Winmostar Operation Manual

----Contents ----



Winmostar
  for Windows

    7/8/10

Copyrightⓒ X-Ability Co. Ltd.
2012-2017 All Rights Reserved

1. Introduction

Winmostar is a GUI software which supports molecule modeling, executes computation programs and visualizes their results.
Maximum number of atoms has been confirmed up to 100,000 atoms.
Each function of Winmostar are explained below.


2. Install / Uninstall / Version-up

2-1. INSTALL

Download the installer exe file and execute it. Files will be automatically extracted to the specified folder. The default install folder is c:\winmos7, which can be changed as you wish.
The Winmostar icon will appear on your desktop and in the start menu.

2-2. VERSION-UP

You can update the program by the same procedure as you installed. You can keep your settings if you select the older winmostar folder as install folder and overwrite it. Please make sure that the existing version is not running before you start update, or you will have an error message.

2-3. UNINSTALL

Simply delete the winmos7 folder and the short-cuts.

3. How to use

3-1. START-UP WINMOSTAR

The program can be started by double clicking the short-cut on your desktop or by [start]> [all programs]> [winmostar].

3-2. START-UP OPTIONS

You can also start Winmostar with options to specify an input file and/or a computation programs.

Use MOPAC -mopac1, -mopac2, -mopac3
Molecular surface area and volume -molsv
Aspect ratio -aspect
Output -o (output filename)


examples
"C:\winmos7\winmostar.exe" "C:\winmos7\samples\dbt.dat" -mopac1
"C:\winmos7\winmostar.exe" "C:\winmos7\samples\dbt.dat" -molsv 1 2.0 0.02
"C:\winmos7\winmostar.exe" "C:\winmos7\samples\dbt.dat" -o pdb
"C:\winmos7\winmostar.exe" "C:\winmos7\samples\dbt.dat" -o gjf adjust hadd clean

When you execute computational programs from Winmostar, it will automatically terminate. Thus, in order to execute them continuously, DOS BAT file will help you.
adjust(adjust coord), hadd(add hudrogen), hdel(delete hydrogen), clean are available with -o filename. See wmjobs.bat for the example of bat file.
In case of Gaussian or GAMESS, consecutive operation can be arranged by [Tools]>[Batch Queue]

3-4. MOUSE OPERATION

Mouse Button functions


Key Left Click Left Drag Right Click Right Up/Down Wheel
None Select Rotate Select and Replace Group Zoom Zoom
Shift Multi Select/Unselect Move View Point Remove - -
Ctrl Multi Select/Unselect Multi Rectangle Select - - -


4. Operation menu

4.1. File

[File]
[New] Ctrl+N refresh display and start editing a new molecule
[Open] Ctrl+O read molecule from a file
[Open Recent] ▶ read a file recently opened
   [Clear History] clear the file history opened recently
[Reload] append a file to the current model
[Appen] Shift+Ctrl+R reload a file currently opened
[Save] Ctrl+S save the molecule in editing window as a file.
[Save As] Shift+Ctrl+S save the molecule with a new file name.
[Import] ▶ import the result of calculation or something. same as in [QM] menu.
   [SMILES] open Import SMILES window to read a SMILES string to generate a molecular structure using conformation search with Balloon.
   [Mopac] MO(mgf)
Charge, Dipole(arc)
Animation(arc)
IRC,STEP(out)
Force(out)
   [GAMESS] Animation
MO, UV, Charge, Dipole, NMR
Hessian,Raman
   [Gaussian] Animation
Anim_Opt(IRC,modred)
MO, UV, Charge, Dipole, NMR
Freq
Fchk(CubeGen)
Cube
   [GAMESS] Animation
MO, UV, Charge, Dipole, NMR
Frequencies,Raman
[Export] ▶ export special format files.
   [SMILES] export SMILES format string.
This is unavailable for multiple molecules.
Cygwin with OpenBabel is required.
   [Structural Formula] export the structural formula of the model as a SVG file.
This is unavailable for multiple molecules.
Cygwin with OpenBabel is required.
   [Image] save the image of the model as a Bitmap or JPEG file.
   [VRML] export a VRML file. A VRML viewer is required to be installed.
[Superimpose]▶ superimpose molecules.
   [Add] Click 3 points (atoms) of the first molecule to specify the plain of superposition. 1st point is the origin, 2nd is on x-axis and 3rd is set on x-y plane.
The display is switched to the superimpose mode.
After [Quit] to return to the editing mode, the second molecule can be added in the same way. The two molecules superposed are shown in the specified plane.
You cannot edit the molecules in the superimpose mode.
The selectetd molecule by [Select] is highlighted. [Shift] is usable to check the molecules if the two molecules are similar structures. [Del] to delete the selected molecule.
When you read a new molecule from a file, it also returns to one-molecule editing mode. To add an new molecule, you must start from the one-molecule mode as described above. You can also view superimposed molecules in 3D viewer pressing [3D].
   [View] switch from the single molecule mode to the superimpose mode.
[Launch Text Editor] open the source file of the current molecule by the text editor program.
[Open Folder] open the folder where the source file of the current molecule exists by the Windows Explorer.
[Save As XYZ] save the molecular structure in Cartesian coordinates for MOPAC.
[My Profile] ▶
   [Load] load and apply the profile stored in a file
   [Save] save the profile into the file.
   [Default] apply the default profile.
[GEMS] use the old file type GEMS to save a file for Nanobox.
[Create Shortcut] create an shortcut of Winmostar on the desktop.
[Exit] finish Winmostar.


