There is a scripting interface as well as the interactive user interface. The scripting interface is usable from the Jython Console module. See the Modelzilla Framework Scripting Interface and the Vincent Van Mol Scripting Interface.

Introducing Vincent Van Mol Vincent Van Mol is a Modelzilla application that makes pretty pictures of proteins. Its original intent was to provide an x-ray protein crystallographer a versatile and at the same time easy way to create pictures to show off their painstaking experimentally determined protein structures, and to give Modelzilla molecular graphics capabilities that would form a basic level of inteligence for doing more specialized stuctural biology applications. As a Modelzilla application, Vincent Van Mol enjoys an integration in the geometric modeling universe inhabited by other Modelzilla applications, while at the same time enjoys the full specialization of a focused application.	Loading Vincent Van Mol
User Interface The basic procedure to using Vincent Van Mol is to load a molecule into memory, and tell it to create renditions the molecule with certain pre defined types of renditions that it offers, and then further specify the details of the renditions. Vincent Van Mol has a data oriented user interface, as opposed to a task oriented user interface. This means that the user can access most of the data controlling the picture and can change these values when ever they want to, as opposed to asking the program to begin a procedure that leads him through a sequence of specifications. Vincent Van Mol has seven main control panels. Each control panel occupies the same space on the screen, with a switching mechanism to control which is shown. We have attempted to arrange the control panels in a logic order that the user uses to get their picture made. As these panels are described, please follow along with your copy of Vincent Van Mol.
The Molecule Panel This panel shows the situation regarding what molecules are currently loaded into memory and has controls for loading, removing, showing, and hiding molecules. The top half of the panel contains the standard Modelzilla file browser. The bottom half contains a list of molecules and a command menu. To load a molecule into memory, select molecule in the file browser and press the "Load Molecule" button. You may also double click on the molecule's file in the file browser to do this. When a molecule is loaded into memory for the first time a default set of renditions is created to give the user confidence it has been loaded correctly. A wire frame of the entire protein is made, and metal atoms are rendered with balls. To remove a molecule, select the molecule in the list and press the remove molecule button. As well as removing the molecule this function removes all representations of the molecule. To hide the representations of the molecule without removing it permanently, press the "Hide Renditions" button. To show the representations of a molecule again, press the "Show Renditions" button. Using the file browser: The file browser has a list of files and directories found under an initial start in directory. Double clicking on a directory lists the contents of this directory in the list box. Double clicking on the two dots on the top of every list move to the parent directory. Double clicking on the file is a convenient shortcut that usually involves some action associated with the file. In this case it will invoke the load molecule function. The file browser also contains a text entry field labeled "Directory". This enables you to type in the directory the file browser should list. The file browser contains a text entry box labeled "File Filter". This enables you to enter a conventional file filter. For Vincent Van Mol, "*.pdb" makes sense.	Molecules Panel
The renditions panel This panel shows the situation regarding existing renditions, and has controls for creating, destroy, and otherwise operating on renditions of molecules. The top area of the panel contains a menu of rendition types. The standard Vincent Van Mol installation offers seven types of renditions: CPK, Molecular Surface, Atom Labels, Tubes, Ribbons, Residue Labels, Wires, and Ball and Stick. Any number of renditions may be created for a molecule, including any number of one type. Renditions are completely independent from one another. To create a new rendition object, press the corresponding button on the renditions menu. The "Fit" function pans and zooms the current view point so that the current rendition just fits into the current view port. The "Center" function sets view port rotation center to the center of the current rendition. The "Hide" function temporarily removes the current rendition from the current view port. The "Show" function puts the current rendition back in the current view port if it has been hidden. The "Delete" function removes the rendition permanently. This "Validate" function re-computes the graphics for the rendition based on its current user data state. Normally this is done automatically when the data changes, but it is possible to turn off this behavior so that many settings can be changed without triggering a possibly computational expense of operation. If this is the case the validate function may be used to update the current rendition.	Renditions Panel
The Element Properties Panel This is where Vincent Van Mol's unique personality begins to come out. Vincent Van Mol is the only molecular graphics program that allows most rendering properties to be specified on a per element basis rather than by simple global properties that are applied across all elements. The Element Properties Panel is used to control the values of properties that may vary per protein element. What the elements are depends on the type of renditions. For CPK rendition, molecular surface rendition, and the atom labels rendition, these elements are atoms. For the tube Trace rendition, a ribbon trace rendition, and residue labels rendition, these elements are residues. For wires and ball and stick, these elements are both atoms and bonds. The top area of the Element Properties panel is used to control which elements are in the current selection set. Note that in the current version of Vincent Van Mol, this selection set is independent of the selection set used by Modelzilla. In the future they may be integrated. The elements selection window contains several lists. The lists are organized in a hierarchical fashion so that when an encompassing element of the list is picked, the elements with in this elements are added to another twist is generally to its left. The simplest type of element selection is the residue selection. The top-level list in this selection is a list of chains. Within this is a list of residues. Upon the selection of a chain, the residues of the chain are added to the residue list, however they are not selected. To add residues to the selection set, it is necessary select the rescues from the residue is by picking them with a mouse off the residue list. As well as selecting elements off a list, it is also possible to select elements by entering an expression in the expression box, or by picking them with the mouse from an existing geometrical model in the view port. The format of the element selection expression is ::, according to the great tradition. In this system, residues selected by the residue expression will be selected within a subset of the chain expression. Likewise the atoms selected by an expression will be selected within a subset of the residue expression. The chain expression is simply a comma delimitated set of chain names, for example "A,B", or the identifier "all" to indicate all chains. The residue expression is a common delaminated set of sub expressions. Each sub expression may be a residue identifier such as "92", a residue range such as "25-28", a residue type filter, like "HIS", or "all" to indicate all residues, "all helix" for all residues in a helix, "all strand" for all residues in a strand, "all turn" for all residues in a turn, "all loop" for all residues in a loop. The atom expression is a comma delaminated set of sub expression. Each sub expression may be an atom identifier, such as "CA", "metal" for any metal, or "hets" for any hetero atom (an atom that is not part of an amino acid). In the upper right of the elements of the selection panel, there is a drop option that controls a geometrical element selection from the view port. The available options in the menu depends on the type of element selection being done. The