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1. ten in other languages It is also easy to extend programs written in other languages with Lua Lua has been used to extend programs written not only in C and C but also in Java C Smalltalk Fortran Ada and even in other scripting languages such as Perl and Ruby Lua is powerful but simple A fundamental concept in the de sign of Lua is to provide meta mechanisms for implementing features instead of providing a host of features directly in the language For example although Lua is not a pure object oriented language it does provide meta mechanisms for implementing classes and inheritance Lua is a powerful fast lightweight embeddable scripting language Lua is a proven robust language and has been used in many industrial application e g Adobe s Photoshop Lightroom http www lua org about html Lua s meta mechanisms bring an economy of concepts and keep the language small while allowing the semantics to be extended in un conventional ways Lua is small Adding Lua to an application does not bloat it The tarball for Lua 5 1 4 which contains source code documentation and examples takes 212K compressed and 860K uncompressed The source contains around 17000 lines of C Under Linux the Lua inter preter built with all standard Lua libraries takes 153K and the Lua library takes 203K Lua is free Lua is free software distributed under a very liberal license the well known MIT license It can2. tion the old content of the volume will get erased Typ ically one would rather use the constructor new function instead of allocate Param x y z with the size of the volumetric map Usage vol volume new vol allocate 10 8 12 better vol volume new 10 8 12 Add the volume data set to the list of documents Name addDoc Desc Add the volume object to the list of documents in Sculptor Param String with the name Usage vol addDoc test situs Set the isosurface threshold level Name setIsoThreshold Desc Set the isosurface threshold level of the volume Param Value of the new isosurface threshold Usage vol setIsoThreshold 1 0 Set wireframe Name setWireframe Desc Enables or disables the wireframe mode of the isosurface volume display Param boolean Usage vol setWireframe true Set color Name setColor Desc Set the color of the isosurface rendering Param red green blue 0 0 1 0 Usage vol setColor 1 0 1 0 1 0 Size of the Map Name size Desc Get the number of voxels in the volume Param None Returns Number Usage size vol size Get a voxel value Name getValue Desc The function retrieves a voxel value from the 3D volume No interpolation takes place x y and z are indices and not coordinates Param x y z index Usage voxel vol getValue 10 8 12 Get a voxel value Name getIntValue Desc This function takes a
3. Arrays Arrays can be accessed using the square bracket operator and start Attention Arrays start with the index 1 with index 1 and not o like in C text Hello print text 1 Strings Strings can be concatenated using two dots text Hello World print text Control the program flow The syntax of if statements if very similar to other programming lan guages if x 5 then print OK end Loops For loops use an index variable and three parameters The first param eters is the starting value of the variable the second is the final value and the third the amount by which the index should increase at every iteration The third parameter is optional and will be 1 by default for i 1 10 2 do print i end Functions Functions can be defined by using the function keyword function f a b print a b end Using the return keyword the function can also return one or several values function definition function f a b print a b return axb atb end now lets test the function c d f 1 2 print c d Print Printf A special lua printf function was added that prints directly to std out instead of into the sculptor log window The behaviour is iden tical to the normal print function Such a printf function is useful for regression test scripts which can output values e g rmsds cor relation that can be piped into files and the
4. Name of the author Cancel sculptor guiGetValue opens a dialog that requests a value Question Resolution of the map Cancel ATOM The atom class encapsulates a single atom An atom object is typically retrieved from a molecule object Get displaymode Name getDisplayMode Desc Retrieves the current display mode of an atom object Param None Returns String with mode name e g CARTOON Usage mode atm getDisplayMode Set displaymode Name setDisplayMode Desc Sets the current display mode of an atom Param String with the display mode e g VDW or CARTOON Usage atm setDisplayMode CARTOON Set get the x coordinate of the position of the atom Name Xx Desc If no parameter is given the function just returns a number otherwise it will set the x coordinate using the parameter provided by the user Param Optional x coordinate Returns If no parameter given it returns a number the x coordi nate Usage atm_a x 15 0 print atm_a x Set get the y coordinate of the position of the atom Name y Desc If no parameter is given the function just returns a number otherwise it will set the y coordinate using the parameter provided by the user Param Optional y coordinate Returns If no parameter given it returns a number the y coordi nate Usage atm_a y 15 0 print atm_a y Set get the z coordinate of the position of the atom N
5. Param Number of milliseconds Usage sculptor sleep 10 Clear log window Name clearLog Desc Deletes all the output from the log window Param None Usage sculptor clearLog Get the current directory Name getCurrentDir Desc Returns the current directory where Sculptor carries out its functions Param None Usage sculptor getCurrentDir Set the current directory Name setCurrentDir Desc Sets the current directory where Sculptor operates Param String with the new current directory Usage sculptor setCurrentDir tmp Save a screenshot to disk Name saveScreenshot Desc Saves a screen shot to disk The routine can save jpg and png files and will attempt to determine the file type using the extension of the filename Param String with the filename of the image file Usage sculptor saveScreenshot scr png Get global scene transformation matrix Name eetlrans Desc Returns the current global scene transformation matrix sim ilar to a camera matrix Param None Returns matrix4 object Usage mat sculptor getTrans mat print Sets global scene transformation matrix Name setIrans Desc Sets the current global scene transformation matrix similar to a camera matrix Param matrix4 object Usage mat sculptor getTrans mat rotate 2 10 sculptor setTrans mat Close sculptor Name quit Desc This function will still check
6. RMSD Before mol_a rmsd mol_b false And now lets see if we can match it mats trn_b match trn_a ewmat mol_b getTrans mult mats 0 mol_b setTrans newmat sculptor redraw Calculate the rmsd after the matching print RMSD After mol_a rmsd mol_b false Flex an atomic model into a volumetric map sculptor clearLog sculptor delAllDocs Load molecule sculptor load molecule pdb mol sculptor getDoc 2 mol setDisplayMode CARTOON mol setColmapMode SOLID 1 Vectorquantize trnMol mol trn 6 Create a synthetic map for tests vol mol blur 3 0 10 0 Flex the molecule for i1 1 100 do vectorquantize with molecule features as starting point trnVol vol trn 6 trnMol OK for fun introduce some random deviations for j 1 6 do atm trnVol getAtom j atm x atm x math random 0 5 10 atm y atm y math random 0 5 10 atm z atm z math random 0 5 10 trnVol setAtom atm end now flex flex mol flexing trnMol trnVol flex addDoc flexingTest pdb flex setDisplayMode CARTOON flex setColmapMode SOLID 2 sculptor redraw sculptor sleep 500 sculptor delDoc 3 end
