| DINO: Visualizing Structural Biology |
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User Manual
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The surface dataset contains information about a molecular surface calculated with an external program, such as MSMS1 or MSP2. It is usually generated by rolling a solvent sphere of a fixed radius around the structure of interest, producing (if possible equidistant) points on the surface which are connected to triangles, approximating the real surface. The spacing of the points is usually adjustable to give the desired resolution. Each point (or vertex) additionally carries a normal vector which is utilized during visualization to smooth the surface, and it appears less coarse than an identical surface with triangular normalization.
The power of the surface dataset lies in its attachment feature: each vertex can be attached to an atom of a structure dataset and inherits that atom's properties (such as name, number, residue, chain, etc ...).
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S3 |
G4 |
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Syntax: .surf attach .struct [-cutoff R] .surf attach none | off
This command will attach the surface dataset surf to the structure dataset struct : each vertex of surf is assigned the closest atom of struct - if this atom lies within the cutoff radius R (default 3.0). As an additional criteria, only atoms that pass the restriction of struct are taken into account (see "5.1.7 Dataset Restriction" on page 25). Vertices that are not assigned an atom are left unchanged, i.e. a previous attachment is not removed. In this way multiple attachments can be issued, possibly with different structure datasets.
To clear all attachment information, attach is called with none or off .
As a result of an attachment, each surface vertex additionally carries the information of a single atom. Atomic properties (as listed in Table 9 (P. 28)) can be used during selection statements involving surfaces (e.g. during new , renew and set ).
// see example in next section
Surface dataset objects are created with the command new:
Syntax: .surf new [-name NAME] [-selection SEL] [-set SET]
There is currently only one object type for the surface dataset, so the type does not need to be specified. NAME defaults to the name of the surface dataset. SEL contains a selection expression, which can contain selectable atom properties if the surface is attached to at least one structure dataset (see Table 9 (P. 28)). Object properties can be defined with -set (see Table 12 (P. 34)).
Example: // example with myo.pdb and myo.face / myo.vert load myo.pdb -name struct load myo -type msms -name surf .surf attach .struct .surf new -name s1 // new object // color surface that lies closest to HEM group .surf.s1 set color=green -sel rname=HEM .surf attach off // reset attachment .struct restrict rname=HEM .surf attach .struct // this time restriction is present .surf new -name s2 // new object // same command as above ! .surf.s2 set color=green -sel rname=HEM // compare surface coloring of s1 and s2 ...
Hint: to select only the part of the surface that carries an attachment, force the selection to evaluate an atom property which is always true.
Example: .surf.all set color=yellow -sel aname=*
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S5 |
G6 |
L7 |
R8 |
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none, unless attached to structure dataset, then all properties from Table 9 (P. 28), but only columns L & R |
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element properties copied from dataset to object, setting on dataset changes default |
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Following are all surface dataset commands:
new : create a new object (see "7.2 Surface Objects" on page 35).
set get : retrieve or modify a dataset property (see Table 12 (P. 34))
Syntax: .surf set PV[, PV ...] .surf get P
restrict : shadow out a subset of the dataset which will not be considered in selection or property setting (see "5.1.7 Dataset Restriction" on page 25).
Syntax: .surf restrict SELECTION
delete : remove one or more objects
Syntax: .surf delete obj [obj2 ...]
attach : attach surface to a structure dataset (see "7.1 Attachments" on page 34).
grab reset fix center : transformation related commands (see "5.1.8 Transformation" on page 25).
Surface object commands are issued as
Syntax: .surf.obj command [parameters]
Following is a list of all surface object commands:
renew : Similar to new command, except the type and name are already determined, so only selection and setting is possible. If either selection or setting (or both) are omitted, the current selection resp. setting is maintained (see "5.1.5 Modifying Objects" on page 23).
Syntax: .surf.obj renew [-selection SEL] [-set SET]
show hide : turns display of the object in the graphics window on or off. Identical to clicking on the object name in the object menu (see "4.12 The GUI" on page 20).
Syntax: .surf.obj show .surf.obj hide
set get : modify or retrieve surface object properties (See Table 12 (P. 34) and see "5.1.5 Modifying Objects" on page 23).
Syntax: .surf.obj get P .surf.obj set PV [-selection SEL] [-range [src=SRC][,PROP=prop][val=VAL1:VAL2]]
Example: .surf attach .myo; .surf new -name all .surf.all set color=green:blue -range prop=rnum,val=1:146
render : modifies the graphical appearance of an object, see below.
The command render changes the graphical appearance of a surface dataset object:
Syntax: .surf.obj render PV [,PV ...]
The render properties applicable are listed in Table 14 (P. 37). Several rendering modes are available, specified as
Syntax: .surf.obj render MODE
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lighting is only applied to the front face, leaving the backside practically unlit and dark |
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Material parameters can be modified with the command material (see "5.1.6 Graphical Appearance" on page 24).