first option in the menu is always "Nothing", indicating that no selection she not be done from the view port. The "Chain" option means that the chain will be identified corresponding to the mouse location in the view port, and when the mouse button is pressed the chain will be added and selected in the chains list. As a mouse is moved over the chain and the view port a visual cue of the extent of the chain drawn. The "Residue" option means that the residue will be identified corresponding to the mouse's location in the view port and when the mouse button is pressed this residue will be added to the residues list. A small ball and stick picture in the view port indicates the residue of the mouse is over. When selecting residues from the view port a special optional when behavior is available: In the general settings there is a setting called "mouseRange". If this setting is true, a residue between the previous mouse click and the next mouse click is added to the selection range. In a future version of the program this option may be controlled by the shift button. The "Atom" option means that atoms will be selected off the view port. A dodecahedron provides a visual cue indicating which atom is selected. The "Bond" selection option means that picking a bond in the view port adds it to the bond list. A visual cue that looks like a dumbbell indicates which bond is selected in the view port. After the residue selection, the next simplest type of element selection is the atom selection. The mechanism for this is just like the residue selection, except for the addition of an atom list. When residues are selected from residue list the atoms they contain are added to the atom list. The atoms in this list must be then selected with the mouse to add the atoms to the selection. The third type of selection interface is the atom-bond selection. This mechanism is just like the atom selection with the addition of a bond selection list. Selecting a residue from a residue list causes the contained atoms and bonds and to be added to the atoms list and the bonds list. The atoms must then been selected from the atoms list to add them to the selection, and the bonds must likewise be selected from the bonds list to add the to the selection. We have experimented with the atom-bond selection interface by linking the atom and bond selection, so that selection atoms would select bonds, and vice-versa. The hope was to alleviate some confusion when creating ball and stick visualizations, because if atoms must turned on separately from the bonds your ball and stick model can have missing bonds or atom. However attempting to link the two brings in as many confusions as it alleviates, therefore the current interface maintains the idea of two distinct sets. The user must simply learn the system. The middle area of the Element Properties Panel controls which property is being set. Vincent Van Mol's offers the usually more than one, and sometimes as many as 10 independently specifiable properties per element. (Remember elements are atoms, residue and bonds). When a rendition is created for the first time, every element is initialized with a default property vector with some safe and fast values that usually results in nothing being drawn, because of the element visibility property is off. Color properties are usually defaulted to grey, and size properties are usually defaulted to some reasonable value. The purpose of specifying an element selection set is to control the set of elements you wish to apply the values of the properties area to. The usage and characteristics of every type of rendition is described below, but for now let's motivate his explanation was an example. The per element properties of the CPK rendition are: "Atom Visibility", "Atom Color", "Atom Radius", and "Atom Shape". Because Vincent Van Mol is not a molecular modeling program, meaning its purpose in life is not to model new and novel molecules, but instead is a molecular graphics program (or call it a visual modeling system), a CPK atom is not added to the view port by a function that adds an atom per se. Instead of the atom's visibility property is turned on. This is because the data already exists. Physical elements of the molecule's cannot be created, destroyed, or changed Vincent Van Mol. To facilitate the assignment of visual properties that vary according to the physical properties of the molecule, Vincent Van Mol uses and a concept of "Schemes". A scheme maps physical properties to visual properties. When select a property in the properties list, the scheme is list is filled with the available schemes for this property. In the future we plan to plan to have the capability of user defined schemes to Vincent Van Mol, however for now on the user will have to be satisfied to pick from a list of scheme options. Although schemes are not entirely user definable, they are at least user modifiable by setting parameters within the schemes. When select a scheme from the schemes list, the parameters of the scheme appear in the scheme parameters list to the right. When a scheme's parameter is picked from this list, a device for setting this value appears in the value area on the bottom of the Element Properties Panel. In general, the input in the Element Properties Panel proceeds from the top down and from left to right. For every property there is a least one kind of scheme, the constant scheme. This essentially means that there's no scheme at all, and at the same value will be applied for the official property regardless of any physical properties across the selection set. This does not mean every element must have the same value. It simply means that every element in the current selection set (which is a subset of the elements of the molecule) will be given the same value. Different values may be assigned by picking different selection sets and assigning different values for the selection sets. The basic behavior of the elements selection panel is as follows: when the selection is changed by any mechanism (list selection, expression selection or view port selection) the current scheme is applied to the selection set. Also, if the value in the value box is changed, the application is done. When the application is done, EVERY property in the properties list is assigned to the elements in the selection set, not only the currently selected property. This has a different effect than only assigning to the single property that is selected. A future version of Vincent Van Mol may contain the option of all reassigning the current property. (An older version had this ability but the ability was removed because it was confusing). Because all properties are assigned together, it is possible to go to each property and set the scheme and the schemes parameters, and then make the selection, and expect all your property changes take effect. This is usually more convenient however it is limiting because it makes impossible to change only one property of an element selection, such as changing the atom radius while leaving the color alone. the future version of the program will probably contain a simple switch the controls whether the one selected property is applied or all properties are applied.	Element Properties Panel
The Object Properties Panel This panel provides a way to control properties that take effect for an entire rendition. The top area of the panel has a list of properties, and the bottom area is the place for devices for setting the value.	Object Properties Panel
The Chart Panel This chart shows the values of per element properties. The chart shows to the values of every property for every element of the set is showing. The current version of the program does not make it possible to set values from the chart. This ability has been removed in an effort to try to clean up and the user interface. Normally these values are set to which the Element Properties Panel. If the "Current Set" option is selected, the chart has a row for every element in the current selection set, showing the properties of the current rendition object. If the "Entire Domain" option is selected, the chart has a row for every element in the domain regardless of the current selection set. The "Domain" option specifies which domain of the current rendition object should be shown if it has multiple element domains. For example the ball and stick rendition has an atom and a bond domain.	Chart Panel
The Saved Set Panel The set development panel will be reworked. It enables one to save an element selection set for later.