7. Simula and J Kangas editors Artificial Neural Networks pages 397 402 North Holland Amsterdam 1991 Laplacian Quantization The laplacian quantization combines the laplacian filter with the vector quantization algorithm yielding in superior performance for volumet ric maps with a low resolution In order to be able to apply the laplace filter the algorithm will convert the high resolution structures into vol umetric maps internally In order to be consistent the algorithm needs to know the resolution and voxel width of the target map when quan tizing a structure Atomic Coordinates This option is typically not useful for a normal multi resolution dock ing application it provides a simple feature extraction based on the atomic coordinates of a molecular structure This is only useful for the comparison of two structures do not use this option and compare the feature vectors with neural gas generated points Feature Extraction Vector Quantization Codebook Size 10 Et Iteration Steps 100000 Res Target Map 10 0 Voxel Width Target Map 3 0 Options Lambda_i Lambada f Epsilon i Epsilon_f Import Export Feature Vectors The feature vectors are stored by default in the Sculptor state file File gt Save State and File gt Load State see the documentation of the File menu If one would like to use already previously calculated feature points from another program for example from
8. Six dials control the six degrees of freedom of a transformation in 3D space The top dials determine the three translation components a translation along the X the Y and the Z axis Each step on one of the dials corresponds to 0 1 Angstroem The lower three dials determine the three components of the rotation along the X the Y and the Z axis Each step rotates the object by 1 degree File Menu Open With the file open menu item one can load data sets into Sculptor In most cases Sculptor automatically recognizes the file type based on the extension Sculptor supports the following file types PDB standard protein data base files Sculptor supports multiple models and interprets the END statement as frame end delimiter for trajectories PDB PSF Sculptor can load in PDB PSF file combos Please select Molecule pdb psf from the file type pull down Now double click on the PDB file first and then double click on the PSF file Sculp tor will immediately reopen the file dialog after the PDB file was se lected PSF DCD Trajectory files based on a protein structure file and a binary DCD file Please select Trajectory psf dcd from the file type pull down Now double click on the PSF file first and then double click on the DCD file Sculptor will immediately reopen the file dialog after the PSF file was selected SITUS Sculptor loads volumetric maps in the Situs format CCP4 MRC MAP Standard MRC files are sup
9. mol setAtomResNum 123 123 Get chain id Name setAtomChain Desc Get chain id information of atom i e g A B C Param Index of the atom Returns String Usage chain mol getAtomChain 123 Set chain id Name setAtomChain Desc Set chain id information of atom i e g A B C Param Index of the atom String with the chain identifier Usage mol setAtomChain 123 A Get icode Name getAtomICode Desc Get icode insertion of residues information of atom i Param Index Returns String Usage chain mol getAtomICode 123 Set icode Name setAtomICode Desc Set icode insertion of residues information of atom i Param Index Usage mol setAtomICode 123 Get occupancy Name eetAtomOccupancy Desc Get occupancy information of atom i Param Index Returns Number Usage occ mol getAtom0ccupancy 123 Set occupancy Name setAtomOccupancy Desc Set occupancy information of atom i Param Index Number Usage mol setAtomOccupancy 123 1 0 Get temperature factor Name eetAtomlTempFact Desc Get temperature factor information of atom i Param Index Returns Number Usage temp mol getAtomTempFact 123 Set temperature factor Name setAtomTempFact Desc Set temperature factor information of atom i Param Index Number with the temperature factor Usage mol setAtomTempFact 123 1 0 Get note Name getAtomNote
10. Desc Get note of atom i Param Index Returns String Usage note mol getAtomNote 123 Set note Name setAtomNote Desc Set note of atom i at least three characters long Param Index of the atom String with the note Usage mol setAtomNote 123 ABC Get segment Name getAtomSegID Desc Get segment id of atom i Param Index Returns String Usage seg mol getAtomSegID 123 Set segment id Name setAtomSegID Desc Set segment id of atom i at least four characters long Param Index of the atom String with the segment id Usage mol setAtomSegID 123 ABCD Get element Name setAtomElement Desc Get element information of atom i Param Index of atom Returns String Usage element mol getAtomElement 123 Set element Name setAtomElement Desc Set element information of atom i at least two characters add a space in front if you need just one Param Index of atom String with the element information Usage mol setAtomElement 123 H Get charge Name geetAtomCharge Desc Get charge of atom i Param Index of atom Returns String Usage element mol getAtomCharge 123 Set charge Name setAtomCharge Desc Set charge of atom i two characters at least Param Index of atom String with the charge information Usage mol setAtomCharge 123 12 Is hydrogen Name isAtomHydrogen Desc Is atom i a hydrogen Par
11. be used for any purpose including commercial purposes at absolutely no cost Just download it and use it Syntax Users familiar with other programming languages should not have any difficulties to learn Lua It is very similar to other high level lan guages A full documentation of Lua is available for free online at http www lua org in addition various books are available for pur chase at bookstores and Amazon In the following the main syntax elements are quickly highlighted Comments Simply start with two hyphens this is a comment Variables Lua knows strings numbers and booleans as basic types As Lua is dynamically typed i e one can just start using variables without having to declare them x 5 text Hello question false There are no integer variables only doubles and variables are by default always global Using the local keyword one can make them local to a function function localTest local counter 0 print counter end More documentation can be found on the Lua website http www lua org docs html There are also several books about Lua available especially Programming in Lua by Roberto Ierusalimschy March 2006 ISBN 85 903798 2 5 can be recom mended as standard textbook Attention Variables are by default global After a function returns the vari ables that were created inside the func tion stay visible unless the local key word is used
12. for new documents that were created but not saved yet and will prompt the user In a test script that might not be desirable just delAllDocs first to make sure that the quit function will succeed without any user intervention Param None Usage sculptor quit Open a file open dialog Name Desc Param Returns Usage file guiFileOpenDlg Opens a file dialog and returns a string with a file name If user cancelled the dialog the string will be empty Message String with selected file name sculptor guiFile0penDlg Please select a file sculptor load file Open a file save dialog Name guiFileSaveDlg Desc Opens a file save dialog and returns a string with a file Param Returns Usage file name If user cancelled the dialog the string will be empty Message String with selected file name sculptor guiFileSaveDlg Please choose a file Open a warning dialog Name Desc Param Usage guiWarning Opens a warning dialog with a message for the user Message sculptor guiWarning Your model only has CA atoms sculptor guiFileOpenDlg opens a file open dialog w Please open a file for loading Look in amp nachina home sbirmanns Documents Tufte i Gm tufte latex 3 5 0 File name Open Filetype Popular supported data formats scl pdb pd Cancel sculptor guiFileSave opens a file save di alog o Please choose a filename f