4.2. Edit

[Edit]
In most case, editing operations act on the selected atom, which is marked by a bold red circle, and the former selected atom, which is marked by a thin red circle, or the multi-selected atoms, which is marked by blue circles.
You can select an atom by clicking the atom on the main view or clicking the line of the atom on the Z-Matrix(XYZ) list. The former selected atom means the atom selected just before the selected atom. To multi-select atoms, click an atom with Ctrl key pressed to add the atom, click an atom in a molecule with Shift key pressed to add the atoms in the molecule, or drag with Ctrl key pressed to add the atoms in the rectangular area. For example, to delete an atom, click the atom on the main view, and click [Edit]-[Atom]-[Delete Atom] menu or [Del] Button. Partially Move, Rotate, Replicate, Delete etc. acts on the multi-selected atoms, or the bonded atoms on the side of the selected atom relative to the former selected atom.
Bonds are generated if the distance of two atoms are smaller than the sum of the covalent radii of the atoms times the bond factor, of which default value is 1.15.
To cancel the editing menu such as Add Atom, Move Atom, Partially Rotate etc., uncheck the menu or press Esc key.
Replace Group is also executed with right-clicking an atom.
Delete Atom is also executed with right-clicking an atom with Shift key pressed.
[Undo] Ctrl+Z cancel the last operation.
[Redo] Ctrl+Y redo the cancelled operation.
[Undo Text] cancel the last operation in the textareas at the right side of the main window.
[Edit Direct] directly edit the file content
[Atom] ▶
   [Add Atom] F4 add an atom, same as [add] button.
   [Move Atom] F5 the target atom can be moved by directly dragging by mouse.
   [Delete Atom] Shift+F4 delete the target atom, same as [Del] button in the case no atoms are multi-selected .
   [Change Element]
   Shift+F5
change the element of the target atom to other kind. same as [Chg]
[Bond] ▶
   [Add Bond] F7 add a new bond between the selected atom and the former selected atom.
   [Delete Bond] F8 remove the bond between the selected atom and the former selected atom.
   [Regenerate] regenerate all bonds
   [Aromatic Ring to
   Single & Double Bonds]
convert bonds of aromatic rings to single bonds and double bonds.
[Add Hydrogens] ▶ add hydrogen atoms
   [Adjust Coords.] Ctrl+J adjust bond length before adding Hydrogen, if the bond length is abnormal.
   [All Atoms (Auto)] Ctrl+H automatically add hydrogens to all atoms.
   [Selected Atom (Auto)] automatically add hydrogens to the target atom.
   [Selected Atom (H1)] add 1 hydrogen atom to the target atom
   [Selected Atom (H2)] add 2 hydrogen atoms to the target atom
   [Selected Atoms (H3)] add 3 hydrogen atom to the target atom.
   [Using pdb2gmx] attach hydrogens to a protein with gmx pdb2mx command in Gromacs
This will fail if the original PDB/GRO file has an atom without the information of amino acid residue. Extra atoms such as ligand or solvent must be removed by [Edit]-[Select Molecules] menu.
cygwin_wm is required to be installed for this menu.
This process runs under the working directory with postfix "_protonate_tmp".
   [Using OpenBabel] attach hydrogens automaticaly to a molecule with OpenBabel
Mainly used for a ligand molecule splitted from a PDB file.
Use [Edit]-[Select Molecules] menu to extract a ligand molecule from a PDB file.
cygwin_wm is required to be installed for this menu.
This process runs under the working directory with postfix "_protonate_tmp".
[Delete Hydrogens] delete hydrogen atoms.
[Partially Edit]
   [Partially Rotate] Ctrl+R rotates the target atom group around the axis from the selected atom to the former selected atom line.
