| menu: File |
| open cell | opens an input file in one of the following four formats: asymmetric unit cell, full unit cell, cartesian unit cell, pure xyz data. The location is assumed to be the subdirectory CELL/ although you may load a file from any location using the file chooser. |
| reload cell | reloads the present inputfile (not for *.SDF files!). This is useful if you edited the input file for specifying polyhedra etc. and you want to activate those changes. |
| load SDF | load the proprietory Structure Description File, which was created by JSV. The default location is the directory SDF/, but a *.SDF file may be opened from any location using the file chooser. |
| write SDF | dump the current state of the displayed structure including colors, modes, edited bonds, edited polyhedra to JSV's Structure Descripton File. The file name has the suffix *.SDF. It is always written to the directory SDF/ and by default opened from there. |
| EDIT file | opens an editor for the current input file. After editing (don't forget "save") the changes may be activated by selecting reload cell from the File menu. SDF files are not supposed to be edited !!!, however you may want to edit the bond properties in the new SDF file format. |
| view file | opens a file viewer for the currently loaded input file (no editing possible) |
| new:
new asymmetric cell |
opens the editor with the template for a new input file for the asymmetric unit cell |
| new:
new full unit cell |
opens the editor with the template for a new input file for a full unit cell |
| new:
new cartesian cell |
opens the editor with the template for a new input file for a full cartesian unit cell |
| import:
MICRO-POWD |
imports *.pwd files of MDI's MICRO-POWD (D.&K.Smith) |
| import:
FAT-RIETAN |
imports *.cif files of RIETANS next release version (F.Izumi) |
| import:
POWDERCELL |
imports *.cell files of POWDER-CELL (G.Nolze & W.Krause) |
| import:
Fullerene Library |
(only in full version) imports *.cc1 files of M.Yoshida's Fullerene Library (download from my website!) |
| import:
Protein Data Bank |
(only in full version) imports *.pdb files |
| import:
MDL |
(only in full version) imports *.mol files of small molecules |
| import:
SHELX |
(only in full version) imports *.res files from SHELX |
| import:
ICSD |
(only in full version) imports *.txt files from the Inorganic Crystal Structure Database |
| save
as: save as GIF |
saves the current display as a GIF file (256 colors). This may sometimes not work if the displayed structure uses more than 256 colors. In such case you have to use JPG. |
| save
as: save as JPG |
saves the current display as a JPG file (more than 65000 colors). (routine by J.R.Weeks) |
| save
as: save as JPG (JDK) |
saves the current display as a JPG file (more than 65000 colors). (using JDK's own JPEG encoder) whereby JSV also asks you for a quality parameter in % |
| save
as: save as PS b/w |
write a black/white PostScript file using my own PostSript libraries. I will improve the quality in future releases. |
| save
as: save as PS color |
write a color PostScript file using my own PostSript libraries. I will improve the quality in future releases. |
| save
as: save as VRML1.0 |
saves the structure in VRML (virtual reality modelling language) format for viewing in a webbrowser or with a stand-alone VRML viewer like GLview3.6 (I highly recommned to download the latter, Windows only). JSV does not use real 3D graphics and may give incorrect images when there are interpenetrating atoms, bonds or polyhedra. Please use this VRML option if you want to see the correct 3D representation. |
| save
as: save as VRML2.0 |
save structure as VRML2.0 (=VRML97) file.The advantage here is that it is possible to have transparent polyhedra. |
| save
as: save as POVRAY |
(only in full version) write file for the free Raytracer program POVRAY |
| save
as: save as Chem3D |
(only in full version) write file in the same format as the Fullerene Library files |
| save
as: write cart.cell |
dumps the current structure to a file in JSV's "cartesian cell" format |
| save
as: write xyz file |
dumps the current atoms to a file with only the x,y,z positions |
| (only Windows/Solaris) prints the current canvas (content of screen) as a raster graphics (!) to a specified printer. This feature is new in the JDK1.2. However, the spooling process is quite slow. You may consider just to save the image as GIF/JPG and then use any other graphics software to view and print the image. | |
| Exit | Quit JSV |
| menu: View |
| sliders | switch the sliders at the top on/off |
| visibility switch | show window with checkboxes for switching atom types ON/OFF |
| memory monitor | show a graph with the RAM usage (code taken from SWING examples) |