13. for the spherical region x y z and radius of sphere Usage vol cutSphere 10 12 8 3 5 Threshold Name threshold Desc Threshold the volumetric map All voxel below and above certain values are cut off and set to those values Param New minimum and maximum values Usage vol threshold 0 3 5 Get Maximal Density Name getMaxDensity Desc Get the maximal voxel value in the map Param None Usage max vol getMaxDensity Get Minimal Density Name getMinDensity Desc Get the minimal voxel value in the map Param None Usage max vol getMinDensity Get the voxelwidth of the volume Name get Voxelwidth Desc Returns the size width of the voxels in the map Sculptor assumes that the maps are cubic and orthogonal Param None Usage vw vol getVoxelwidth Set the voxelwidth of the volume Name set Voxelwidth Desc This will not re interpolate the map but only set the inter nal voxelwidth variable See interpolate function Param Nmber new voxelwidth Usage vol setVoxelwidth 3 0 Get the size of the volume in x dimension Name getSizeX Desc Returns the size number of voxels in x direction Param None Usage sizex vol getSizeX Get the size of the volume in y dimension Name getSizeY Desc Returns the size number of voxels in y direction Param None Usage sizey vol getSizeY Get the size of the volume in z dimens
14. inform the program which of the files is the target map for the multi resolution fitting Once the document is selected a small icon next to its file name will also show its special state as target map The volumetric map which was loaded last will automatically be selected as target map ke loel situs Set Probe Molecule is As one can load multiple data sets into Sculptor the user has to inform the program which of the files is the probe molecule for the multi resolution fitting The structure which was loaded last will automatically be selected as probe molecule Cross Correlation to determine the agreement or similarity of two signals It can be used In signal processing cross correlation is an established criterion in the context of multi resolution fitting as scoring function to compare multiple docking solutions Select two volumetric maps from the list of documents and click on the cross correlation menu item The program will calculate and report the cross correlation coefficient between the two maps If a structure was docked into a map and the quality of the fit should be measured using the CCC the structure has to be converted into a volumetric description first Please click on the document and selected Structure gt Blur to generate a volumetric map The resulting volume can then be utilized in a second step for the correlation coefficient calculation Feature Extraction The items in the sub me
15. the Situs qpdb and qvol tools or if one would like to export the coordinates to other programs one can use Sculptor to import or export the points in PDB format Render Feature Vectors The visualization of the feature vectors can be turned on or off with this menu item Render Displacements In addition to the normal feature vector rendering one can also render the deviation of two feature point sets using arrows for example in order to visualize the conformational change between two data sets Please select two documents in the document list hold down the ctrl key and click onto the two documents The two documents have to have feature point sets associated with them for example from a feature extraction with the neural gas algorithm Once you click on the menu item the visualization should change and arrows between the two point sets will appear Visualization Volume Rendering Iso Surfaces Direct Volume Rendering The before mentioned iso surface renderings convert the volumetric data into a triangular mesh This is done by essentially thresholding the map wherever the voxel densities reach a certain threshold trian gles are added and the surface is drawn Unfortunately thresholding essentially converts the floating point data set into a simple binary map all the density variations are lost not shown in the triangular iso surfaces An alternative representation for volumetric data is Map Explorer The
16. Sculptor Scripting Interface Introduction SCULPTOR VERSION 1 3 and above features an embedded Lua in terpreter which is used as scripting language Sculptor internally is fully implemented in C which is a standard object oriented com piled language We are happy with C and do not plan to switch to Lua or any other interpreted lanuage for our main algorithm develop ment Lua as a true scripting language on the other hand allows us to quickly test new ideas that we later might port to C It is also very useful for end users as they can implement their own molecular mod eling techniques without having to set up a C programming envi ronment In fact Lua routines can be programmed directly in Sculptor in the internal script editor and can be executed immediately without any compilation step The scripting interface is also very convenient to automize certain routine procedures like for example loading a se ries of files and setting up their visualization Why Lua and not XXX fill in your favorite interpreted programming language here There are literally hundreds of scripting languages available whereby most of them nowadays are not only praised and advertised for light pro gramming tasks but also for real application development If one intends to write a significant portion of the code of a larger applica tion in a scripting language this changes the requirements and makes certain languages more attractive than others On
17. The visibility can also be toggled by clicking directly into document list onto the eye icon Top A The top most document in the document list determines the origin of the entire scene its origin will be the origin of the Sculptor 3D scene and all other documents will be positioned relative to this one If the origins of your files are very different this can also mean that only some files are visible Other are positioned so far away that they cannot be seen By moving the document to the top position one can inspect those files View Menu Add Clipping Plane J The clipping plane cuts the 3D visualization into two areas ev erything left of the plane will not get rendered anymore The clip ping plane is stored as a standard document that can be manipulated moved around rotated visibility on off etc like any other docu ment To facilitate the positioning of the clipplane a semi transparent rectangle is drawn on top of the plane The rendering of the rectangle can be turned off in the property dialog of the clipplane document Save Screenshot K Saves the content of the 3D window as a jpg or png file to disk Please make sure that the 3D window is not occluded by any other window or dialog box Export as Wavefront OB file Saves the 3D visualization as alias wavefront obj file The file format is supported by most 3D rendering packages which can be utilized to create high quality images The format does not