   [Change Angle] Ctrl+A Modify the bond angle around the former selected atom. Since atomic group of the target atoms rotates in the view plane, you can modify the molecule in various ways.
   [Partially Move] Ctrl+M move the target atom group
   [Partially Rotate (Free)] Ctrl+F rotate the target atom group freely
   [Partially Clean] Ctrl+L optimize the target group by simple molecular force field method.
   [Partial Center of Mass] make a dummy atom at the center of the target group.
   [Partially Orientate] orientate the target group to the specified axis or plane.
   [Partially Cut] Ctrl+X cut the target group to the clipboard
   [Partially Copy] Ctrl+C copy the target group to the clipboard
   [Partially Paste] Ctrl+V paste the target group of the clipboard
   [Partially Replicate] replicate the target group with the specified position and number
   [Partially Delete] Ctrl+X delete the target atom group.
   [Partially Fix/Free] Ctrl+I modify optimization indices of the target atoms.
[Set] ▶
   [Length] change the distance between the selected two atoms to the specified value
   [Angle] change the angle of the selected three atoms to the specified value.
   [Dihedral Angle] change the dihedral angle of the selected four atoms to the specified value
[Build Ring] F9 build a ring between the selected two atoms, automatically adding -CHCH- or -CH-.
[Group] ▶
   [Replace Group] F6 replace the target atom with the group shown in group combo-box. You can also replace by right-clicking the atom.
"-CHCH-" and "-CH-" are the parts for polycyclic structures which will be added more closer to the "former atom"
same as [Repl] button.
   [Save Group] save the editing molecules as a group. The selected must be an terminal atom.
   [Delete Group] delete a group in the list.
[Exchange Indices] exchange the indices of the selected atom and the former selected atom.
[Reorder Indices] reorder atoms so that the hydrogen atoms are placed backside of the atom list.
[Orientation]▶  
   [Set] set currently shown orientation in the view as X,Y,Z direction.
   [Set (3 points)] set X-Y plane to the plane defined by the 3 points indicated by click prior to this operation.
   [Set Origin] set the target atom as origin.
[Z-Matrix]▶  
   [Add Atom] add an atom. Click where you want to place the atom on the screen, and click 3 atoms with which you want to form Z-Matrix connectivity following instructions on screen.
   [Add Dummy Atom] add a dummy atom.
   [Change Dihedral] change dihedral angle in Z-matrix
   [Change Connectivity] change connectivity of Z-matrix
   [Move Atoms] move an atom. All atoms which has Z-matrix connectivity to the atom moves.
   [Regenerate Z-matrix] refresh Z-matrix. The Z-Matrix connectivity is also reconstructed.
[Clean] Ctrl+G optimize the whole structure with simple molecular force field method.
[Mirror Image] convert the molecule to the mirror image by reversing the coordinates.
[Duplicate Enantiomer] generate and add the mirror image of the molecule.
[Select Molecules] multi-select the same kind of molecules. Operations such as "Partially Delete" are available after the selection. For example, you can extract a protein or a ligand structure from a PDB file of protein-ligand complex.
[Sort by Molecule Species] sort atoms in order to make molecules of same kind are sequential.
[Create/Edit Cell] create and/or edit a unit cell for MD etc.
When no cell exist, pressing [Create] button first to make a cell.
Then, extend the cell by pressing [Expand] button or edit values directly.
Representation of the cell is changed by Box Vectors, Lattice Constants, or LAMMPS Tilt Factors.

