
  3. Atom Labels Visible
  4. 2D Draw
  5. 2D to 3D Conversion
  6. Delete Atom
  7. Delete Fragment
  8. Delete Bond
  9. Undo Last Operation
  10. Read 3D Fragments
  11. 3D Sketch
  12. Make Bond
  13. Make Hydrogen Bond
  14. Set Bond Order
  15. Join 3D Fragments
  16. Fuse 3D Rings
  17. Change Atoms
  18. Alter Geometry
  19. Add Hydrogens

Change Atoms

  1. Dismiss
  2. Redraw Automatically
  3. Atom Labels Visible
  4. Adjust Bond Lengths
  5. Auto Names
  6. Auto Serial Numbers
  7. Auto Group Numbers
  8. Auto Sequence No's
  9. Clear Auto Settings
  10. Set Atom Picking
  11. Rename Atoms (Untermenü)
  12. Rename Segment
  13. Reparameterise Segment
  14. Set Label Style

Set Atom Picking

  1. Dismiss
  2. Confirm Picked Atoms
  3. Individual Atoms
  4. by Entry
  5. by Group Number
  6. by Atomtype
  7. by Segment
  8. by Residue Range
  9. by Fragment
  10. List of Atoms
  11. all Atoms
  12. Prompt (Menu)
  13. Prompt (Keyboard)

Alter Geometry

  1. Dismiss
  2. Redraw Automatically
  3. Set Atom Coordinates
  4. Set Bond Length
  5. Set Bond Angle
  6. Set Torsion (1 Atom)
  7. Set Torsion (Twist)
  8. Invert Chirality
  9. Set Atom Picking
  10. Rebuild Segment

Add Hydrogens

  1. Dismiss
  2. Redraw Automatically
  3. Add 1 Hydrogen
  4. Add 2 Hydrogens
  5. Add 3 Hydrogens
  6. Add 4 Hydrogens
  7. Add by Valency

Crystal Symmetry

  1. Dismiss
  2. Redraw Automatically
  3. Unit Cell Visible
  4. Unpack Before Pack
  5. Read Data
  6. Set Unit Cell
  7. Symmetry Options
  8. Packing Options
  9. List Packing Setup
  10. Pack - all Operators
  11. Pack - 1 Operator
  12. Unpack Structure
  13. Calculate Bonds
  14. Set a View
  15. General Display Style

Geometry

  1. Dismiss
  2. () Range of Values
  3. Prompt For Range
  4. Bonded Atoms
  5. Non-Bonded Atoms
  6. () Any Atoms
  7. Set Atom Picking
  8. Calculate Distance
  9. Calculate Angle
  10. Calculate Torsion
  11. List Geometry
  12. Alter Geometry
  13. Monitor Structure
  14. Vectors as Arrows
  15. Set Atom-Atom Vector
  16. Find Best Plane
  17. Find Centroid
  18. Set Scalars, Vectors
  19. List Dummy Atoms

Energy

  1. Dismiss
  2. Modify VdW Energy
  3. Modify MM Energy
  4. Modify Atomtypes
  5. Charges
  6. H-Bonding
  7. Restraints
  8. Include Entries
  9. Set VdW Minimisation
  10. Set MME Optimisation
  11. () MM2 Interface
  12. () Amber Interface
  13. Calculate Gasteiger Charge
  14. Calculate VdW Energy
  15. Calculate MM Energy
  16. Calculate Contacts
  17. () Calculate ChemLib Energy
  18. () Set ChemLib Routine
  19. () Minimise VdW Energy
  20. Optimise MM Energy

H-Bonding

  1. Dismiss
  2. Calculate Automatically
  3. Donor-Acceptor
  4. Hydrogen-Acceptor
  5. Set Length Range
  6. Set Angle Range
  7. Set Colour
  8. List Setup
  9. Reset Setup
  10. Calculate H-Bonds
  11. List H-Bonds
  12. Print H-Bonds

Restraints

  1. Dismiss
  2. Restrain to Value
  3. Match Variable
  4. Replace MM Variable
  5. Atom Position
  6. Distance
  7. Angle
  8. Torsion Angle
  9. Define Rigid Group
  10. Symmetry Restraints
  11. Remove One Restraint
  12. Clear Selected Type
  13. Clear Rigid Groups
  14. Clear all Restraints
  15. Set Atom Picking
  16. Fix Atom Position
  17. Release Fixed Atom
  18. Free all Fixed Atoms
  19. List Restraints