18. ain GUI window the place where one can adjust most of Boel pdb the global properties of the program and also a number of settings relating to an individual document Here you will find only a basic description of the icons of the main document window details about the usage of the features of the pro gram are described in the other tutorials The icons can also be found as functions in the menubar i io Y enables or disables the rendering of this document the menu item data view can also be used to toggle the state the transformation If the document is rotated for example by using if this icon is displayed the document will be the center of the mouse the rotation will be around the geometrical center as pivot point Attention The coordinates of the document will change if a rotation is applied If the Sculptor Scene document is the center a global rotation around the center of the 3D scene will get carried out In that case the actual coordinates of the documents will not change only the viewpoint gets adjusted One can change the center of the transformation by selecting a doc ument and by clicking on the menu item data gt move Alternatively one can also directly click into the document list into the area where the crosshair would be The m key on the keyboard also allows to toggle the status of the current document if is already the center the scene will be the new center I
19. am Index of atom Returns Boolean Usage hydro mol isAtomHydrogen 123 Is atom codebook vector Name Desc Param Returns Usage hydro isAtomQPDB Is atom i a codebook vector Index of atom Boolean mol isAtomQPDB 123 Is water molecule Name Desc Param Returns Usage hydro isAtomWater Is atom i part of a water molecule Index Boolean mol isAtomWater 123 Is carbon alpha Name Desc Param Returns Usage hydro isAtomCA Is atom i a carbon alpha Index Boolean mol isAtomCA 123 Is atom 1 on the backbone Name isAtomBackbone Desc Is atom i part of the backbone Param Index of atom Returns Boolean Usage hydro mol isAtomBackbone 123 Is atom i a nucleotide Name isAtomNucleotide Desc Is atom ia nucleotide Param Index of atom Returns Boolean Usage hydro mol isAtomNucleotide 123 Get mass Name getAtomMass Desc get the atomic mass Param Index of atom Returns Number Usage mass mol getAtomMass 123 Set mass Name Desc Param Usage setAtomMass Set the atomic mass of an atom Index of atom Number mol setAtomMass 123 1 2 Adjust the atomic mass based on a simple periodic table Name Desc Param Usage adjustAtomMass Automatically adjust the atomic mass of an atom using a simple periodic table Index of atom mol adjustAt
20. ame Z Desc If no parameter is given the function just returns a number otherwise it will set the z coordinate using the parameter provided by the user Param Optional z coordinate Returns If no parameter given it returns a number the z coordi nate Usage atm_a z 15 0 print atm_a z Print content to stdout Name print Desc Prints information about the atom to the sculptor log win dow Param None Usage atm print Measure distance to another atom Name distance Desc Measures the distance from one atom to another one Param Atom object Returns Number Usage dist mol getAtom 123 distance mol getAtom 124 Powell refinement Name powell Desc Compute the powell off lattice refinement of an array of molecules against a volume object The user has to specify an array of molecules which of course can just consist of a single molecule In case of multiple models in the array a simultaneous refinement is carried out Param array of molecule objects volume object number with resolution of volumetric map boolean should the model be low pass filtered or not at tention takes significantly more time Usage sculptor load sculptor_powell scl vol sculptor getDoc 2 a ali sculptor getDoc 3 al2 sculptor getDoc 4 al3 sculptor getDoc 5 al4 sculptor getDoc 6 union sphere correlation blur false sculptor powell a vol 10 fal
21. d 5 10 Remove all atoms Usage mol delAllAtoms Remove all bonds Usage mol delAllBonds Match two point clouds Name match Desc Param Usage mats This function should not be used directly on atomic mod els but only on feature point clouds First use vector quantization to extract a small number of feature points from both data sets models and then match those feature points The resulting transformation matrix can then be applied to the original atomic models Returns an array of matrices with the first matrix representing the most likely match Other molecule object tolerance for anchor point determination 15 0 nearest neighbor matching zone 12 0 zonesize 3 wildcards o trnmol_a match trnmol_b 15 12 3 O realmol_a setTrans realmol_a getTrans mult mats 1 Flex a molecule Name Desc Param Returns Usage flex flexing Flex a molecule according to the coordinates of two feature point sets The first feature point set describes the molecule in its original conformation the other one the target con formation for example from a cryo em map Two molecule objects New molecule object mol flexing trn_a trn_b VOLUME The volume class encapsulates a single volumetric data set Allocate memory Name allocate Desc This function throws the current map of the object away and allocates memory for a new volumetric map Atten
22. ferent colors whereas the low color palette changes smoothly over the range of the values The following two dialog boxes show the same region of the high contrast and low contrast palette Sculptor Selecta m a Sculptor Selecta T an x Closed Surfaces at Clip Planes This menu item can be used to close the borders of surfaces at clip planes default off Docking Menu The docking menu includes various tools with which one can accom plish a multi scale fitting In the process a high resolution structure from now on called probe molecule is docked into a low resolution target map volumetric map The program implements a variety of established techniques most of which are reviewed in the following paper about hybrid modeling methods Willy Wriggers and Pablo Chac n Modeling Tricks and Fitting Techniques for Multi Resolution Structures Structure 2001 Vol 9 PP 779 788 The efficient feature based M to N docking algorithm is described in the following article Stefan Birmanns and Willy Wriggers Multi Resolution Anchor Point Registration of Biomolecular Assemblies and Their Compo nents J Struct Biol 2007 Vol 157 pp 271 280 The user manual describes the individual menu items one by one the tutorial section reports in a more application oriented fashion how one can carry out a multi resolution fitting Set Target Map ss As one can load multiple data sets into Sculptor the user has to
23. ing and rapid prototyping Why choose Lua Lua is a proven robust language Lua has been used in many industrial applications e g Adobe s Photoshop Light room with an emphasis on embedded systems e g the Ginga mid dleware for digital TV in Brazil and games e g World of Warcraft Lua is currently the leading scripting language in games Lua has a solid reference manual and there are several books about it Lua is fast Lua has a deserved reputation for performance To claim to be as fast as Lua is an aspiration of other scripting languages Several benchmarks show Lua as the fastest language in the realm of interpreted scripting languages Lua is fast not only in fine tuned benchmark programs but in real life too A substantial fraction of large applications have been written in Lua Lua is portable Lua is distributed in a small package and builds out of the box in all platforms that have an ANSI ISO C compiler Lua runs on all flavors of Unix and Windows and also on mobile devices such as handheld computers and cell phones that use BREW Symbian Pocket PC etc and embedded microprocessors such as ARM and Rabbit for applications like Lego MindStorms Lua is embeddable Lua is a fast language engine with small foot print that you can embed easily into your application Lua has a sim ple and well documented API that allows strong integration with code written in other languages It is easy to extend Lua with libraries writ