The options panel This panel has settings controlling the behavior of Vincent Van Mol. autoApply - if the auto apply setting is turned on, the per element properties will be applied automatically when the element selection is changed or a property value is changed. If this setting is turned off, nothing will happen with the selection is changed or the property's value is changed, and it will be necessary to use the manual apply button in the element properties panel. Turning this option off is useful if you are planning on making a lot of incremental changes to the selection set and you are not interested in seeing your changes updated in the viewport, possibly because you are working on a slower computer. autoValidate: if auto validate is turned on, rendition objects will be invalidated through Modelzilla when per element properties are changed, and when object wide properties are changed. If the auto validate setting is turned off, no invalidation will be done when the settings are changed and the visual object in the view port will not be updated. This is a similar effect to turning off the auto apply setting, however it is safer to keep the auto apply setting is on, and the auto validate setting off, because you are sure property changes are at least being done even though the visual model is not being updated. To validate the visual model, use the validate button in the renditions panel. Turning off auto validation is useful if you are working on a slow computer, or adjusting a large and complicated model. The auto apply setting is kept around because it may be useful for some special needs in setting element properties. enableToggle: if the enable toggle setting is turned on, Vincent Van Mol does a special trick when elements are removed from an element set. Property changes are normally only applied to elements currently in the selection set. For example if you are changing the atom visibility property for a CPK rendition, if you have the visibility property turned on, and you are adding elements to your atom selection, every atom selected will receive a ball around it. If you start removed elements from the selection, the balls will not go away because settings are applied only to elements that are in selection. To remove balls you would normally have to turn the visibility property off and add the atoms to the selection that you don't want to see. However you might intuitively expect that if you were to remove atoms from the atom selection, that the property changes you had recently made would be un-done in the atoms would disappear. You might expect similar behavior if you were adjusting the atom color or shape. Property value toggling attempts to provide this intuitive behavior. If the toggle setting is turned on, elements removed from this selection get their previous property values put back. mouseRange: if the mouse range setting is turned on, selecting an element from the view port will cause every element between this element in the previously the selected element to be filled in. This is relevant only to residue selections because residues are a natural sequence.	Settings Panel
Undo system Vincent Van Mol makes use of the undo system offered by Modelzilla. Undoable events include: any change to a per element property. keep in mind that the undo tracking for the per element properties requires a lot of memory. When using Vincent Van Mol, the undo limit should be kept to a minimum, such as 10 events. any change to a per object property the visibility property of an object to the creation of eight rendition object the deletion of rendition object the creation of a molecule object the deletion of the molecule object
File saving Vincent Van Mol stores its data in the Modelzilla database. That is, it stores data that was entered or is modifiable by the user in the Modelzilla database. Computed data is stored by its own specialized mechanisms. Data in the database for Vincent Van Mol includes the loaded molecules, rendition objects, the object wide properties of the rendition objects, and the per element properties of the rendition objects. The sequence of events to create the renditions is not stored, only the resulting data, just like a document from a word processor. All data in the Modelzilla database can be saved to a file and opened from a file. (The database files have the extension .MVG, which is means Modeling Vector Graphics. This is an unusual name considering the file contains no graphics information such as triangles or lines directly. It turns out that in a modeling program storing the graphics is a useless thing to do, because the graphics are usually computed from the model. So the name MVG is correct when you consider that the model data is rendered to vector graphics). When a Modelzilla database file is opened, the computer logic that created the data re-computes any derived data as well. In the case of Vincent Van Mol, it re-computes the renditions based on the model data. Technical details aside, to save a file, go the "Model Files" panel in the Modelzilla controls, and hit the "Save" button. To open a file, hit the "Open" button.
3D-Printing Any Modelzilla application has the capability of sending a geometrical model to a stereo lithography printer. (aka 3D printer) This is done by exporting a .STL file, or a .VRML file. .VRML is needed if your printer prints in color. To do this, in the Modelzilla controls, go to the "Exports" panel and invoke the "Export STL" or "Export VRML" function.
The Renditions The protein in the examples The following descriptions are sometimes in terms of a protein that comes in the demo files Vincent Van Mol. It is the beta barrel 1ema.pdb. To load this protein into memory go to the molecules panel. Select this file in the file browser. Invoke the "Load Molecule" function. A wire frame rendition is created for the molecule. Note that when the Vincent Van Mol application is loaded in Modelzilla, it automatically turns on the depthCue and autoDepthQue setting. This is why the wire frame rendition appears perfectly brighter in the front. Depth cue is very important for molecular graphics. Other defaulted renditions may appear such as a CPK for seeing the metals, or maybe a tube trace. Go to the renditions panel and remove every rendition except for the wire frame by using the "Remove Rendition" function.
