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ICM Graphical User Interface Guide v.3.0by Ruben Abagyan, Andrew Orry, Eugene Raush, Levon Budagyan, and Maxim Totrov
Copyright © 2007

Mar 18 2008

Table of contents

1 Introduction1.1 ICM Specifications and Recomendations1.2 Products and Features1.3 Requesting an ICM license and Installation2 Graphical User Interface Overview - RECOMMENDED READING FOR NEW ICM USERS2.1  How to load a PDB Structure2.2  How to Move a Structure in the Graphical Display2.3  How to Make Selections2.4  How to Change the Selection Level and Mode2.5  How to Check What is Selected2.6  How to use the ICM Workspace Panel2.7  How to Display a Molecule2.8  How to Change Protein Representation2.9  How to Color2.10 How to Save an ICM Object2.11 How to Save an an ICM Project File2.12 How to Manage the GUI Windows2.13 GUI Helpful Tips2.14 Quick Start: Sequences and Alignments2.15 Quick Start: Protein Structure2.16 Quick Start: Cheminformatics3 File Menu3.1  New3.2  Open3.3  Extract from ICB3.4  Load3.5  Save Project3.6  Save Project As3.7  Quick Image3.8  Write Image3.9  Preferences3.10 Recent Files3.11 Recent PDB Codes3.12 Quit4 Graphics Move Tools4.1 Keyboard and Mouse Shortcuts4.2 Move Buttons5 Display Tab5.1 Display and Undisplay Hydrogens5.2 Structure Representation5.3 Hydrogen Bonding5.4 Coloring5.5 Labeling5.6 Displaying Tethers5.7 Displaying Distance Restraints5.8 Superimpose5.9 Display Clash6 Light Tab7 Labels Tab7.1 Customized Label 2D or 3D7.2 Displaying Distances7.3 (Un)display Origin8 PDB Search Tab8.1 Searching the PDB8.2 Finding a PDB Structure8.3 Querying PDB by Keyword or PDB Code8.4 Querying PDB by Sequence Pattern8.5 Sensitive PDB Similarity Searches8.6 Working with PDB Search Results8.7 Converting PDB Files Into ICM Objects9 Meshes Tab9.1 Surfaces9.2 Meshes and Macroshape10 View Menu and Tools10.1  Undisplay All10.2  Clear-Display-and-Planes10.3  Selection Level10.4  Selection Mode10.5  Fog10.6  Side-by-Side Stereo10.7  Hardware Stereo10.8  Full Screen10.9  Perspective10.10 Full Scene Antialias10.11 High Quality10.12 Easy Rotate10.13 Shadows10.14 Animate View10.15 Drag Res Labels10.16 Antialias Lines10.17 Color Background10.18 Save Viewpoint10.19 Center10.20 Macro Shape10.21 Select by Purple 3D Box10.22 Clipping Tools10.23 Mesh Clipping11 Making Selections11.1 Graphical Selections11.2 Workspace Selections11.3 Selecting Neighbors11.4 Alignment and Table Selections11.5 Making Links12 Working with Tables12.1 Standard ICM Tables12.2 Molecular Tables12.3 Plotting Table Data12.4 Principal Component Analysis12.5 Learn and Predict12.6 Cluster13 Working with Sequences13.1 Load Sequence13.2 Sequence Alignments14 Bioinfo Menu14.1  Residue Content14.2  Predict Secondary Structure14.3  Six Frame Translation14.4  Set Sequence Type14.5  Align Two Sequences14.6  Sequence Structure Alignment14.7  Align DNA vs Protein14.8  Multiple Sequence Alignment14.9  Link to Structure14.10 Extraxt Sub-Alignment As Is14.11 Cut Vertical Alignment Block14.12 Reorder Sequences14.13 Extract Unique Sequences14.14 Search and Align15 Tools Menu - Xray15.1 Crystallographic Neighbor15.2 Crystallographic Cell15.3 Biomolecule Generator15.4 Get Electron Density Map15.5 Map's Original Cell15.6 Contour Electron Density Map15.7 Convert Xray Density to Grid16 Tools Menu - 3D Predict16.1 Assign Helices and Strands16.2 Protein Health16.3 Local Flexibility16.4 Protein Interface by ODA16.5 icmPocketFinder17 Tools Menu - Analysis17.1 RMSD17.2 Contact Areas17.3 Closed Cavities17.4 Surface Area17.5 Distance17.6 Planar Angle17.7 Dihedral Angle17.8 Ramachandran Plot18 Tools Menu - Superimpose18.1 Display and Select Proteins for Superposition18.2 Proteins by 3D18.3 Multiple Proteins18.4 Arrange as Grid19 Homology Menu and Modelling Tools19.1 Homology Modeling Introduction19.2 Build Model19.3 Display Loops19.4 Loop Modeling19.5 Regularization19.6 Refine Side Chains19.7 Making a