24. ion Name getSizezZ Desc Returns the size number of voxels in z direction Param None Usage sizez vol getSizeZ Normalize the map Name normalize Desc Normalize the voxel values in the volumetric map to o 1 Param None Usage vol normalize Mask with another volume object Name mask Desc Applies a mask to the volume All the voxels in this vol are multiplied with the mask volume voxels multiplied by o for not overlapping voxels Param Mask volume object Usage vol mask maskvol Create a binary mask Name makeMask Desc Create a binary mask using a threshold value Every voxel below the threshold will get set to o the rest to 1 Param Number threshold value Usage vol makeMask 1 0 Interpolate map to different voxelsize Name interpolate Desc Interpolate the map to a different voxelsize Param Number new voxelsize Usage vol interpolate 2 0 Convolve map Name convolve Desc Convolve map with another volume kernel Param Volume kernel Usage vol convolve kernelvol Create Gaussian Kernel Name createGaussian Desc Create a Gaussian kernel volume within SigmaFactorfSigma Attention This will overwrite the current content of the volume object with the filter kernel It will allocate the memory internally Param sigma of map and sigma factor Usage kernel createGaussian sigma sigmafactor Create Laplacian Kernel Name crea
25. ion of the document files like pdb or mrc files If the location of the files changes the state cannot be restored properly The state files are ascii xml files so by editing in a text editor one might be able to restore the file J Cross Sections DVR info Disable tsosurface E came R a Nicaea coca A eee eee A comer cer c 1 2 3 4 5 Level 2 60808 Steps 1 Create Triangles 720 Wireframe Flat Shading illuminated Two Sided Culling Transparency Global rendering settings In Sculptor you can find under the view submenu all the global set igi iQ QO td 4 W tings and rendering functions One can take screenshots of the ren derings change the background color zoom in and out or change to orthographic mode The settings should be self explanatory Transformations Add Transformation In multi scale modeling applications a very precise control over the Tramslation X Translation T Tramslation Z transformations applied to the probe molecule is necessary to ensure an accurate docking result Therefore Sculptor provides two basic modes of interactions With the mouse molecular structures can be ag moved on the X Y plane right mouse button on the X Z plane mid Rotation x Rotation Y Rotation 2 dle mouse button and rotate around the origin left mouse button if precise control is needed a transformation dialog can be o amp J 6 activated menu Docking gt Transformation
26. m None Usage mol updateRendering Save the molecule to disk Name save Desc This function saves the atomic model to disk as a pdb file Param Filename Usage mol save test pdb Load an atomic model from disk Name load Desc The molecule will not get added to the document list of Sculptor can be done later using the addDoc function This function is therefore not identical to the function load of the Sculptor class which one typically would call The function here is useful if one needs to have access to a cer tain atomic structure temporarily and would like to avoid loading it into Sculptor as a real document for which e g a visualization is created etc Param Filename Usage mol molecule new mol load test pdb Vectorquantization Name vectorquant Desc Create codebookfeature vectors using the neural gas TRN algorithm Param None Usage mol vectorquant Set displaymode Name setDisplayMode Desc Set the global display mode of the molecular structure Param String with the name of the display mode e g CAR TOON Usage mol setDisplayMode CARTOON Set colmapmode Name setColmapMode Desc Set the color mapping mode Param Colormapping mode e g SOLID Number of color from the Sculptor palette Usage mol setColmapMode SOLID 5 Project Mass Correlation Name projectMassCorr Desc This routine only projects the atoms
27. m disk Name load Desc Loads a volume from disk The volume will not get added to the document list of Sculptor can be done later using the addDoc function Typically one would prefer to use the sculptor load function Param Filename Usage vol volumw new vol load test situs Compute Feature Vectors Name vectorquant Desc Create codebookfeature vectors using the neural gas TRN algorithm Returns a new molecule with the feature vec tors Can start from an already existing configuration and will in that case also return a matched feature point set can be used to flex the molecule The start configuration is in that case the second parameter of the function call Param Number of feature vectors Usage vectors vol vectorquant 10 Cross Correlation Name correlation Desc Calculate the correlation with another volume object Param Other volume object The second parameter specifies if the correlation coefficient should only be computed under the current molecule aka local correlation or over the entire volume Boolean if true only under the molecule false standard correlation Default false standard cc Usage cc vol_a correlation vol_b Delete a spherical subregion Name cutSphere Desc Remove set to o a spherical subregion within the volume Useful for example for virus maps where one might only be interested in the capsid for docking Param center voxel coordinate
28. me Desc Param Usage atm addAtom The atom is stored as a new atom in the molecule will therefore get a new svt index Atom mol getAtom 123 atm x 10 5 mol addAtom atm Add an array of atoms to the molecule Name addAtoms Desc The atoms are stored as new atoms in the molecule and will therefore get a new svt index Param Array of atoms Usage atm mol getAtoms 123 135 atm 1 x 10 5 mol addAtoms atm Get the number of atoms in the molecule Name Returns Number Compute RMSD Name rmsd Desc Compute the rmsd with another molecule object Param molecule object boolean align the two structures before rmsd true false Usage rmsd mol rmsd mol2 false Create volumetric map Name blur Desc Blur an atomi model by convoluting it with a Gaussian kernel Param voxelwidth resolution Returns a volume Usage vol mol blur 3 0 10 0 Get transformation matrix Name eetlrans Desc Get the transformation matrix Returns matrix4 object Usage mat mol getTrans mat print Sets the transformation matrix Name eetlrans Desc Set the transformation matrix Param matrix4 object Usage mat mol getTrans mat rotate 2 10 mol setTrans mat Update the rendering of the molecule Name updateRendering Desc Updates the visual rendering of the molecule Should be called if the data was manipulated internally Para
29. n a visual multi scale docking process one very often wants to adjust the position of one or multiple probe molecules relative to a 3D volumetric map To check the position and orientation of the molecule it is often beneficial to alternate between a local and global transformation This can also be accomplished very efficiently by selecting the probe molecule in the document list and by M toggeling the status via the key deletes the selected document s lected document can be adjusted See other tutorials for details opens a dialog box with which the visualization of the se moves the selected document up in the document list The geometric center of the first item will at the same time also be the origin of the 3D scene That way the first document will always be clearly visible after being loaded If more documents are loaded the origin can be changed by moving another file up and thereby the first in the list moves the selected document down in the document list makes the selected document the top in the document list Save and Restore States Sculptor can store the current state of the program in an xml file with the extension scl This state file will keep all the information about the current documents and the visualization modes and settings One can save and load a state file with the menu items File gt Load State and File gt Save State Attention The state file will only store the locat