The CPK Rendition The CPK rendition draws balls around the atoms. The atoms have a larger radius so that they intersect one another. This rendition is named after the biologists who first used this type of physical model, Corey, Pauling and Koltun. The first step in using the CPK rendition is to go to the renditions panel and creating new CPK object by hitting the picture that looks like atom balls. The new object shows no atoms. Per element properties in Vincent Van Mol are changed by applying schemes to a set of elements. For the CPK renditions, this set of elements is an atom set. In Vincent Van Mol parlance, we say the domain set of the CPK renditions is the atom set. The end goal of the elements selection for the CPK rendition is to specify a set of atoms. The Show Atom Property This is a true or false property. It controls whether or not the atom is included in the CPK rendition. This property offers the following schemes: Constant Atom Visibility: This constant scheme applies a true or false value when irrespective of the physical properties of the atom. Showing Waters Maybe is interesting to find out where the crystallographer thought water molecules should go. To see the water molecules in the example protein, select the second chain, select all the residues of this chain (these "residues" are only residues by PDB file convention; they are really just individual waters), then select all the atoms of the atom list. In the view port there should be waters scattered around the periphery of the protein like berries on a bush. Removing Waters Choose the Show Atom property, move down to the value area, and make the "show" value false. This will apply the false value to the current selection, which still has the waters. Make sure the current selection has the waters. The waters should disapear from the CPK rendition. Showing central complex by picking off viewport It is possible to select atoms by picking them off the view port. Of course to take elements off models in the view port you need to have an existing model of the atoms you want to pick. Fortunately the wire frame will do. Change the mouse selection mode to select atoms. The mouse selection mode is controled by the drop down option labeled "Mouse" in the top of the element properties panel. Click the mouse over any atom in the wire frame you would like to be CPK'ed. As you move the mouse over the wire frame it is hard not to notice the large atom cursor that is shaped like a dodecahedron. This indicates the atom that will be added to the list if you click the mouse button. Now change the mouse option to select residues. Entire residues will be CPK'ed by picking them off the wire. If you can find the central complex (a chromophore) in the beta barrel, pick it with the mouse. It is instantly and effortlessly CPK'ed. When picking elements off the view port, the identity or type of the renditions you are picking is not important. Only that an atom or residue may be derived from the current mouse position is important. It is also possible to pick off the rendition that you are currently specifying. The Atom Color Property This color property controls the color of the atoms drawn in the CPK rendition. The following schemes are offered: Constant Atom Color: The constant scheme applies a color value irrespective of the physical properties of the atom. Atom Type Atom Color: This scheme has a lookup table that associates atom element to color. This scheme has a parameter for every common element found in protein. One could use this scheme to elucidate the location of all the atoms of a certain type. Residue Type Atom Color: This scheme has a table that associates the type of residue of the atom to color. This scheme has a parameter for every type of residue in protein, that controls a color associated with this element. One could use this scheme to elucidate where all the residues of a certain type are. Chain ID Atom Color: This scheme associates the chain of an atom to color. This scheme has settings that control the color associated with each chain index. One could use this scheme to see the large-scale structure of the protein chains. Temperature Factor Atom Color: This scheme associates temperature factors with colors. This scheme should have a setting controlling a general scalar value to color mapping, however currently it has no settings because our general general scalar value to color mapping code resides within a different extension module (GridZilla) at this time. We plan to move it to the Modelzilla framework. Coloring by residue type The best way to demonstrate the color properties of the CPK rendition is show what happens when the scheme of a small set of CPK'ed residues is changed. Turn off all atoms from the current CPK rendition, or if you find it easier, simply go to the renditions panel and delete the entire CPK object and create a new one. Select the first chain, select the first five residues, and select all atoms in the atom set. Notice as you add a selection to the residue list the member atoms are added to the atoms list. Select all the atoms from the atoms list. You should see a clump of atoms on the "bottom side" of the beta barrel. The currently selected scheme is "Color by Element Type". Change the scheme to "Color by Residue Type". In the event that the new values are not automatically applied, use the "Apply Selection" button to force an application. You should now see the atoms colored by residue type in the view port. The easiest way to select all of the elements in a list is to hit the "all" button. The easiest way clear the selection is to hit the "none" button. If you find that the lists are too short for your convenience, and they can be made taller by grabbing the grabbable traction bars below the list area and dragging downwards. By this method the list can be made almost the entire height of the computer screen. Assigning arbitrary colors Often it is useful to set the colors of individual atoms irrespective of physical properties. To make the CPK with the golden crown as pictured, apply the "Color by Atom Type" scheme to the current selection. Clear the atom selection. Choose the "Constant Atom Color" scheme. Change the color to some new and recognizable color such as bright orange. Change the mouse selection mode to select atoms. Now click the mouse over every atom to color orange. The Atom Radius Property This is a scalar property. It controls the radius of the atoms drawn in the CPK rendition. This property offers the following schemes: Constant Atom Radius Scheme: This constant scheme applies a radius irrespective of the physical properties of the atom. Atom Type Atom Radii: This scheme has a look up table associating atom element type to atom radius. It has a parameter for every element in its lookup table. Connolly Radii: This scheme is essentially the same as the Atom Type Atom Radii scheme, except that it uses a specialized mapping that is ideal for solvent accessible surfaces. The two schemes will likely be combined into one scheme with different initial settings. Assigning arbitrary radii Changes to the atom radius are best demonstrated with the water atoms because they are well separated from one another. Turn off any atoms that are CPK'ed. CPK the waters. Selected the atom radius property. Clear the atom selection. Select the constant radius scheme and use a large radius like 2.5 angstroms. Change of the mouse option to select atoms. Now pick the atoms off the view port that need to be bigger. The Atom