disulfide bond.20 Working with Chemistry Tools20.1 Reading Chemical Structures20.2 Working with Chemical Spreadsheets.20.3 Molecular Editor20.4 Saving Chemical Structures and Images21 Chemistry Menu21.1  Calculate Properties21.2  Standardize Table21.3  Build Prediction Model21.4  Predict21.5  Convert Smiles to 2D21.6  Convert Structure to Smiles21.7  2D Depiction21.8  Convert to 3D21.9  Generate 3D Conformers21.10 Generate Tautomers21.11 Convert to Racemic21.12 Generate Stereoismers21.13 Align/Color by 2D Scaffold21.14 Cluster Set21.15 Compare Two Sets21.16 Merge Two Sets21.17 Sort Table21.18 Select Duplicates21.19 Enumerate by Markush21.20 R-Group Decomposition21.21 Enumerate by Reaction21.22 Superposition21.23 Chemical Search21.24 Pharmacophore Drawing and Searching21.25 Find and Replace21.26 Generating Chemical Fragments21.27 Molcart22 Docking22.1 Small Molecule Docking22.2 Flexible Receptor Docking and Multiple Receptor Conformations22.3 Template Docking22.4 Virtual Ligand Screening22.5 ICM X-Ray AutoFit - Automated Model Building into Density22.6 Protein-Protein Docking23 Making Molecular Animations, Slides, and Documents23.1 Molecular Animations and Transitions23.2 Making Molecular Slides23.3 Making Molecular Documents24 Movie Making24.1 Movie Making Options24.2 Screen-grabbing Movie24.3 View-Defined Movie Making25 Frequently Asked Questions25.1 FAQ Installation25.2 FAQ Hardware25.3 FAQ Graphics and Display25.4 FAQ Structure25.5 FAQ-Docking25.6 FAQ-Cheminformatics25.7 FAQ-Simulations25.8 FAQ-Script25.9 Troubleshooting26 Tutorial - Working with the Graphical Display26.1 Getting Started26.2 Making Graphical Selections26.3 Making Sequence Selections in the ICM Workspace26.4 Making a Spherical Selection.26.5 Filtering a Selection.26.6 Propogating a selection to all atoms in a residue.26.7 Coloring and Molecule Representations26.8 Labeling and Annotation27 Tutorial - Molecular Documents27.1 Making a Molecular Document27.2 How to Incorporate Tranistion Effects Between Slides28 Tutorial - Working with PDB Protein Structures28.1 PDB Searching28.2 Converting a PDB File into an ICM Object28.3 PDB Preparation - Symmetry28.4 PDB Preparation - Occupancy and B-Factors29 Tutorial - Working with Sequences and Alignments29.1 Pairwise Alignments29.2 Sequence Drag and Drop and the Alignment Editor29.3 Multiple Sequence Alignments29.4 Boxing Shading and Annotating an Alignment30 Tutorial - Ligand Binding Pocket Analysis Examples30.1 Displaying only the residues that surround the ligand binding pocket.30.2 Displaying the sequence conservation around the ligand binding site.30.3 Displaying hydrogen bonds between a ligand and receptor.31 Tutorial - Homology Modeling and Structure Analysis Tools31.1 Homology Modeling31.2 Making an amino acid mutation31.3 Protein Health31.4 Superimpose Structures32 Tutorial - Crystallographic Analysis Tools32.1 Crystallographic Symmetry32.2 Biomolecule Generator33 Tutorial - Working with Chemical Tables33.1 Reading and Displaying Chemical Structures33.2 Adding more information (Columns) to a Chemical Table33.3 Creating a grid view with multiple columns.33.4 Sorting a table column33.5 Filtering the table by the values contained within a column.33.6 Renaming a Column and Adding Data.34 Tutorial - Working with the Molecular Editor34.1 Draw Chemical34.2 Edit Chemical35 Tutorial - Chemical Searching35.1 Chemical Similarity Searching35.2 Advanced Chemical Similarity Searching35.3 3D Pharmacophore Searching35.4 2D Pharmacophore Searching36 Tutorial - Docking and Virtual Ligand Screening36.1 Re-Dock Biotin to the Streptavidin Receptor36.2 Re-Dock an Inhibitor to Ricin Crystal Structure36.3 Virtual Ligand Screening to Ricin Receptor36.4 Virtual Ligand Screening to Cyclooxygenase36.5 Docking a Markush Library36.6 Multiple Receptor Conformation Ensemble Docking Example

[ 本帖最后由 downsea 于 08-3-31 15:32 编辑 ]

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