| show info | show title and number of atoms on the bottom left of the display area. When exporting GIF and JPG it is sometimes better to switch this information off. |
| center to screen | center the shown structure to the screen center after you moved it around with the Shift-Zoom mode |
| fit to screen | try to show the whole structure on the screen (eg.after you zoomed) |
| atom
style: draw Spheres |
shows atoms as spheres (precalculated 2D images of spheres) |
| atom
style: draw Discs |
draws atoms as filled disc in the specified colors with depth cueing |
| atom
style: draw Circles |
draws atoms as empty circles |
| bond
style: draw triangle |
draw bonds as triangles, the bond radius slider may be used to change the thickness of the bonds |
| bond
style: draw thin lines |
draws bonds as simple thin lines (draws faster than the other bond types!) |
| bond
style: draw thick lines |
draws bonds as thick lines (imitating shaded cylinders) |
| bond
style: draw half & half |
draws bonds as thick lines whereby each half of the bond has the colour of the attached atom. |
| atom radius: ... | sets the specified atom radius in [%] |
| zoom: ... | sets the specified zoom factor for the structure display in [%] |
| background: gradient background 1 |
shows a color gradient as background with grad.col A at the top/bottom and grad.col B at the center |
| background: gradient background 2 |
shows a color gradient as background with grad.col A at the top to grad.col B at the bottom |
| background: uniform background |
shows a monocolor background with the specified canvas color |
| Java3D window | requires
Java3D to be installed ! This opens another window in which the present structure is displayed as true 3D graphics using the Java3D libraries for the JDK1.2.This allows you to see interpenetrating atoms correctly and transparent polyhedra. |
| menu: Cells |
| 1 x 1 x 1 | draws the shown numbers of unit cells |
| 2 x 1 x 1 | along |
| 1 x 2 x 1 | a-, b- and c-direction |
| 1 x 1 x 2 | |
| 1 x 2 x 2 | (keep in mind that I limited the maximum |
| 2 x 1 x 2 | number of atoms to 5000) |
| 2 x 2 x 1 | |
| 2 x 2 x 2 | |
| 3 x 3 x 3 | |
| 4 x 4 x 4 | |
| 5 x 5 x 5 | |
| custom | specify range along a-, b- and c-direction (also non-integer values allowed) |
| menu: Rotation |
| around X: 90 deg | rotate 90 degrees around screen normal |
| around X: -90 deg | rotate -90 degrees around screen normal |
| around X: custom | specify angle around screen normal |
| around X: auto | start animation around screen normal |
| around Y: 90 deg | rotate 90 degrees around horizontal axis |
| around Y: -90 deg | rotate -90 degrees around horizontal axis |
| around Y: custom | specify angle around horizontal axis |
| around Y: auto | start animation around horizontal axis |
| around Z: 90 deg | rotate 90 degrees around vertical axis |
| around Z: -90 deg | rotate -90 degrees around vertical axis |
| around Z: custom | specify angle around vertical axis |
| around Z: auto | start animation around vertical axis |
| stop auto rotation | stop animation (it is faster to use hit SPACE key) |
| new rotation center | lets you select any atom as center of rotation by clicking at it |
| menu: Option |
| view cell data | opens a list which displays the cell contents and other data. (this is actually the contents of the file tmp.ucc, which is always written for use in the diffraction calculations ) |
| atom radii/colors | opens a periodic table from where you may choose/edit the atom radii and select atom colors. The 34 colors are specified in the file lib/color.pal . So if you are familiar with RGB colors you may edit those values to create another color palette. (don't change the number of colors =34) |
| color settings | opens a color chooser. Click first on the top color bar to select a hue and then in the square area to select the color. The combo box lets you select what the color is used for. This is not for atom colors. Those are specifies under atom radii/colors |
| space group info | open a window with information on the space group of the currently loaded structure (if space group number is given, eg.asymmetric unit cell) |
| X-ray diffraction | calculates the x-ray intensities for the present structure (asymmetric/full unit cell or SDF file derived from an asymmetric/full unit cell input) This calculation requires the unit cell content as saved in the file tmp.ucc . The file tmp.ucc (temporary unit cell content) is written when the space group symmetry operations generate the atom positions. It is also appended to a SDF written from an asymmetric/full unit cell, so that diffraction intensities can be calculated from the SDF file as well. |
| Search interstitials | opens the interstitial search dialog and then the interstitial viewer. (see also here) |