Shape Property This is an integer property. It controls the shape of the objects representing an atom. Possible values are "Sphere", "Cube", "Octahedron", "Tetrahedron", and "Icosahedron". This property offers the following schemes: Constant Atom Shape Scheme: This constant scheme applies a shape value irrespective of the physical properties of the atom. Assigning arbitrary shapes Select the atom shape property. Selected the "Constant Atom Shape" scheme. Change the shape to tetrahedrons. This is a good distinctive shape. If you have any atoms in the atom set they are now tetrahedrons. Add atoms to the set to make them tetrahedrons. CPK Object Wide Properties maxBalls: this controls the maximum number of balls the CPK rendition is allowed have before it drops back to a simpler form of rendering the atoms. Usually CPK'ing an entire protein will bring the graphics hardware to its knees. This setting is a sanity check. sphereDis: this controls the vertex density of the sphere geometries if the latitude-longitude sphere topology is used. transparency: this controls the transparency sent to the graphics system visibility: this controls whether a the CPK object is visible in any view port	Showing waters Showing a central complex Coloring by residue Coloring by atom, then constant Changing atom radii Changing atom shapes
The Molecular Surface rendition The molecular surface rendition, otherwise known the solvent accessible surface, is an imaginary surface that shows the bounds of the protein accessible by a water molecule. Vincent Van Mol makes use of MSMS by Sanner, a very good implementation of the solvent accessible surface algorithm. This algorithm stitches together a surface composed of the inside surfaces of toruses that run through the saddle area between atoms on the protein surface, and the outer surfaces of spheres that crown the outer sides of the surface atoms. The idea is that this is the surface of an imaginary a water molecule that moves around touching everywhere it can. Vincent Van Mol considers a molecular surface renditions to be analog of the CPK rendition. It's domain is the atom set. Its element properties are the same as the CPK, with the exception of the removal of the atom shape setting, and the addition of the atom surface inclusion setting. To start a molecular surface rendition go to the renditions panel and hit the picture that looks like a molecular surface. The initial molecular surface rendition includes no atoms. The Show Atom Property This is a true or false property. If the property is true for an atom, the atom is included in the input to MSMS, so that it takes part in the molecular surface computation. Of course if it in the interior of the protein, it will not come through to the resulting surface. Surfacing a protein What better to do when you have a new protein on your hands then to see its molecular surface! The finest of the computational protein models! A most beautiful and exhaled wonder of nature and information processing! To show the molecular surface of the beta barrel, select the first chain, select all the residues, and select all that atoms. This creates a wiz-bang a molecular surface in the view port. Surfacing a piece of a protein Suppose we didn't actually want show the entire molecular surface of this protein. Although it is an unnatural thing to do, it is possible to put a molecular surface around any subset of the atoms in the natural protein. This might help one answer the question, what would be the general shape of this protein if this site chain wasn't here. What would the protein be like if this loop was removed (assuming this didn't alter the structure in other places). Remove the molecular surface from all the atoms by changing the "show" value at the bottom of the control panel to false. Now deselect all the atoms. Select few sequential residues. Making selections with the "show" property set to false will prevent unnecessary molecular surface computations. Select all the atoms in the atom list. With the atom set made, change the "show" property to true. A small molecular surface of this imaginary mini protein in should appear in the view port. Note that if you wish to create molecular surface that forms a discontinuous volume, it seems that surface computer we're using does not handle this very well, and is best to treat them as two separate objects within Vincent Van Mol. Removing a piece of a protein Of course no one is interested in seeing a molecular surface of a few isolated residues. The possibility of removing a side chain from a protein is more interesting. Remove this surface and create a new one. Select the first chain, select all the residues, and select all the atoms , and if the show atom property is not already turned on make it so. Clear the atom selection. Chains the mouse selection mode to select residues. Pick a side chain that is forming a peninsula jutting from the surface. Remove the backbone atoms from the atom selection list, and change the show atom property to false. This removes the effect of the side chain. After the surfaces been re-computed, you should see the wire frame poking through the area where the service was removed. The Atom Radius Property This is a scalar property. It controls the atom radius given the molecule surface computation. The best scheme to use for this property is the "Conolly Radii" scheme. The Atom Color Property This is a color property. It controls how the surface in this atoms vicinity is colored. Coloring by residue To color by residue, change the color scheme to "Color by Residue" Arbitrary surface colors To highlight a particular region of the molecule surface, you may wish to change the colors of the associated atoms. Selected the "Atom Color property . Clear the atom list. With the constant color scheme selected, change the color to something distinctive such as orange. Change the mouse selection mode to select atoms . Now every atom you touch on a molecular service will become orange. Vincent Van Mol has the Midas touch. Color mapping To map a measurement field value such as electric potential on to the molecular surface, you need to use the separate GridZilla application, which is a Modelzilla extension. GridZilla can map fields onto any surface, so we have not duplicated this ability in Vincent Van Mol. The Atom Inclusion Property This is a true or false property. It controls whether or not the surface generated by the surfacing algorithm is included in the vicinity of this atom. This property does not effect the input to the surfacing computation. If the property is false, the surface in not drawn, leaving a hole. Leaving a hole Choose the "Atom Inclusion" property. Clear the atom list. Change the mouse selection mode select atoms. Change the "include atom" value to false. Now touch every atom on surface for which you would like to remove the surface. A jagged hole should be left upon every touch, which is useful to like to see through the surface to show something underneath in a diagram. Molecular surface object wide properties atomOffset: this quantity is added to the radius of every atom that is sent to the molecular surface calculator. We found this setting useful for creating hollow shells of molecular surfaces with our three-dimensional printer. A positive value makes the atoms bigger. A negative value makes the atoms smaller. atomScale: this quantity is multiplied by the radius of every atom (before the atomOffset is applied) and that is sent to the molecular surface