_________________________________________________________________ RASMOL info _________________________________________________________________ This is an info-file, i.e. it contains both some basic information and some open questions about the graphical visualization code RASMOL. These information are intended as a fast recipe for pedestrians and are kept to the minimum size. Questions represent information we do not know, so if you know the answer let us know. Of course all the basic information about RASMOL can be obtained by typing 'help' in the RASMOL window or from a RASMOL manual (for RASMOL manual web page see http://www.umass.edu/microbio/rasmol/distrib/rasman.htm or http://www.bernstein-plus-sons.com/software/rasmol/doc/rasmol.html#go_canvas) However, RASMOL was designed with biochemistry requirements in mind, so it may be useful to have some notes on how to use RASMOL tools to draw particles of arbitrary type, such as those one one studies in molecular dynamics or similar simulations. _________________________________________________________________ STARTING AND QUITTING START currently one can start RASMOL by the command: - rasmol (version 2.6) - rasmol27 (for version 2.7) NOTE A single window is sufficient to work with RASMOL, because if it is run in background: - rasmol & then the X-window works as a normal one when it is active, and as the rasmol command window (i.e. where everything typed is redirected) when the RASMOL window is active QUIT to quit from RASMOL type: - quit _________________________________________________________________ INPUT FILES AND LOADING RASMOL can read several formats, here only XYZ format is considered. DESCRIPTION OF XYZ FORMAT 1st line: n (1 field = int. number = number of particles) 2nd line: whatever (the name for RASMOL), maybe not used... n following lines: ab x y z t (5 fields, additional fields ignored...) where: ab = atom label (not more than 2 characters, whatever), x = x coordinate, y = y coordinate, z = z coordinate, t = (called) "temperature" field (used to vary the colour/size, see below) and has this restriction (negative values are not considered here): (-3.0) 0 < t < +3.0 if real (-750) 0 < t < +750 if integer, values out of range are ineffective To load an xyz file type: - load xyz filename where "filename" is an xyz file which does not have to have an .xyz extension Before loading a new file (a new system), the command: - zap is needed. Presently RASMOL loads 1 file at time ________________________________________________________________ THE GRAPHICAL REPRESENTATION When RASMOL loads a file, the initial draw of the particles may look strange, at least for two reasons. Consider that: 1) RASMOL automatically tries to calculate (chemical) bonds if particles are close enough to each other. This may turn out to be a very long process if there are many particles. QUESTION: can one disable the bond calculation ?? NOTE:-) Since bonds are calculated if the distance of particles is < 2.0, one can disable bonds by rescaling coordinates with a suitable factor To remove bonds ondce they have been made, type: - WIREFRAME OFF 2) The first picture appears by default "from the bottom" :-) namely this is the default frame you see: -Y +Z | / | / |/ -X -------o------- +X /| / | / | -Z | +Y The monitor is the X-Y plane (note: Y axis going downwards), the Z axis perpendicular to the monitor (+ direction inward, - outward). ________________________________________________________________ LIST OF INTERACTIVE COMMANDS Here is a list of commands which can be given interactively when the RASMOL window is active: ROTATIONS - right bar: rotates around current x axis - lower bar: rotates around current z axis - Shift-Mouse3: rotates around current y axis - Mouse1: acts like right + lower bars at the same time the equivalent commands (useful for a fine tuning or repeated operations) are: - rotate x n: rotate around current x axis of n degrees (n can be floating) - rotate y n: rotate around current y axis of n degrees (n can be floating) - rotate z n: rotate around current z axis of n degrees (n can be floating) - set picking center: after this command, left-clicked particles become center of rotatation, useful if you want to inspect a small subsystem TRANSLATIONS - Mouse3: translate the system ZOOM - Shift-Mouse1: zoom in or out BALL RADIUS - spacefill r: specifies ball radii current limits are either 0.0 Temperature) NOTE if you want to use the t-field for colours you can get all the colours by setting t from t = 1.1 (blue) to t = 1.8 (red) QUESTION: how does RASMOL decide the colour for arbitrary t ? - colours cpk: uses the first field (ab = label) to assign colours (from the panel: Colours -> CPK) A simple way to get the most of the colours is to use real atom labels in the first field (ab) and the 'colours cpk' command (even if they have nothing to do with the real particles studied). Here is a short correspondences list for the most common colours: --------------------------------------- approx.category symbol colour --------------------------------------- white&greys -> H white -> C light grey -> Ca dark grey blues -------> Na blue -> N light blue greens ------> B light green -> Mg forest green yellows -----> S yellow -> Si goldenrod orange/reds -> P orange -> O red pinks -------> He light pink -> I purple -> Unknown deep pink browns ------> Cu brown -> Li firebrick (If, on the other hand, you want to know which colour corresponds to a given atom or have an arbitrary colour, refere to the manual) NOTE For some reasons colours appearing in the RASMOL window are different from those appearing in the output postscript file (check!) QUESTION: Why? - background white (black/green/etc): changes colour of background SLAB - slab (on): activates the slab, i.e.: 1) it shows a thin section parallel to the monitor, if section slabmode is active, 2) it shows all the specimen behind a certain section, if the reject slabmode is active - slab off: deactivates the slab - set slabmode section: activate section slabmode - set slabmode reject: activate section reject - slab n: where n is an integer, specifies the slab % - Ctrl-Mouse1: varies continuosly the percentage of the slab when the slab is active FRAME - set boundbox on/off displays or not the box - set axes on off displays or not the Cartesian axes ________________________________________________________________ EXPORTING PICTURES Picture can be exported from the panel EXPORT -> POSTSCRIPT for postscript files, just give a name for the file when asked ________________________________________________________________ SCRIPT It is possible to execute a set of commands consecutively and automatically by writing them in a standard text file and then running the file (called e.g. "filename") with: - script filename The command: - pause can be useful in writing scripts. It stops the execution of the script until any button is pressed NOTE If you have a code producing different snapshots of the system at different times representing a time evolution, you can make the code also update a file "filename" with the proper RASMOL commands at every snapshot. At the end of the run, you can run RASMOL and type: - script filename to see all the snapshots consecutively. ________________________________________________________________ here is an example of script: zap load xyz WIGNER_0 wireframe off rotate x 90 rotate y 45 rotate x 20 colour cpk spacefill temperature pause zap load xyz WIGNER_1 rotate x 90 rotate y 45 rotate x 20 wireframe off colour cpk spacefill temperature pause zap load xyz WIGNER_2 wireframe off rotate x 90 rotate y 45 rotate x 20 colour cpk spacefill temperature pause zap load xyz WIGNER_3 wireframe off rotate x 90 rotate y 45 rotate x 20 colour cpk spacefill temperature pause ________________________________________________________________