| hole radius at [x,y,z] | search for the free radius around a given point to search for the possibility of accomodating another atom there |
| generate nanotube | (only in full version) opens dialog for generating atom coordinates of nano tubes, nano cones and sheets. After the atoms are displayed you can generate bonds using the bond menu. |
| redefine atom | lets you change the atomic number of a atom species after clicking at one. This new atomic number is then used to obtain radius and atom color. This change is however neither saved in the input file nor is it considered in the X-ray diffraction simulation. |
| cut spherical region | lets you click at an atom in order to cut out its environment in a spherical volume section. The radius of the section can be adjusted using the slider which appears on the right side of JSV's display. Thus you can study for example atom shells around some atom. (you can also turn this central atom into the center of rotation with [Rotation][new rotation center] ) |
| uncut all cut atoms | After you have removed (set invisible) several atoms in the Cut Atoms mode, you may set all their flags to visible again. (atoms are never really removed since the bonds/polygons depend on the atom numbers) |
| uncut within 10 pix | click any point, then any cut atoms within 10 pixel radius will be made visible again. This is usefull if you accidently cut some atom. |
| uncut by atom type | After you have removed (set invisible) several atoms in the Cut Atoms mode, you may set the atoms having a particular atom label to visible again. |
| menu: Polygons |
| add triangle | lets you add a triangular
polygon (all polygons in JSV are triangles!). Switch to mode
numbers so that you can see the numbers of the
atoms. Then select three which are to form a polygon and
enter those three numbers in the dialog box (with a space
between the numbers). The order has to be such that if
the polygon faces towards you the numbers should be in
clock-wise order. That ensures that the normal of the
polygon faces to you. If the normal of a polygon faces
away from you the polygon will not be drawn. (saves
drawing time) . Polygons are supposed to form a closed
polyhedron. Otherwise JSV's drawing routine is
insufficient (painter's algorithm). If you just want to create a VRML file, you may of course create individual polygons, because VRML will always show them correctly. You may also make rectangular polygons by deviding them into two triangles! |
| remove triangle | lets you remove a polygon by specifying the atom numbers of its three vertices |
| reverse last triangle | reverse the normal of the last added polygon. (in case you chose counter-clockwise) |
| remove last triangle | removes the last added polygon |
| !!!!!! the following items let you manually add/remove individual polygons/polyhedra. Symmetry equivalent ones will NOT be generated in this case. I used this technique to create the High-Tc superconductor gallery. Please note that the atom numbers on the vertices have to be given in a special order, in order to make sure that the corners of the individual triangles are ordered counter-clockwise (for producing the correct face normal) |
|
| add square | adds a plane square using 4 triangles (2 towards each side) to make sure it is being displayed. An individual triangle is only displayed if its normal faces towards you the viewer. |
| remove square | |
| add pentagon | |
| remove pentagon | |
| add tetrahedron | |
| remove tetrahedron | |
| add octahedron | |
| remove octahedron | |
| add square pyramid | |
| remove square pyramid | |
| add cube | |
| remove cube | |
| specular light | uses an additional white lamp for the polygons only (if selected) |
| polygon edge | draws a darker contour of the polygon (if selected). This might only be desirable if all polyhedra only have triangular facets |
| remove all polygons | removes all polygons |
| menu: Bonds |
| make single bond | click two atoms to create single bonds. End mode with [Mode][Rotate] or by clicking the rotate LED |
| make all bonds (atom types) | click two atoms to create equivalent bonds for that length and only using a pair of the same atom types. End mode with [Mode][Rotate] or by clicking the rotate LED (you may set a bond length margin with set deviation) |
| make all bonds (lengths) | click two atoms to create equivalent bonds, whereby atom types are neglected and only this length is used . End mode with [Mode][Rotate] or by clicking the rotate LED (you may set a bond length margin with set deviation) |
| set deviation | set allowed deviation for bond lengths (default dl=0.01). In order to get a larger number of equivalent bonds you may have to increase this value. |
| undo last make | removes last created single bond/equivalent bonds |