4.3. View

[View]
[Full Window] F10 expand the main view, select again to back to the original size.
[Centering] adjust the view point so as to the molecule is at center of the view
[Three View] switch whether to show as Three View or not
[Rotation] ▶
   [Free] rotate the view point freely by dragging mouse
   [X,Y,Z-Axis] rotate the view point along with x,y,z-axis by dragging mouse
   [Eye Vector Axis] rotate the view point along with the eye vector axis
[Dipole/Trans.Moment]▶
   [View] display dipole moment of MOPAC data
   [Scale] set the scale of the dipole arrow
   [Trans.Moment] set visible/invisible and the scale of the dipole moment and the transision moment.
[Select] ▶ set whether to show components on the main view or not
   [Mesh] display grids
   [Index/Charge] display atom indices or charge values.
   [Charge] ▶ set how to express charges
      [Numerical] display value of charges.
      [Graphical] display blue and red circles to express the amount of charges.
      [Scale] set scale for blue and red circles.
   [Dummy Atoms] display all atoms including dummy atoms.
   [Information] display the information of the molecule in the main view.
   [Marker] display red and blue circles on the selected atoms and the multi-selected atoms
   [Axis] display coordinate axes.
   [Multi.Bond] display multiple bonding
   [Backbone] display only backbone atoms
   [Cell] display cell
[Method] select a ball & stick model from Defaut or Slim, and Plain, Normal or Wire.
[Zoom In/Out] F3/F2 expand/reduce the size of the molecular image
[Space-Filling Model] display the space-filling image of the molecule
[Perspective] display the molecule in a perspective view
[Pack in PBC Cell] ▶
   [None] do not pack atoms into the periodic boundary cell
   [Atom] pack atoms into the periodic boundary cell in an atom unit
   [Molecule] pack atoms into the periodic boundary cell in a molecular unit
[3D] display a 3D image with a new window
[External Viewer] ▶ display a 3D image with an external application.
   [Jmol] start Jmol
   [VRML] view VRML (VRML viewer should be installed)
   [Mercury] start Mercury, read a CIF file in the case the CIF file is currently opened.
   [ChemscapeChime] start MDL Chime in a new window, if installed
   [Ray Tracing (PovRay)] display an image with ray tracing method, if PovRay is installed.
   [OpenSCAD] export a scad file, and start OpenSCAD if it is installed
[Copy Image] Ctrl+Alt+C copy the image to the clipboard.


4.4. Semi-Empirical

[MOPAC]
[MOPAC Keywords Setup] display the window to set MOPAC keywords
[Import Keywords] import keywords from a file
[Run with JM] launch Job Manager when running MOPAC if checked
[(1)Start MOPAC6] generate keywords and input data table of the current molecule, and start computation. The output file will be automatically opened by the editor specified at Editor Program Path on [Tools]-[Preference] window.
[(2)Start MOPAC7] generate an input data file for MOPAC7, and start MOPAC7 or the program specified at (2)MOPAC Program Path on [Tools]-[Preference] window.
[(3)Start MOPACX] generate an input data file for MOPAC, and start an other version MOPAC specified at (3)MOPAC Program Path on [Tools]-[Preference] window. This menu is disabled if the program is not available.
[Edit .out File] Open a MOPAC standard output file (.out) by the editor.
[Edit .arc File] Open a MOPAC summary file (.arc) by the editor.
[Import] ▶
   [MO(mgf)] display the orbital image of the molecule if graphic output is assigned (keyword: GRAPHF). 3D display is available.
   [Charge,Dipole(arc)] read a .arc file and show electrostatic charge or dipole moment.
   [Animation(arc)] read a .arc file and show the structure or the animation image of the molecule.
   [IRC,STEP(out)] read a structural data of IRC output and show the continuous figure of the molecule.
   [Force(out)] read a result from vibration analysis and show IR spectrum and vibration profile.
[CNDOS]
[CNDO/S Keywords Setup] set up parameters for CNDO/S
[Import Keywords] import keywords from an existing CNDO/S file
[Start CNDO/S] start CNDO/S
note:
CNDO/S has been introduced by former JCPE as "P083(CNDO/S:conputational program for UV/Visible absorption spectrum)".
The two programs were combined and modified to be executed from Winmostar.
The program was compiled with gfortran to cndosw.exe.
[UV-VIS Spectrum] show UV/VIS spectrum and molecular orbitals from a CNDO/S output file.
[Edit .lst File] open the output file of CNDO/S by the editor.
[MOSF]
[MOSF Parameter] set MOSF parameters to replace keywords.
[Start MOSF] run MOSF.
[UV-VIS Spectrum] show UV/Vis spectrum from MOSF output.
[Edit .oms(mut) File] open an output file of MOSF by the editor.