30. n be compared with pre computed values The test script can then be started from the command line sculptor test lua and as last statement the script kills the sculptor application with sculptor quit One can run series of those regression tests before a new release to make sure that the introduction of new features did not break any older algorithms The information above should enable you to write simple scripts for a more in depth description of Lua please go to http www lua org or buy one of the books about the language Reference Manual In the following the special Sculptor Lua classes are documented and their member functions are listed with a simple example that illus trates their Usage The molecule volume and matrix classes are all normal dynamic classes which means that one first has create ob jects instances before one can use them The Sculptor class is different in this respect as there is always a sculptor object available and one should not attempt to create any new object of the type sculptor The idea is that the sculptor object represents the main application pro gram whereas one of course can create and delete molecular models or volume data dynamically New objects of the types volume molecule and matrix are typically created using get functions of other objects For example vol sculptor getDoc 2 returns the second document One can also generate new objects using the constructor vol volume ne
31. normal angstroem world coordinate and interpolates the voxel values tri linearly Param x y z angstroem coordinate Usage voxel vol getIntValue 11 5 8 24 12 21 Set a voxel value Name setValue Desc The function allows to directly manipulate a single voxel value No interpolation takes place x y and z are indices and not coordinates Param x y z index and value Usage vol setValue 10 8 12 0 567 Copy Name copy Desc Copies the current volume data set It will not automati cally get added to the list of loaded documents but stays initially just on the Lua side and will get deleted again once the Lua interpreter finishes AddDoc can be used to push the new object into the Sculptor document list and make it permanent Param None Usage volCopy vol copy Crop the volume Name crop Desc Cuts the volume to a smaller size by removing voxels from each dimension Param min max x min max y min max z Usage vol crop 2 12 5 24 3 34 Update rendering Name updateRendering Desc Update the rendering of the volume data Should be called if the data was manipulated internally for example with setValue so that the rendering will reflect the new changed data Param None Usage vol updateRendering Save the volume Name save Desc This function writes the volume data to a file on the disk Param Filename Usage Usage vol save test situs Load a volume fro
32. nu extract feature points from multi resolution data sets These feature points can then in a second step be utilized to find solutions to the multi resolution docking problem see feature based docking below Feature points can be determined using the neural gas algorithm or laplacian quantization The algorithmic details are described in the following article Stefan Birmanns and Willy Wriggers Multi Resolution Anchor Point Registration of Biomolecular Assemblies and Their Compo nents J Struct Biol 2007 Vol 157 pp 271 280 Neural Gas The neural gas is a classic artificial neural network algorithm from the category of the self organizing maps The neural net is trained to represent the original data in a best possible way least information loss After clicking on Feature Extraction gt Neural Gas the following dialog box appears Feature Extraction Vector Quantization Codebook Size 10 ba iteration Steps 100000 3 Options Lambda i 0 7 Lambda f 0 02 pi Epsiloni Epsilon f 0 001 OK Cancel The main parameter is the size of the codebook which determines the number of the features the algorithm will extract from the data The other parameters concern the inner workings of the algorithm they should not be changed in common docking applications The following article describes the algorithm and the parameters A neural gas network learns topologies In T Kohonen K Mak isara O
33. omMass 123 Get vdw radius of atom 1 Name Desc Param Returns Usage getAtomVDWRadius Get the van der Waals radius of an atom Index of atom Number rad mol getAtomVDWRadius 123 Get a model from the molecule Name Desc Param getModel Returns a new molecule object with an extracted model from the current molecule Modelnumber Returns Molecule object Usage mol_b mol getModel 1 Get a chain from the molecule Name getChain Desc Extracts a chain from a molecule and returns it as a new molecule object Param Chain ID Returns Molecule object Usage mol_b mol getChain A Compute Internal Model Information Name calcAtomModels Desc Builds an internal array with the different atom model num bers typically this array is automatically build during loadPDB If a pdb is build by hand call this function af ter assembly of the structure Param None Usage mol calcAtomModels Add another molecule Name add Desc Add a another molecule to this molecule object Param Molecule object Usage mol_a add mol_b Add a bond between two atoms Param Index a and index b of the two atoms Usage mol addBond 5 10 Is there a bond between two atoms Param Index a and index b of the two atoms Usage bond mol isBond 5 10 Remove a bond between two atoms Param Index a and index b of the two atoms Usage mol delBon
34. omRemoteness Desc Set remoteness information for atom i e g alpha for a carbon alpha atom Param Index Usage mol setAtomRemoteness 123 Get branch information Name gsetAtomBranch Desc Get branch information of atom i Param Index Returns String Usage branch mol getAtomBranch 123 Set branch information Name setAtomBranch Desc Set branch information of atom i Param Index Usage mol setAtomBranch 123 Get alternate location indicator Name getAtomAltLoc Desc Get alternate location indicator information of atom i Param Index Returns String Usage alt mol getAtomAltLoc 123 Set alternate location indicator Name setAtomAltLoc Desc Set alternate localtion information of atom i Param Index Usage mol setAtomAltLoc 123 Get residue name Name eetAtomResName Desc Get residue name information of atom i e g alanin Param Index Returns String Usage res mol getAtomResName 123 Set residue name Name setAtomResName Desc Set residue name information of atom i e g alanin Param Index Usage mol setAtomResName 123 ALA for ALA for Get residue number Name cetAtomResNum Desc Get residue number information of atom i Param Index Returns Integer Usage res mol getAtomResNum 123 Set residue number Name setAtomResNum Desc Set residue number information of atom i Param Index Usage
35. onto the volume object and calculates the correlation it will not convolute the molecule with a Gaussian to bring it to the same resolution as the volumetric data Param Volume object Usage cc mol projectMassCorr volume Get secondary structure information Name getAtomSecStruct Desc Retrieve the secondary structure information of atom i Param Index Returns String Usage ss mol getAtomSecStruct 123 Get atom type information Name getAtomType Desc Get the atom type information for a specific atom in the molecule Param Index Returns String Usage type mol getAtomType 123 Set atom type information Name setAtomType Desc Set the atom type information for a specific atom in the molecule Param Index String with type information Usage mol setAtomType 123 H Get atom model information Name setAtomModel Desc Get atom model information for atom i Param Index Returns Integer Usage model mol getAtomModel 123 Set atom model information Name setAtomModel Desc Set atom model information for atom i Param Index Integer with the new model identifier Usage mol setAtomModel 123 3 Get remoteness information Name eetAtomRemoteness Desc Get remoteness information for atom i e g alpha for a carbon alpha atom Param Index Returns String Usage rem mol getAtomRemoteness 123 Set remoteness information Name setAt