Include Entries

  1. Dismiss
  2. Intra Entry Set1
  3. Intra all Entries
  4. Inter Set1 & Set2
  5. Inter Set1 & all
  6. Inter all & all
  7. Total Set1 & Set2
  8. Total Set1 & all
  9. Total all & all
  10. List Settings
  11. Calculate VdW Energy
  12. Calculate MM Energy

Set VdW Minimisation

  1. Dismiss
  2. Display During Calculate
  3. Report VdW Energy
  4. Save Intermediates
  5. Set Output Frequency
  6. VdW Minimisation Option
  7. Bond Options
  8. Peptide/Polymer Bonds
  9. Add Auto Bonds
  10. Add Path Bonds
  11. Add One Bond
  12. Add Fragments
  13. List Setup
  14. Remove One Variable
  15. Clear all Variables
  16. Open DBS Database
  17. Minimise VdW Energy

Parameterisation

  1. Dismiss
  2. Substructure Parameterisation
  3. Fix Bond Order
  4. Fix Atom Types
  5. Create Param Dummies
  6. Modify Atomtypes
  7. MM Parameters
  8. VdW Parameters
  9. Charge Parameters
  10. Read Parameter File
  11. List Parameters
  12. Set Segment Picking
  13. Reparameterise Segment

Quantum Mechanics

  1. Dismiss
  2. Icon8
  3. () CNINDO
  4. Ampac
  5. Mopac
  6. () Gaussian
  7. () Gamess
  8. Read QM Results File
  9. List Summary Results
  10. QM Map Calculation
  11. QM Label Options
  12. Label - QM Property
  13. Mo Diagram
  14. Draw MO Diagram

Icon8

  1. Dismiss
  2. Basic Eht (Extended Hückel)
  3. Charge Iteration
  4. Vsie Charge Iter'n
  5. Vsie With Madelung
  6. Apply Weighting
  7. Set Huckel Constant
  8. Select Output Level
  9. Set Title
  10. Read Template File
  11. Write Template File
  12. List Setup
  13. Reset Setup
  14. Calculate In Batch
  15. Select QM Atoms
  16. Write Input Files
  17. Run Calculation
  18. Repeat Calculation

Ampac

  1. Dismiss
  2. Select Method
    1. Cancel
    2. Keyboard
    3. AM1
    4. MINDO3
    5. MNDO
  3. Set Scf Option
    1. Cancel
    2. Keyboard
    3. RHF
    4. UHF
    5. Open Shell Occupancy
    6. Number of C.I. MO's
  4. Set Multiplicity
    1. Cancel
    2. Keyboard
    3. Singlet
    4. Doublet
    5. Triplet
    6. Quartet
    7. Quintet
    8. Sextet
  5. Select Run Type
    1. Cancel
    2. Keyboard
    3. Check Input
    4. Single Energy
    5. Force
    6. Saddle Point
    7. Optimisation
  6. Optimisation Options
  7. Set Control Option
  8. Set Output Option
  9. Add Extra Keywords
  10. Set Title & Comment
  11. Set Cpu Time Limit
  12. Read Template File
  13. Write Template File
  14. List Setup
  15. Reset Setup
  16. Calculate In Batch
  17. Select QM Atoms
  18. Write Input Files
  19. Run Calculation
  20. Repeat Calculation

Mopac

  1. Dismiss
  2. Select Method
    1. Cancel
    2. Keyboard
    3. AM1
    4. MINDO3
    5. MNDO
    6. PM3
  3. Set Scf Option
    1. Cancel
    2. Keyboard
    3. RHF
    4. UHF
    5. Open Shell Occupancy
    6. Number of C.I. MO's
  4. Set Multiplicity
    1. Cancel
    2. Keyboard
    3. Singlet
    4. Doublet
    5. Triplet
    6. Quartet
    7. Quintet
    8. Sextet
  5. Select Run Type
    1. Cancel
    2. Keyboard
    3. Check Input
    4. Single Energy
    5. Force
    6. Saddle Point
    7. Optimisation
  6. Optimisation Options
  7. Set Control Option
  8. Set Output Option
  9. Add Extra Keywords
  10. Set Title & Comment
  11. Set Cpu Time Limit
  12. Read Template File
  13. Write Template File
  14. List Setup
  15. Reset Setup
  16. Calculate In Batch
  17. Select QM Atoms
  18. Write Input Files
  19. Run Calculation
  20. Repeat Calculation

Optimisation Options

  1. Dismiss
  2. Enable Optimisation
  3. all Variables
  4. Apply Restraints
  5. Selected Variables
  6. Set Restraints
  7. Set Initial Chain
  8. Optimise Distance
  9. Optimise Angle
  10. Optimise Torsion
  11. Set Symmetric Dist
  12. Set Symmetric Angle
  13. Set Symmetric Tors'n
  14. List Z-Matrix
  15. Set Label Colour
  16. Label Distance