4.5. QM

[Remote Job Submission] execute remote job control of Linux (Unix) computers through ssh. Gaussian98/03/09, GAMESS, NWChem, Gromacs and LAMMPS can be executed. PBS and LSF are supported.
[GAMESS]
[GAMESS Keywords Setup] show the window for entering GAMESS keywords.
[Import Keywords] import GAMESS keywords from a GAMESS data file.
[NCPUS] set the number of CPUs (cores) to be uses for the computation.
[NODES(Firefly)] set the directories of computing nodes for Firefly.
[PDB]▶
   [Edit PDB File] edit the molecule, such as deleting atom, keeping the indformation of residues, etc.
   [FMOutil] launch FMOutil.
[Start (1)GAMESS] generate the input file of the current molecule with the keywords and start computation.
If you want to use external basis function ($BASIS EXTFIL=.T.), place basis.lib in the same directory of the GAMESS program file.
For WinGAMESS, insert “setenv EXTBAS ../basis.lib” in runscript.csh.
[Start (2)GAMESS] start program specified at (2)GAMESS Program Path on [Tools]-[Preference] window
[Edit .out(log) File] open an GAMESS standard output file (.out) by the editor.
[Import] ▶
   [Animation] read an GAMESS standard output file (.out) and show stepwise change of co-ordinates during optimization process.
    [MO,UV,Charge,
      Dipole,NMR]
read an GAMESS standard output file (.out) and show the image of molecular structure or molecular orbitals. 3D display is also available. Available basis functions are limited to STO -3G, 3-21G(*), 6-31(+)G(*), and 6-31G(d,p).
   [Hessian,Raman] read the result of vibration analysis and show IR-Raman spectrum and vibration profile.
   [$VEC from punch] read $VEC from a punch file.
   [$HESS from punch] read $HESS from a punch file.
   [RESP charge from punch] read a punch file and calculate RESP charges.
[Gaussian]
[Gaussian KeywordsSetup] display the window to set Gaussian keywords
[Import Keywords] import parameters from an existing Gaussian data file.
[Start Gaussian] generate the input data file of the current molecule and the keywords, and execute computation.
[Edit log(out)] open an Gaussian output fileby the editor.
[Import] ▶
   [Animation] read an Gaussian standard output file (.out) and show stepwise change of co-ordinates during optimization process.
   [Anim_Opt(IRC,modred)] read an Gaussian standard output file (.out) and show the optimized structure of the molecule.
   [MO,UV,Charge,Dipole,NMR] read an Gaussian standard output file (.out) and show the structure and the orbit of the molecule. Available basis functions are limited to STO-3G, 3-21G(*), and 6-31(+)G(*).
   [Freq] read the result of vibration analysis and show IR-Raman spectrum and vibration profile.
   [Archive] read precise corrdinates from the archive part of an output file.
[FormChk] execute Formchk in G03W utility and generate a formatted file .fch from the .chk file, then open it.
[Import Fchk(CubeGen) File] execute Cubegen in G03W utility and generate a Cube file from the .fch file.
[Import Cube File] visualize a Cube file.
3D is available.
In case of GAMESS, a .pun file is converted to Cube format.
[PIO]▶
   [with Gaussian] set parameters for PIO (paired interacting orbitals) analysis by Gaussian and execute computation.
   [with GAMESS] set parameters for PIO (paired interacting orbitals) analysis by GAMESS and execute computation.
[NWChem]
[NWChem Keywords Setup] show the window to set NWChem keywords
[Import Keywords] import NWChem keywords from a NWChem data file.
[Start NWChem] generate the input file of the current molecule with the keywords, and start NWChem.
[Edit .out File] open a NWChem standard output file (.out) by the editor.
[Import] ▶
   [Animation] read a NWChem standard output file (.out) and show stepwise change of coordinates during optimization process.
   [MO,Charge,Dipole] read a NWChem standard output file (.out) and show an image of molecular structure or molecular orbitals.
3D view is also available.
   [Frequencies,Raman] read a NWChem standard output file (.out) and show frequencies and raman spectrum.