36. or saving Look in amp nachina home sbirmanns Documents Tufte i f tufte latex 3 5 0 File name Save File type Popular supported data formats scl pdb pd Cancel sculptor guiWarning opens a warning dialog Warning Your model only has CA atoms OK Open an information dialog Name guilnfo Desc Opens an information dialog with a message for the user Param Message Usage sculptor guiInfo Your model only has CA atoms Open a yes no question dialog Name guiYesNo Desc Opens a yes no dialog with a question for the user Param Message Returns Boolean with the value true if the user clicks on Yes Usage answer sculptor guiYesNo Do you really want to quit Open a free text question dialog Name guiQuestion Desc Opens a question dialog where the user can reply with a text Param Message Returns String with answer Usage answer sculptor guiQuestion Name of the author Open a value question dialog Name euiGetValue Desc Opens a dialog where the user can type in a value Param Message Usage answer sculptor guiGetValue Resolution of the map sculptor guilnfo opens an information dialog ial Information 4 i Do you really want to quit OK sculptor guiYesNo opens a dialog box with a question for the user Lg Question 4 Ep Do you really want to quit No sculptor guiQuestion opens a question dialog Question
37. ported We have tried to be consistent with most data files and other programs that are available Unfortunately the file format is not really standardized and therefore incompatibilities can exist Sculptor only supports orthogo nal maps Save As The selected document can be saved using the Save As menu item in the file menu The program will always open a file dialog to give you a chance to specify a new file name to avoid overwriting your original data Load and Save State Sculptor is able to save and restore it s current state This will restore all loaded documents all visualization settings and all docking re sults Attention If one generates a completely new data set in Sculptor for example by blurring a high resolution structure into a volumetric map this new document needs to be saved before the state is written out into a file User Manual Data Menu All menu items in the Data sub menu will always change the currently selected documents in the document list The document list is a list of loaded files in the top left corner of the Sculptor window Close i Closes the selected documents they will get removed from the list of loaded files Properties Opens the properties dialog of the selected document View Toggles the visibility of the selected document If the Sculp tor Scene document is currently selected all documents will be set to invisible Sculptor Scene E Monomer pdb
38. re 10 10 10 10 0 vol_a addDoc cutSphere situs Create a 10x10x10 volume with a cube vol volume new 10 10 10 for x 1 10 do for y 1 10 do for z 1 10 do if x gt 2 and x lt 8 and y gt 2 and y lt 8 and z gt 2 and z lt 8 then vol setValue x y z 10 end end end end vol addDoc demo situs vol setIsoThreshold 0 5 Extract only the helices from an atomic model sculptor clearLog sculptor delAllDocs sculptor load monomer pdb mol_a sculptor getDoc 2 mol_b molecule new for i 1 mol_a size do if mol_a getAtomSecStruct i H then mol_b addAtom mol_a getAtom i end end mol_b addDoc helices pdb Do a powell refinement only on a single chain lt to be written gt Matching This example code will load two molecules vectorquantize them and match them sculptor clearLog sculptor delAllDocs Load molecule A sculptor load mol_A pdb mol_a sculptor getDoc 2 mol_a setDisplayMode CARTOON mol_a setColmapMode SOLID 1 trn_a mol_a trn 6 trn_a addDoc TRN_A pdb trn_a setDisplayMode VDW trn_a setColmapMode SOLID 1 Load molecule B sculptor load mol_B pdb mol_b sculptor getDoc 4 mol_b setDisplayMode CARTOON mol_b setColmapMode SOLID 2 trn_b mol_b trn 6 trn_b addDoc TRN_B pdb trn_b setDisplayMode VDW trn_b setColmapMode SOLID 2 sculptor redraw Calculate the rmsd before the matching print
39. sculptor biomachina org SCULPTOR VERSION 2 UsER MANUAL March 26 2010 Sculptor has been developed from 2001 2012 at biomachina org with contributions from the following authors in alphabetic order Stefan Birmanns Maik Boltes Paul Boyle Jan Deiterding Frank Delonge Sayan Ghosh Jochen Heyd Oliver Passon Mirabela Rusu Francisco Serna Zbigniew Starosolski Manuel Wahle Willy Wriggers and Herwig Zilken The main reference for Sculptor v 2 is e Stefan Birmanns Mirabela Rusu and Willy Wriggers Using Sculptor and Situs for Simultaneous Assembly of Atomic Components into Low Resolution Shapes J Struct Biol Vol 173 pp 428 435 2011 In addition we list here some relevant published articles that describe specific visualization features of Sculptor e Mirabela Rusu and Willy Wriggers Evolutionary Bidirectional Expansion for the Tracing of Alpha Helices in Cryo Electron Microscopy Reconstructions J Struct Biol Vol 177 pp 410 419 2012 e Manuel Wahle and Stefan Birmanns GPU Accelerated Visualization of Protein Dynamics in Ribbon Mode SPIE Proceedings Vol 7868 Visualization and Data Analysis 2011 Pak Chung Wong Jinah Park Ming C Hao Chaomei Chen Katy Borner David L Kao Jonathan C Roberts Editors e Oliver Passon Maik Boltes Stefan Birmanns Herwig Zilken and Willy Wriggers Laplace Filter Enhanced Haptic Rendering of Biomolecules In Proceedings Vision Modeling and Visuali
40. se MOLECULE The molecule class encapsulates a single molecule i e a Sculptor atomic model document Add the molecule to the list of documents Name addDoc Desc Add a Lua internal molecule to the Sculptor list of docu ments Param String with the name Usage addDoc test pdb Get an atom from the molecule Name eetAtom Desc Retrieve a specific atom out of all the atoms of the molecule Param Index Returns An atom object Usage atm mol getAtom 123 Set an atom in the molecule Name setAtom Desc The atom contains the index so it knows where it was re trieved from and will go back to exactly the same position If a new atom is supposed to be stored in the molecule please use addAtom Param Atom object Usage atm mol getAtom 123 atm x 10 5 mol setAtom atm Get a series of atoms from the molecule Name Desc Param Returns Usage getAtoms Retrieve a subset of atoms from the molecule Two indices An array of atoms atm mol getAtoms 123 135 Set an array of atoms in the molecule Name Desc Param Usage setAtoms The atoms contain the index so they know where they were retrieved from and will go back to exactly the same position If a new atom is supposed to be stored in the molecule please use addAtom Array of atoms atm mol getAtoms 123 135 atm 5 x 10 5 mol setAtoms atm Add an atom to the molecule Na