calculator. Using this setting is a good way to test the robustness of MSMS. baseColor: this is the color is applied to the surface if vertex colors are turned off. probeRadius: this quantity is used in the molecular surface calculation. It should be about the radius of a water molecule if it's possible to give it a single radius. (About 1.5 angstroms.) It is the radius of the torus forming the saddle area between atoms. Setting this quantity to zero will the molecular surface look like a union of CPK balls, however the molecular service will have several times fewer triangles. Making this value large, such as 5 angstroms will create something something closer to the convex hull of the protein, with groves and holes removed. transparency: this sets a transparency value given to the graphics system for drawing entire surface. We plan on giving a future version of Vincent Van Mol the ability to independently specify the transparency for every atom forming the surface, or perhaps a transparency applied via texture map. vertex Colors: this controls whether or not the surface is colored on a per vertex basis. It may be useful to disable this setting when using a slow computer. vertexDensity: this quantity is used in molecular surface calculation. A higher number will result in a smoother surface with lots of small triangles that can form a smooth bends. A lower number result in a rough surface it and it may be faster to draw, especially and if you are running Vincent Van Mol on a system with slower graphics hardware. visibility: this controls whether this service is show at all in any view port.	Surfacing a protein Surfacing part of a protein Coloring by residue Arbitrary colors Holes
The Atom Labels rendition The atom labels rendition is a convenient way to label atoms. Like the CPK rendition and the molecular surface rendition, its domain is the atom set. To create a new set of atom labels, go to the renditions panel and hit the picture that looks like labeled atoms. The rendition is initialized with no atoms shown. The Show Atom Property This property controls which atoms receive labels. To label atoms, simply add atoms to the atom selection, using the list, expression, or mouse selection mechanism. The Label Color Property The label color property controls the colors of the labels. This property has the same assignment schemes as the atom color property of the CPK and molecular surface renditions. Changing the label colors is done in a manner similar to changing the atom colors the CPK and molecular surface. The Label Text Property This property controls the text of the labels. The following schemes are available: Constant Label Text: Use this scheme to set the label text irrespective of the physical properties. Atom Text by Identity: Use this scheme to make the label text the same as the atom name Atom Text by Type: Use this scheme to set the label text to follow the atom element type Atom Label object wide properties font: this is the font that is applied to all labels transparency: this is the transparency value that is given to the graphics system when drawing the labels. visibility: this controls whether the labels are shown in any view port.	Labeling a tube
The Tube Backbone Trace rendition The tube trace is a long tube connecting the alpha carbons of the protein backbone. It is useful for showing the organization of internal protein structure. The domain of the tube rendition is the residue set. To create a tube trace rendition, go to the renditions panel and hit the picture the looks like a tube trace. The initial to trace is empty. The Show Residue Property This property controls which residues are visualized by a tube trace. Long contiguous ranges of residues should be turned on to make a trace meaningful. Tracing the entire protein Select the first chain, and select all the residues in the chain. The organized structure of the beta barrel should appear in the view port. Tracing helicies It is possible to show limited ranges of the backbone with a tube trace. This example uses the protein 2gep in the demo directoy. Create a new tube trace rendition. Enter the selection expression: ":all helix:". Tracing ranges with mouse The tube can also be built by picking with the mouse. If you know where the pieces of the protein you would like to see are geometrically, the easiest way to put to trace through these residues is to change the mouse selection mode to select residues, and pick a range of residues of the view port. For this to work there will need to be an existing model including these residues. A wire frame model will work nicely. At the bottom of the element properties panel turn the "show" value on. Pick a residue off the wire frame. Pick another residue several residues down the backbone. When picking residues with the mouse, if the general setting "mouseRange" is true, every residue between the recently picked residue and the previously selected residue will be added to the selection set. As you pick residues the tube trace should grow. A sequence of residues in a completely different piece of the protein may picked as well. The best way to be sure that the mouse ranges are applied separately from the first region and the second region, is to clear the residue list before beginning the new selection. The Residue Color property The residue color property controls the color assigned to the tube in the area of each residue. The colors are piecewise averaged from residue to residue. Being able to change the color of the trace residues is useful for seeing the physical significance of certain residues if you or mapping from physical properties to colors. It is also useful for highlighting certain residues in diagrams if you're going to assign colors irrespective of physical properties. Coloring a tube arbitraraly Select the residue color property, change to the constant residue color scheme, change the constant value to a boring shade of gray, and select all of the residues of the protein. A grey tube trace should wind throughout the chain. Now clear the residue selection. Change the constant color to a bright orange. Change the mouse selection mode to select residues. Every residue you pick and on the trace should turn orange. Imagine your picture in a journal article says "this bright orange area here is where we believe our new drug binds to inhibit this enzyme". Tube Trace object wide properties lineWidth: this controls the width the lines drawn in the rendition if lines are drawn at all. The value corresponds to the pixel width of the lines. Most scaling values in a vector based modeling system such as this one control a floating point value that are screen resolution independent. However this value controls the size and actual pixels which can be a problem for scaling the picture, because if the picture is made very small the lines appear to be too thick and if the pictures made very big the lines appear to be a very thin. Therefore careful adjustment of its value may be necessary sometimes. offset: this is an angstrom scale factor that controls on the computation of the elbowed tube option. The value is proportional to the elbow radius. radius: this is the radius in angstroms of the tube. pathDiscretization: this controls the vertex density given to the tube along the path. A higher value and gives a smoother and better looking tube, and increases memory requirements, and may slow graphics performance. sectionDiscretization: this controls the vertex density around the circumference of the tube. A