4.6. MD

[Remote Job Submission] Same of [QM]-[Remote Job Submission].
[Solvate/Build Cell] put water or solvate molecules saved as a mol2 file around the molecule shown on the main window, Mainly used to build liquid phase.
[Generate Ions] replace water molecules with monoatomic ions
Mainly used to neutrize a protein system.
[Gromacs]
[Keywords Setup] set parameters for Gromacs.
[Start Gromacs] execute Gromacs.
[Import .gro File] import a Gromacs GRO file (gmx_tmp_mdrun.gro).
[Import Trajectory] import a Gromacs trajectory file (gmx_tmp_mdrun.trr).
[Energy Plot] display an energy graph from a calculation result .edr file.
[Radial Distribution Function] display a graph of radial diffusion function computed from simulation result.
[Mean Square Displacement] display a graph after calculating mean square displacement from simulation result and calculate self diffusion coefficient.
[Root Mean Square Deviation] draw a graph of time change of Root Mean Square Deviation against initial coordinates especially in a protein system.
[Radius of Gyration] display a graph of time change of Radius of Gyration especially in a protein system.
[Scattering Function] display a graph of scattering function from Gromacs output TRR, TPR and NDX files.
[Solubility/Chi/DPD Parameters] compute Solubility, Chi and DPD aij parameters from Gromacs output.
[Start ER] compute free energy using Energy Representation (ER) method.
[Import ER] display results from the free energy calculation using ER.
[Start BAR] compute free energy using Bennett Acceptance Ratio (BAR) method.
[Import BAR] display results from free energy calculation using BAR.
[LAMMPS]
[Keywords Setup] set parameters for LAMMPS.
[Start LAMMPS] Start LAMMPS
[Import Trajectory] import trajectory coordinates from a LAMMPS dump file.
[Energy Plot] display a energy graph from a log file of calculation result.
[Radial Distribution Function] display a graph of radial diffusion function computed from a simulation result XTC file.
[Mean Square Displacement] display a graph of mean square displacement from a simulation result XTC file.
Self diffusion coefficient is also computed.
[Amber]
[LEaP Keywords Setup] set parameters for LEaP.
[Start LEaP] make a coordinate(crd) file and a toporogy(prmtop) file with tLEaP.
[sander Keywords Setup] set parameters for sander.
[Start sander] start sander.
[Import Coordinate File] import an Amber format coodinate(crd) file and a toporogy(prmtop) file.
[Import Trajectory] import an sander output trajectory file.
[Energy Plot] display graphs of various kinds of energy from a sander output log file.
 
[Polymer] ▶
   [Register Monomer] register a monomer.
   [Homo Polymer Builder] build a homo polymer.
   [Block Polymer Builder] build a block polymer.
   [Random Polymer Builder] build a random polymer.
   [Polymer Cell Builder] build polymers packed in a cell.
   [Map Monomer] map registerd monomers to DPD particles to obtain all atoms.
   [Setting] set the each folder path to save monomers and polymers in.
[DPD] ▶
   [DPD Cell Builder] Build a DPD polymer cell.
   [DPD Potential Editor] edit and set the potentials to be used for DPD.
[Interface Builder] start Interface Builder
[Bond/Angle Calculator] calculate and show a time change of bond lengths, angles or dihedral angles.
call this function when the animation window is present.
[Fragment ER] show Fragment ER window.


4.7. Solid

[Remote Job Submission] Same of [QM]-[Remote Job Submission].
[Crystal Builder] Build an crystal model.
[Quantum ESPRESSO]
[Keywords Setup] set calculation conditions for the ab-initio computation program Quantum ESPRESSO(QE).
[Start Quantum ESPRESSO] start QE.
[Edit .pwout File] open a QE output .pwout file by the specified editor.
[Animation(pwout)] display energy change of optimization process from a QE output .pwout file.
[Lowdin Charge] display isosurface of electric density with a specified QE output folder.
[Potential Energy Distribution] display potential energy distribution along z-axis with a specified QE output folder.
[Band Structure] display band structure with a specified QE output folder.
[Density of States] display density of states with a specified QE output folder.
[Difference Densty/Energy (esm1)] display distribution of difference energy/density along z-axis with specified QE output folders using ESM with two different conditions.
[Animation(pos)] display change of atom coordinates from a QE output .pos file.
[Energy Plot(evp)] display graphs of various kind of energy from a QE output .evp file.
[FDMNES]
[Keywords Setup] set calculation conditions for the XAFS spectrum computation program FDMNES.
[Start FDMNES] start FDMNES.
[XAFS spectrum] display a graph of XAFS spectrum.