Set Control Option (Ampac)

  1. Cancel
  2. Keyboard
  3. Molecular Charge
  4. No. of Optim Cycles
  5. Override Geom Checks
  6. Use Pulay Converger
  7. Restart Calculation
  8. Use Powell Minimiser
  9. Use Precise Criteria
  10. Thermo Rot Symmetry
  11. Symmetry Constraints
  12. Cpu Time Limit

Set Output Option (Ampac)

  1. Cancel
  2. Keyboard
  3. Bond Order Matrix
  4. Eigenvalues in Iter
  5. File For Graphics
  6. Localised Orbitals
  7. Final C.I. Matrix
  8. Mulliken Analysis
  9. Sigma and Pi Bonds
  10. Thermodynamic Prop's
  11. Eigenvectors

Set Control Option (Mopac)

  1. Cancel
  2. Keyboard
  3. Molecular Charge
  4. Fit Esp to Dipole
  5. Esp Calculation
  6. Override Geom Checks
  7. MM Bond Correct'n
  8. No MM Correction
  9. Use Precise Criteria
  10. Use Pulay Converger
  11. Restart Calculation
  12. Thermo Rot Symmetry
  13. Read Setup File
  14. Symmetry Constraints
  15. Cpu Time Limit

Set Output Option (Mopac)

  1. Cancel
  2. Keyboard
  3. Bond Order Matrix
  4. Restart File Freq'cy
  5. Eigenvalues in Iter
  6. File For Graphics
  7. Localised Orbitals
  8. Final C.I. Matrix
  9. Mulliken Analysis
  10. Sigma and Pi Bonds
  11. Calculate Polarisability
  12. Thermodynamic Prop's
  13. Eigenvectors

List Summary Results

  1. Dismiss
  2. List to a File
  3. Set QM Energy Units
  4. Summary of Calculate
  5. Summary of all MOs
  6. QM Charges
  7. Coeff's - Homo
  8. Coeff's - Lumo
  9. Coeff's - Other MO
  10. S'deloc - Homo
  11. S'deloc - Lumo
  12. S'deloc - Other MO
  13. S'deloc - Occ Mos
  14. S'deloc - Unocc Mos

QM Map Calculation

  1. Dismiss
  2. Automatic Window
  3. Wavefunction
  4. () Electron Density
  5. Potential (Vss)
  6. () Potential (Denpot)
  7. Homo
  8. Lumo
  9. Other Orbital
  10. Occupied Orbitals
  11. Alpha
  12. Beta
  13. 2-D Map
  14. 3-D Map
  15. Set Grid Points (default 10, besser 20)
  16. Set Title
  17. List Setup
  18. Run Calculation Now
  19. Submit to Batch
  20. Examine Chem QM Map

QM Label Options

  1. Dismiss
  2. Charge Lab's Visible
  3. QM Labels Visible (Vorsicht!)
  4. Use Default Cutoff
  5. S'deloc
  6. Coefficients
  7. Sum Coeff's Squared
  8. Set QM Energy Units
  9. Homo
  10. Lumo
  11. Other Orbital
  12. all Occupied MOs
  13. all Unoccupied MOs
  14. Set Label Colour
  15. List Setup
  16. Carbon Atoms
  17. Heteroatoms
  18. Hydrogen Atoms
  19. Apply Label Style

Mo Diagram

  1. Dismiss
  2. Show Spin Arrows
  3. Auto Energy Range
  4. Set QM Energy Units
  5. Alpha (Uhf)
  6. Beta (Uhf)
  7. Code by Energy
  8. Code by Occupancy
  9. Single Colour
  10. Auto Colour Coding
  11. Include Orbitals
  12. Remove Orbitals
  13. Include all Orbitals
  14. Remove all Orbitals
  15. List Orbitals
  16. List Setup
  17. Restore Auto Setup
  18. Draw MO Diagram

Maps

  1. Dismiss
  2. Redraw Automatically
  3. Current Map Visible
  4. Global Map Setup
  5. Set Map Property
  6. Set Contours/Coding
  7. Set Atom Picking
  8. Select Atoms
  9. Select Current Map
  10. List Current Map
  11. Write Current Map
  12. Read Map File
  13. Tie Map to Atom
  14. Add Map Extremes
  15. Combine Maps
  16. List Volumes, Areas