higher value and gives a smoother and better looking tube, and increases memory requirements, and may slow graphics performance. sharpColors: this controls whether colors are smoothly blended between residues. If the value false there is a sharp color change at the midpoint between the trace atoms of residues of different colors. smoothOrder: this controls the order of a polynomial is used in the piece wise smoothing function that computes the tube colors position. surface: this controls the to the surface is realized. The "Shaded" option makes the tube a shaded surface. The "Lines" option realizes the tube as four lines going down the length of the tube, evenly spaced around the section. The shaded lines option realizes the tube as both of the lines and a surface, with the surface dropped back a pixel or two to ensure that it does not occlude the lines. traceAtoms: this controls the atom and each residue that the tube will pass through. "CA" (the default): tube passes through CA atoms. "N": tube passes through N atoms. "O" tube passes through O atoms. "N-CA-C": tube passes through all three backbone atoms. The N and the O option may be useless, however we believe the option of passing them through all three back bone atoms, especially if the elbow and smoothing type is used, is a nice option for showing exactly where the backbone is. transparency: this controls a transparency value that is sent to the rendering system for the entire tube object. visibility: this controls whether or not the tube is shown in any view port	Tracing a protein Tracing helicies Coloring arbitraraly
The Ribbon Backbone rendition The ribbon rendition and shows an overview of the protein structure by drawing a long sinuous ribbon through the alpha carbons along the backbone. It highlights the secondary structure the protein by changing the shape and orientation of the ribbon according to whether it is running through a helix, a sheet, or a turn-loop. The domain of the ribbon rendition is the residue set. To create a new ribbon rendition, go to the renditions panel and hit the picture that looks like a ribbon. The initial ribbon is empty. The Show Residue Property The show residue property controls which residues are included in the ribbon. The ribbon will be more meaningful if these residues are along contiguous ranges. Ribboning an entire protein To draw a ribbon diagram throughout the entire beta-barrel (1ema.pdb in the examples), select the first chain, and select all the residues of this chain. A nice ribbon diagram should appear in the view port. Building a ribbon gradually The example picture uses the protein 2gep.pdb, which has a greater variety of secondary structure. Load the protein, remove the CPK rendition of the metals if it is annoying you. Create a new ribbon rendition. Gradually add residues to the residue list and they should be gradually built in the view port. Try selecting other contiguous ranges of residues to see that you have complete freedom of where you want the ribbon to appear. The Residue Color property The colors corresponding to the residues can be reassigned independently. To reassign the residue colors, select the residue color properties, pick a reasonable scheme, and began selecting residues. The Residue SS Type property Vincent Van Mol does not assume the secondary structure that it finds for the protein is the best true secondary structure. We have made the secondary structure determination a scheme just like the residue color determination. The default scheme for secondary structure determination is to look up in the PDB file. However sometimes the secondary structure given the PDB file doesn't start and stop that are very appealing, sometimes giving turns of only one element, which looks comical. Setting secondary structure To demonstrate that it is possible to change the secondary structure that is rendered in the ribbon diagram, select the Residue SS Type property. Clear the residue selection. Choose the constant scheme. Change the constant value to "Helix". Find a helix in the diagram that you think should be longer, and selected residues at the end of the helix. You can make a secondary structure rendered in the ribbon just like you intend in this matter. The Helix Width property Vincent Van Mol allows independent specification of the width of the helices is on a per residue basis. The helix width refers to the width of the ribbon along the helix axis. A small value results in a very artistic and delicate looking helix. A large value results in a robust helix that is especially fit for making a three-dimensional print. If the helix is made too wide it may intersect were wrapped around, which may be desirable if you were trying to make a very strong helix for a three-dimensional print. Someone with a great deal of artistic flair can use this control to give every helix residue a different width. The different widths are smoothly blended together so that no discontinuity exists between residues. Notice that this property is in fact applied to all residues whether or not they are rendered as helices. This is because in general all of the properties in Vincent Van Mol are orthogonal with one another. Offering a helix width property only for the residues that are helices would have required relating the secondary structure property with a helix width property. The Helix Thickness property The helix thickness can be specified on a per residue basis. The helix thickness refers to the thickness of the helix ribbon along the radial access. Using this property is like using any other per residue property, just select the width you want and select the residues to apply it to. The Strand Width property The width of strands can be specified on a per residue basis. The strand width with refers to the width of one of the strands across the width of the sheet, along the direction perpendicular to the backbone sequence. Using this property is like using any other per residue property, just select the width you want and select residues to apply it to. The Strand Thickness property The thickness of the strands can be specified on a per residue basis. This strand thickness refers to the thickness of a strand sheet along the direction perpendicular to the local plane of the sheet. Using this property is like using any other per residue property, just select the thickness you want and select residues to apply it to. The Tube Thickness property The thickness of tubes can be specified on a per residue basis. Using this property is like using any other per residue property, just select the thickness you want and selected residues to apply it to. The Ribbon object wide properties arrowMajorSize: this is the width in angstroms of the arrows at the end of strands. Plans for the future include making this setting a multiplying factor of the strand width of the residue in the vicinity of the arrow, because if the strand may vary in width on a per residue basis, giving the arrow a constant width may make it out of proportion and some places. arrowMinorSize: this is the width in angstroms of the point of the arrow. This should be kept about equal the tube thickness. arrows: this true or false property controls whether or not arrows are drawn. circularTurns: if this property true, turns and loops will have a circular or cross section. If this property is false, turns will have a square cross section that blends more smoothly with the adjoining helices and strands. fancyBlend: the color of helix or strands is determined both