4.8. Tools

[Tools]
[Preference] open the environment preference window.
[Conformation Search(Balloon)] start conformation search with Balloon.
[Launch CONFLEX] launch CONFLEX.
CONFLEX is required to be installed.
[Molecular Surface Area & Volume] calculate molecule's surface area and volume.
[Aspect Ratio] calculate aspect ratio defined as L/D, where L and D are the length and the diameter of the smallest cylinder which the molecule internally contacts.
[Radius of Gyration] calculate Radius of Gyration.
[Sterimol Parameter] calculate the sterimol parameter for the multi-selected (blue circled) atoms in the main view.
Start calculation when "Calculate" button is pressed.
[Point Group Analysis] (1) detect point group of the molecule.
(2) resolve distortion and symmetrize the coordinates, with the information of detected point group symmetry.
(3) convert symmetric unit and asymmetric unit each other.
[Grep] search keywords from an output file of computation, and output the lines to an excel or text file.
[Job Manager] launch Job Manager.
[Batch Queue] make a batch file and execute it.


4.9. Help

[Manual] F1 show this manual.
[Web Manual] link to the Winmostar online manual page.
[Periodic Table] show a periodic table.
[winmostar.com] move to the Winmostar website.
[About] show the version and the expiration date of installed Winmostar.
[Debug] open the debug information window.


[Basic]
[Language] select a language.
[Show Advertisement] switch whether to show the advertisement image or not.
[License Code] set a license code.
[Edit]▶
   [Bonding Factor] set the bonding factor to be used whether generate each bond or not.
   [Keep Z-Matrix
   Connectivity]
keep Z-Matrix connectivity while editing the molecule if checked.
   [Convert Aromatic
   to Single & Double
   Bonds for MOL File]
convert bonds of aromatic rings to single and double bonds for saving a MOL file.
[Calculation]▶
   [Run MOPAC with
   Job Manager]
same of [Semi-Empirical]-[MOPAC]-[Run with JM].
   [Run the Other Progmras
   with Job Manager]
set whether to use Job Manager to execute other programs than MOPAC or not.
   [GAMESS NCPUS] same of [QM]-[GAMESS]-[NCPUS].
   [Firefly NODES] same of [QM]-[GAMESS]-[NODES(Firefly)].
   [NWChem MPI Procs] specify the number of MPI processes to execute NWChem.
[View]
[Color Set] select a default color set among Winmostar, GaussView, Jmol, Rasmol Old Winmostar, and Patent(White).
[Color]▶
   [Selected Atom] change the color for the element of the selected atom.
   [Bond] change the color of bonds.
   [Background] change the color of the background.
   [Background] change the color of the background of the 3D view.
   [Text] change the color of the text on the main view.
[VDW Radius of Selected Atom] change the VDW radius for the element of the selected atom.
[Charge Scale] same of [View]-[Select]-[Charge]-[Scale].
[Select] same of [View]-[Select]
[Program Path]
set a program path of each program.



New File Ctrl+N Add Bond F7 Partially Copy Ctrl+C
Open File Ctrl+O Delete Bond F8 Partially Paste Ctrl+V
Save File Ctrl+S Build Ring F9 Partially Delete Ctrl+L
Save File As Shif+Ctrl+S Adjust Coordinates Ctrl+J Partially Fix/Free Ctrl+I
Export Image Ctrl+Alt-I Add Hydrogens
(All Atoms)
Ctrl+H Clean Ctrl+G
Undo Edit Ctrl+Z Partially Rotate Ctrl+R Replace Group F6
Redo Edit Ctrl+Y Change Angle Ctrl+A Full Window F10
Add Atom F4 Partially Move Ctrl+M Zoom In F3
Move Atom F5 Partially Rotate
(Free)
Ctrl+F Zoom Out F2
Delete Atom Shift+F4 Partially Clean Ctrl+L Copy Image Ctrl+Alt+C
Change Element Shift+F5 Partially Cut Ctrl+X Manual F1