Regular Search

  1. Dismiss
  2. Regular Search
  3. Torsion Dynamics
  4. XYZ Dynamics
  5. () Amber Dynamics
  6. () Distance Geometry
  7. Search Options
  8. Define Minimisation
  9. Set Rejections
  10. Bond Options
  11. () Peptide/Polymer Bonds
  12. Add Auto Bonds (Untermenü)
  13. Add Path Bonds
  14. Add One Bond
  15. Add Fragments
  16. List Setup
  17. Remove One Variable
  18. Clear All Variables
  19. Open DBS Database
  20. Search Conformations

Torsion Dynamics

  1. Dismiss
  2. Regular Search
  3. Torsion Dynamics
  4. XYZ Dynamics
  5. () Amber Dynamics
  6. () Distance Geometry
  7. Torsion Dynamics Options
  8. Bond Options
  9. () Peptide/Polymer Bonds
  10. Add Auto Bonds (Untermenü)
  11. Add Path Bonds
  12. Add One Bond
  13. Add Fragments
  14. Set Time Interval
  15. Set Temperature
  16. List Setup
  17. Remove One Variable
  18. Clear All Variables
  19. Open DBS Database
  20. Execute Dynamics

Plot Conformations

  1. Dismiss
  2. Plot Conformations
  3. Display Conformations
  4. Read Conformational Data
  5. Redraw Automatically
  6. Display Legend
  7. Display Symbols
  8. Display Contours
  9. Plot Display Style
  10. Alter Plots
  11. Combine Plots
  12. Study Variables
  13. Display Plot
  14. List Displayed Plots
  15. List all Plots
  16. Label Point
  17. Append Conformation
  18. List to a File
  19. List Conformation

Display Conformations

  1. Dismiss
  2. Plot Conformations
  3. Display Conformations
  4. Read Conformational Data
  5. Bonds Visible
  6. Atoms Visible
  7. Alter Display Style
  8. Define a Map
  9. Combine Conf Maps
  10. (-) Review Answer Set (Vorsicht!)
  11. Load Frames
  12. Exclude Frames
  13. Include Frames
  14. Clear all Frames
  15. List Setup
  16. Display Conformations

Read Conformational Data

  1. Dismiss
  2. Open DBS Database
  3. Replace Structure
  4. Append One Segment
  5. Select Conformation
  6. Read Archive File
  7. () Read Conform File
  8. Read Fca File
  9. Read Amber .Cse File
  10. Update to New Format

Plot Display Style

  1. Dismiss
  2. Redraw Automatically
  3. 1-D Plots
  4. 2-D Plots
  5. 3-D Plots
  6. Display Legend
  7. Display Contours
  8. Display Fit Line
  9. Display Symbols
  10. Use Symbols
  11. Use Segment Names
  12. Set Contour Grid
  13. Set Box Colour
  14. Set Fit Line Colour
  15. List Plot Style

Alter Plots

  1. Dismiss
  2. Redraw Automatically
  3. Auto Energy Coding
  4. Rebuild Auto Plots
  5. Display Plot
  6. Current Plot Visible
  7. Select Current Plot
  8. Select Segment
  9. Alter Plot Name
  10. Study Variables
  11. List Variables
  12. Set X-Axis
  13. Set Y-Axis
  14. Set Z-Axis
  15. Alter X-Axis Range
  16. Alter Y-Axis Range
  17. Alter Z-Axis Range
  18. Set Error Bars
  19. Set Coding Variable
  20. Set Coding Levels
  21. List Current Plot

Study Frames

  1. Dismiss
  2. Structure
  3. Information
  4. Loop
  5. Auto-Reverse
  6. Forward
  7. Backward
  8. Superimpose
  9. Set Delay
  10. Set Step Size
  11. Go
  12. Step
  13. Clear Frames
  14. Reset View
  15. Reset
  16. List
  17. Help

Surfaces

  1. Dismiss
  2. Redraw Automatically
  3. Calculate Surface Visible
  4. Read-In Surf Visible
  5. Field Surface
  6. Set Vector Length
  7. Auto Density Calculate
  8. Use Read-In Surface
  9. Colour by Element
  10. Single Colour
  11. Coded by Potential
  12. Set Coding
  13. Set Surface Radius
  14. Set Atom Picking
  15. Surface Atoms
  16. Unsurface Atoms
  17. List Setup
  18. Read Surface File
  19. Write Surface File
  20. () Connolly Surfaces

Motion

  1. Dismiss
  2. Move all Atoms
  3. Move Selected Atoms
  4. Origin On Atom
  5. Screen Centre Origin
  6. X Rotation
  7. Y Rotation
  8. Z Rotation
  9. Rotate About Vector
  10. X Translation
  11. Y Translation
  12. Z Translation
  13. Shift Along Vector
  14. Set a View
  15. Bonds and Fragments
  16. Assign Dials
  17. Monitor Structure