by the color of the local residues, and the identity of the side of the helix or strand. This could be the front, back or side of the helix or strand. This quantity controls whether proportionally more of the local residue color will be used or proportionally more of the back-front-side color will be used. Set the value to 1.0 to make the back and front dominate completely. Set the value to zero to make the residue color dominate completely. fancyHelix: this is a true or false setting that controls whether or not color blending between sides and residue colors should be used. Turning this value off is equivalent to setting the fancyBlend value to 0.0. fancyStrand: this is a true or false setting that controls whether or not color blending sides and residue colors should be used. Turning this value off is equivalent to setting fancyBlend value to 0.0. helixInsideColor: this is the color used to draw the inside of helices, if fancy helix coloring is enabled. helixOutsideColor: this is the color used to draw the outside of helices, if fancy helix coloring is enabled. helixSideColor: this is the color used to draw the sides of the helices, if fancy helix coloring is enabled. lineWidth: this is the width the trace lines that may optionally run along the length of the ribbon. lineColor: this is the color of the trace lines that may optionally run along the length of the ribbon. polygonization: this controls the vertex density of the length of the ribbon. strandBottomColor: this is the color of the bottoms of the strands if fancy strands are enabled. strandTopColor: this is the color of the tops of the strands if fancy strands are enabled. strandSideColor: this is the color of the sides of the strands if fancy strands are enabled. surface: this controls how surface is realized. Shaded: this shaded option will draw the ribbon as a shaded surface. Lines: the lines option will draw the ribbon as four trace lines along the corners of the helix sections, the corners of strand sections, and four lines spaced equally apart around a circumference of circles or sections of turns and loops. Shaded and Lines: this option draws both the shaded surface and trace lines at the same time, offsetting the surface down a pixel or two so that it does not occlude the lines. transparency: this controls the general transparency of the entire ribbon. tubeDis: this controls the vertex density around the circumference of the circular tubes. vertexColors: this controls whether vertex colors are used at all. If this setting is disabled, a simpler ribbon diagrams with only a few colors is made. visibility: this controls whether the ribbon appears in any view ports.	Tracing a protein Tracing a protein Building a ribbon with mouse
The Residue Labels rendition The residue labels rendition is a convenient way to label residues. Its domain is the residue set. To create a new set of residue labels, go to the renditions panel and hit the picture that looks like labeled residue. The rendition is initialized with no residue shown. The Show Residue Property This property controls which residues receive labels. To label residue, simply add atoms to the residue selection, using the list, expression, or mouse selection mechanism. The Label Color Property The label color property controls the colors of the labels. This property has the same assignment schemes as the residue color property of the tube and ribbon renditions. Changing the label colors is done in a manner similar to changing the residue colors of the tube and ribbon renditions. The Label Text Property This property controls the text of the labels. The following schemes are available: Constant Label Text: Use this scheme to set the label text irrespective of the physical properties. Residue Text by Identity: Use this scheme to make the label text the same as the residue name Residue Text by Type: Use this scheme to set the label text to follow the residue type Residue Label object wide properties font: this is the font that is applied to all labels transparency: this is the transparency value that is given to the graphics system when drawing the labels. visibility: this controls whether the labels are shown in any view port.	Residue labels
The Wire Frame Rendition The wire frame rendition shows a detailed network of atoms and bonds, rendered entirely with lines. Because wire frame renditions do not print well, their main purpose in Vincent Van Mol is a geometry for picking atoms, bonds, and residues off, as well a cheap way to show a lot of information. The domain of the wire frame rendition is the atom-bond set. To create a new wire frame rendition, go to the renditions panel and hit the picture that looks like a wire frame. The initial wire frame is empty. The Show Atom Property This property has no effect. It is here because of some generalizations we made to the properties across all renditions. The Atom Color Property This controls the colors of the lines attaching the atoms. It is used like the atom colors property of the CPK rendition. The Show Bond Property This controls whether a bond is rendered with a line. This is the property you use to control what part of the protein will have a wire frame. This property is assigned to the bond set. Wire frameing 10 residues To put a wire frame around the first 10 residues in a protein, select the first chain, and select the first 10 residues. This should fill both the atoms list and the bonds list. Select all the bonds in the bonds list to show the wire frame. Attached atoms are automatically so the atoms will have their colors assigned. The Wire Frame Object Wire Properties halfBonds: this true or false setting will cause a sharp color change at the mid point between atoms of it is true. lineWidth: this controls the width of the lines in pixels. transparency: this is the transparency value that is given to the graphics system when drawing the wire frame. visibility: this controls whether the wire frame is shown in any view port.	A small wire frame
The Ball and Stick Rendition The ball and stick rendition show atoms and bonds as solid spheres and cylinders, which is easier to see than the lines of the wire frame. The domain of the ball and stick rendition is the atom-bond set. To create a new ball and stick rendition, go to the renditions panel and hit the picture that looks like a ball and stick. The initial ball and stick is empty. The Show Atom Property This controls whether an atom is shown, just like the CPK rendition. It is possible to turn off an atom so that a bond cylinder leads to nothing. This might be useful if the atom is in the way. The Atom Color Property This controls the color of the atom balls, just like the CPK rendition. The Atom Radius Property This controls the radius of the atom balls, just like the CPK rendition. The radius is scaled by 0.25 compared to the regular radius schemes. The Show Bond Property This controls whether a bond is shown as a cylinder. The Bond Color Property This controls the color of the bond if atom colors are not used. The Bond Thickness Property This controls the thickness of the bond. The Bond Halfness Property If this is true for a bond, it is colored according to the atoms of the bond. The Ball and Stick Object wide properties transparency: this is the transparency value that is given to the graphics system when drawing the ball and sticks. visibility: this controls whether the ball and sticks are shown in any view port.	Ball and stick of beta barrel protein Heme and some liganding residues