41. support all features of the opengl rendering shown in the interactive 3D window the direct volume rendering is an example of a Sculptor rendering which cannot be exported using the alias wavefront format The image on the right was exported from Sculptor and rendered with the free 3D modeling package Blender Change Background Color Opens a color chooser dialog with which one can set a new back ground color Zoom In Zoom Out cis 5 Scales the entire Sculptor scene Center Mode If center mode is enabled the rotations are applied around the center of the document this is the default If the mode is disabled the ro tations are relative to the mouse point or the coordinate of the input device tracking device etc Orthographic Projection E Switches between perspective projection default and ortho graphic projection The following example shows the same system first in perspective projection and then in orthographic projection Show 3D Coordinate System Turns the coordinate system on or off Show 3D Cursor Turns the 3D cursor on or off High Contrast Palette The coloring of the molecular structures is based on a standard palette properties of the structure for example the b factor chain ID etc are mapped to a color using a palette With the menu item one can switch between a high and low con trast palette If the high contrast palette is selected adjacent values are mapped onto very dif
42. teLaplacian Desc Create a laplacian kernel volume 3x3x3 Param None Usage kernel createLaplacian Set Get Position Name xX y Z Desc Set get the x y z coordinate of the position of the map If no parameter is given the function just returns a num ber otherwise it will set the x y z coordinate using the parameter provided by the user Param Set functions Coordinate in Angstroem Usage vol x 15 0 print vol x vol y 5 0 print vol yQ vol z 1 0 print vol z Examples Hello World print This is a very simple Sculptor script print Sculptor version sculptor version Animation mat sculptor getTrans for j 1 10 do mat rotate 0 1 sculptor setTrans mat sculptor redraw sculptor sleep 20 end Number of atoms mol_A sculptor getDoc 2 mol_B molecule new mol print Mol_A mol_A size print Mol_B mol_B size Save a screenshot sculptor saveScreenshot tmp test png os execute display tmp test png This can be easily combined with the animation script above to create a movie In that case one would use a movie encoder like ffmpeg in the os execute command to create the final movie file Creation of a synthetic cryo EM map and cut out a spherical region sculptor clearLog sculptor delAl1Docs sculptor load monomer pdb mol_a sculptor getDoc 2 vol_a mol_a blur 3 0 10 0 vol_a cutSphe
43. the other hand as mentioned above Sculptor is implemented in C and the scripting language is used by users and collaborators to write small external routines and short scripts For Sculptor it is therefore important that the language can be embedded seamlessly into the main application that it does not create any problems when it is ported to other plat forms and that it does not create any links to external libraries Lua is ideal in this respect as it is very compact and stable Lua is fully em bedded into Sculptor and does not rely on any other operating system components or external libraries Sculptor version 1 3 and above features an embedded Lua interpreter which is used as scripting language See http www lua org for more informa tion Sculptor itself is fully implemented in C Why Lua The following text from http www lua org about html summarizes important properties of the Lua scripting language and thereby indi rectly provides some additional reasons why we chose Lua over other alternatives What is Lua Lua is a powerful fast lightweight embeddable scripting language Lua combines simple procedural syntax with pow erful data description constructs based on associative arrays and exten sible semantics Lua is dynamically typed runs by interpreting byte code for a register based virtual machine and has automatic memory management with incremental garbage collection making it ideal for configuration script
44. ument Name Desc Param Usage delDoc Deletes a document from the main program This is equiv alent to clicking on Data gt Close or clicking on the little trash can icon Index of the document First document is the Sculptor scene so the first document loaded by the user is index 2 sculptor delDoc 2 Delete all documents Name Desc Param Usage delAllDocs Delete all documents in the main program None sculptor delAllDocs Get the sculptor version number Name version Desc Returns a string with the version number Param None Usage print sculptor version Print the current svt tree Name printTree Desc Prints the internal svt tree to the log window This function is only useful for internal debugging Param None Usage sculptor printTree Make a document visible Name show Doc Desc This function makes a document visible and is equivalent to clicking on the eye symbol Param Number of document Usage sculptor showDoc 2 Hide a document Name hideDoc Desc This function makes a document invisible and is equivalent to clicking on the eye symbol Param Number of document Usage sculptor hideDoc 2 Redraw of the 3D window Name redraw Desc This function triggers a redraw of the 3D window Param None Usage sculptor redraw Sleep Name sleep Desc Lets sculptor sleep for a certain number of milliseconds
45. w 10 10 10 SCULPTOR The Sculptor class encapsulates the main application program and al lows the user to load and retrieve documents and to make global ad justments to the program Load a file Name load Desc Loads a file into the main application This function call is equivalent to clicking on File gt Load in the graphical user interface The extension of the file will be used to de termine the file type e g in case of file pdb Sculptor will attempt to load the file as an atomic model The loaded file will appear in the document list just like any other file loaded interactively through the main user interface Param String with the filename Usage sculptor load test pdb Save the sculptor state Name save Desc Saves the state of the Sculptor program in a scl state file Param String with the filename Usage sculptor save current scl Get the number of currently loaded documents Name numDoc Desc Returns the number of currently loaded files existing documents in Sculptor Param None Usage num sculptor numDoc Get a document Name Desc Param Usage getDoc Retrieves a document from the main applications and re turns it either as a volume or molecule object to the Lua program Index of the document First document is the Sculptor scene so the first document loaded by the user is index 2 mol sculptor getDoc 2 Delete a doc
46. zation G Greiner J Hornegger H Niemann M Stamminger Editors 2005 pp 311 318 amp 516 IOS Press Netherlands ISBN 1 58603 569 X e Stefan Birmanns Maik Boltes Herwig Zilken and Willy Wriggers Adaptive Visuo Haptic Rendering for Hybrid Modeling of Macromolecular Assemblies In Proceedings Mechatronics and Robotics P Drews Editor 2004 Vol 4 pp 1351 1356 Eysoldt Verlag Germany ISBN 3 938153 30 X e Stefan Birmanns and Willy Wriggers Interactive Fitting Augmented by Force Feedback and Virtual Reality J Struct Biol 2003 Vol 144 pp 123 131 Contents Sculptor 5 Visualization 19 The Sculptor Scripting Interface 21 NOTE For the latest information see the online tutorials and online documentation Sculptor Concept Graphical User Interface Main Window The Sculptor window is partitioned into two columns with the left column showing the current list of loaded documents and their prop erties whereas the right column is reserved for the 3D and text output The columns are separated with thin dividers that can be moved to ad just the size of the different areas of the GUI They can also be used to completely collapse sub elements which is useful to maximize the space for the 3D window Of course the collapsed elements can be brought back by moving the divider again Document Window The document window maintains a list of all loaded data sets It is D sculptor scene also the m
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