Fitting

  1. Dismiss
  2. Define Auto Fit
  3. Auto Fit
  4. (-) Auto Conform Fit (Vorsicht!)
  5. View Results
  6. Use VdW Minimisation
  7. Use MME Minimisation
  8. Prompt for Weighting
  9. Set Fit Restraint
  10. List Fit Restraints
  11. Remove Fit Restraint
  12. Clear Fit Restraints
  13. Rigid Fit
  14. Define Minimisation
  15. Flexible Fit
  16. Distance Geometry

Polymers

  1. Dismiss
  2. Build Polymers
  3. Generate Conformations
  4. Analyse Spectra
  5. () Use ChemPolymer
  6. Homopolymer
  7. Co-Polymer
  8. Repeating Sequence
  9. Use Reaction List
  10. Read Monomer
  11. Define Reactions
  12. Alter Configuration
  13. List Configuration
  14. Build Polymer

Read Structure

  1. Dismiss
  2. Offset Structure
  3. CSSR
  4. PDB (Brookhaven Protein Data Bank)
  5. Smiles
  6. Fragment Library
  7. DBS Database
  8. Cambridge CSD (Cambridge Structure Database FDAT)
  9. Maccs (MOL von MDL)
  10. () Darc F1
  11. Chemlab-I
  12. Tribble
  13. North
  14. Select Compound File
  15. Select Fragment Lib
  16. Read Archive File
  17. Replace Structure
  18. Append Structure

Write Structure

  1. Dismiss
  2. Include Dummy Atoms
  3. CSSR
  4. PDB (Brookhaven Protein Data Bank)
  5. () DBS Database
  6. Maccs (MOL von MDL)
  7. Chemlab-I
  8. Tribble
  9. Select DBS Database
  10. Rename Chem-X Segment
  11. Change Directory
  12. Write Archive File
  13. Write Structure

Display Styles

  1. Dismiss
  2. Atom Style
  3. Bond Style
  4. Label Style
  5. Entry-Coloured Stick
  6. Atom-Coloured Stick
  7. Ball and Stick
  8. CPK Solid
  9. () Backbone by Residue
  10. () Backbone by Secondary
  11. () Schematic Protein
  12. Picture Style
  13. Stereo & Perspective
  14. Visibility
  15. Bonds and Fragments
  16. Assign Dials
  17. Monitor Structure
  18. Draw all Segments
  19. Draw Active Segment
  20. Redraw Picture

Calculate Energy

  1. Dismiss
  2. VdW Energy
  3. MM Energy
  4. VdW Contacts
  5. () ChemLib Energy
  6. Skorczyk Charges
  7. Gasteiger Charges
  8. Apply to all Entries
  9. Intra-Entry En'gy
  10. Inter-Entry En'gy
  11. Intra+Inter Energy
  12. Calculate Energy

Set MME Optimisation

  1. Dismiss
  2. Display During Calculate
  3. Save Intermediates
  4. Report MM Energy
  5. Report Large Shifts
  6. Include Cell Lengths
  7. Include Cell Angles
  8. Set Output Frequency
  9. MME Optimisation Options
  10. List Setup
  11. Reset Setup
  12. Open DBS Database
  13. Optimise MM Energy

MME Optimisation Options

  1. Dismiss
  2. Set First Atom Shift
  3. Set Maximum Atom Shift
  4. Set First Cell Shift
  5. Set Maximum Cell Shift
  6. Set Number of Cycles
  7. Set Convergence
  8. List Setup
  9. Reset Setup

Map

  1. Dismiss
  2. Redraw Automatically
  3. Current Map Visible
  4. Global Map Setup
  5. VdW Surface
  6. Coded VdW Surface
  7. VdW Cavity
  8. Coded VdW Cavity
  9. Potential
  10. Steric Probe
  11. Charge Probe
  12. Set Contours/Coding
  13. Set Contour Density
  14. List Current Map
  15. Clear Map
  16. Draw Map

Worked Examples

  1. Dismiss
  2. () Building Structures
  3. Display Styles
  4. Manipulating Struc's
  5. () Saving Structures
  6. Geometry Calc's
  7. Crystal Packing
  8. Maps (Problem am Ende)
  9. Surfaces
  10. Energy Calculations
  11. () Minimising Energy
  12. Generating Conformations
  13. Study Conformations (Problem am Ende)
  14. Quantum Mechanics
  15. () Fitting Structures
  16. Combining Maps
  17. Combining Plots
  18. () Database Searches

Zum Beginn dieses Dokuments

Kurzinformation zu Chem-X

Burkhard Kirste, 1993/11/30