| remove single bond | click two bonded atoms to remove that bond. End mode with [Mode][Rotate] or by clicking the rotate LED |
| remove equivalent bonds | click two bonded atoms to remove all equivalent bonds. End mode with [Mode][Rotate] or by clicking the rotate LED |
| remove all bonds | kill all bonds |
| remove identical bonds | removes identical (duplicate) bonds if present (may reduce number of bonds for faster drawing) |
| menu: Mode |
| Note that clicking at the corresponding
labels on the LED bar at the bottom of JSV is equivalent
to selecting the display mode from this menu ! Several modes, which require to click atoms may be switched off by clicking at the Rotate label on the LED bar! |
|
| Rotate | rotation mode:
press left mouse button and drag to rotate about y-,z-axis;
right mouse button around the x-axis KEYS: you can also use the CURSOR KEYS or SHIFT+CURSOR KEY to perform the rotations. However you might have to click at the display area first, in order to give it the keyboard focus. |
| Shift-Zoom | use left mouse button+drag for zooming and right mouse button+drag for shifting the image around |
| Perspective | toggle between orthonormal projection and perspective projection. The slider for the perspective factor lets you adjust the degree of perspective |
| Stereo | toggle between mono and stereo pair display. By default the stereo mode is in parallel view. You may go into shift-zoom mode and use right mouse button+drag to adjust the distance between the images or reverse sides to cross-eyed view. |
| Cellbox | switch display of the cell boundary on/off |
| Bonds | switch display of bonds on/off (if there are any) |
| Polyhedra | switch display of polyhedra on/off (if there are any) |
| Labels | show atom labels as given in the input file |
| Numbers | show individual atom numbers needed for specifying polygons/polyhedra |
| Distance | click two atoms to measure their distance. End mode with [Mode][Rotate] or by clicking the rotate LED |
| Angle | click at three atoms to measure the enclosed angle. End mode with [Mode][Rotate] or by clicking the rotate LED |
| Cut Atom | Start the cut atoms mode. You may click at individual atoms to set them invisible. Also existing bonds with those atoms will become invisible. End this mode by choosing [Mode][Rotate] or by clicking the rotate LED at the bottom. Atoms are never really removed since the bonds/polygons depend on the atom numbers. Even if you write a SDF file the cut atoms are still there and you may set them to visible again with show cut atoms from the menu Option. |
| economy | SPEED UP ROTATIONS! when this checkbox is checked rotations will be faster, because during rotation by mouse drag or cursor keys the display mode is changed to simple circles without any bonds or polyhedra. When you release the mousebutton or the cursor key the original display mode is used again. |
| individual bonds | JSV can display bonds using the globally set properties (bond color and style [view][bond style][draw..] ) or when this checkbox is checked then the bond color and bond style , which are specific to each individual bond are used. Of course There you only can see a difference if you specified individual properties. See also bondproperty.html . |
| menu: Modules |
| Reciprocal space viewer | start the XRDL modul as a stand-alone modul without specifying an input file (*.xrd). You then may open a *.xrd file of your choice. |
| Stereographic projections | Opens the JWulff modul whereby the unit cell parameters of the presently loaded structure is used as start setting. This modul allows you to plot stereographic projections onto a Wulff net. You may plot the poles of planes (hkl) or the poles of zone axes [uvw]. |
| Unit cell visualizer | Opens the JUnitCell modul which is based on my JCell applet. The unit cell parameters of the presently loaded structure are used as the start unit cell. |
| Periodic Table | Opens a periodic table of elements which gives the most important properties for each element. The graph shows the value of a chosen property for all elements. The vertical line (at a certain atomic number) indicates the location of the chosen element. You may click either at the table itself or on the graph to select another element. |
| Interstitial space viewer | Opens a 3D viewer for *.jfm files, which contain grid point positions within a unit cell which are not occupied by atoms. Several search criteria influence the number of displayed points. |
| CMB,MDI-diffractogram viewer | Viewer for MICRO-POWD's *.cmb files and MDI's *.mdi files |
| Rietan-diffractogram viewer | Rietveld difference plot viewer for FAT-RIETANS's IGOR files |
| VRML97 viewer | start VRML97 viewer (requires Java3D to be installed) - only works for VRML97,VRML2.0 files and NOT for VRML1.0 files !!! |