Prime User Manual - ISP

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12 Chapter 2: Using Prime–Structure Prediction Font Size The font size of letters and numbers in the sequence viewer can be changed using this option. The font size options are: • Small • Medium • Large • Huge View Structure The options for showing structures in the Maestro Workspace include: • All • None • Predicted Only View SSA This option controls whether secondary structure assignments are shown in the sequence viewer. The default is not to show secondary structure assignments. Legend Choose this menu option to open the Legend panel, which includes the assignment of each color and symbol used in each color scheme and sequence representation. Click the Colors tab and select a Color scheme from the list, or click the Symbols tab and select a type of Sequence data, such as Pfam/HMMER or SSP. This option is also available when you right-click on a sequence in the sequence viewer. Preferences Choose this Display menu option to open the Proximity dialog box: • Proximity cutoff: The value entered in this text box defines proximity for the Proximity color scheme. The default is 4.00 Å. 2.3.4 The Step Menu The Step menu provides another way to navigate between steps in Prime. It includes the following options: Prime 2.1 User Manual
Guide Chapter 2: Using Prime–Structure Prediction When this check box is selected, the Prime Guide is displayed (the default). Deselect the check box to hide the Guide. Input Sequence Click this option to go to the Input Sequence step. Find Homologs Click this option to go to the Find Homologs step. There is an option to click to go to each step in Prime–SP. A red diamond is displayed next to the option to go to the current step. Options to go to steps that are not available are dimmed. 2.4 The Prime Toolbar The Prime toolbar is the row of buttons just under the Prime menu bar. The Prime toolbar provides convenient access to commonly used Prime tasks. Pause the mouse over a button to see its description. These task modes are also available as options in the Edit and Display menus. The toolbar buttons are shown below as they appear on the toolbar, with their names and functions. Select (Edit menu): Select a region of the sequence to see the corresponding residues highlighted in the 3D Workspace. Crop (Edit menu): The cropping tool, which can be used in the Build Structure step to select ends of the query sequence that are not to be used for building. Edit SSP (Edit menu): Edit secondary structure predictions. Highlight a region of the SSP, and then type either H for α-helix, E for β-strand, or - for loop. Set Template Regions (Edit menu): If more than one template was selected in the Find Homologs step, use this button in the Build Structure step to proceed to the mode that allows selection of template regions for building. Slide Freely (Edit menu): Use this button to edit the alignment between query and template. Selecting a residue and sliding to the right creates N-terminal gaps. Selecting a residue and sliding to the left creates C-terminal gaps. Slide As Block (Edit menu): Use this button to edit the alignment between query and template. Selecting a residue and sliding to the right creates N-terminal gaps. Selecting a residue and sliding to the left slides all residues as a block to the left. Prime 2.1 User Manual 13
Page 1 and 2: Prime User Manual Prime 2.1 User Ma
Page 3 and 4: Contents Document Conventions .....
Page 5 and 6: Contents 5.3 Running the Build Stru
Page 7 and 8: Contents 11.7 ssp—Secondary Struc
Page 9 and 10: Document Conventions In addition to
Page 11 and 12: Prime User Manual Chapter 1: Introd
Page 13 and 14: 1.3 Running Schrödinger Software C
Page 15 and 16: Prime User Manual Chapter 2: Using
Page 17 and 18: Chapter 2: Using Prime-Structure Pr
Page 21: Chapter 2: Using Prime-Structure Pr
Page 27 and 28: Prime User Manual Chapter 3: Prime-
Page 29 and 30: 3.2 Find Homologs Step Chapter 3: P
Page 31 and 32: To identify a family for the query
Page 33 and 34: Table 3.1. Homologs table data Colu
Page 35 and 36: Chapter 3: Prime-Structure Predicti
Page 37 and 38: Prime User Manual Chapter 4 Chapter
Page 39 and 40: 4.3 Initial and Imported Alignments
Page 41 and 42: Chapter 4: Comparative Modeling: Ed
Page 43 and 44: 4.5.2 Align Program Technical Detai
Page 45 and 46: Prime User Manual Chapter 5 Chapter
Page 47 and 48: Chapter 5: Comparative Modeling: Bu
Page 53 and 54: Prime User Manual Chapter 6: Fold R
Page 55 and 56: Figure 6.2. The Fold Recognition pa
Page 57 and 58: Figure 6.3. The Fold Recognition-Op
Page 59 and 60: Chapter 6: Fold Recognition potenti
Page 61 and 62: Prime User Manual Chapter 7: Prime-
Page 63 and 64: Chapter 7: Prime-Refinement If your
Page 65 and 66: 7.2 Using the Refinement Panel Chap
Page 67 and 68: 2. Click New Membrane (Auto-Place).
Page 69 and 70: Figure 7.3. The Refine loops task i
Page 71 and 72: Chapter 7: Prime-Refinement Figure
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Figure 7.6. The Structure Refinemen
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Chapter 7: Prime-Refinement The tex
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Chapter 7: Prime-Refinement ment, w
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7.11 Output of Refinement Jobs Chap
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Prime User Manual Chapter 8: Maestr
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Alignment Section Chapter 8: Maestr
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Chapter 8: Maestro Protein Structur
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Prime User Manual Chapter 9: Dockin
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Chapter 9: Docking Covalently Bound
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Prime User Manual Chapter 10: Prime
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Table 10.1. Options for the prime_m
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Prime User Manual Chapter 11: Comma
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Table 11.2. Keywords for the blast
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Table 11.3. Keywords for the bldstr
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Chapter 11: Command Syntax The alig
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Chapter 11: Command Syntax • Outp
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Table 11.5. Keywords for the multir
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Chapter 11: Command Syntax It is no
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Table 11.6. General keywords for th
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Table 11.7. Protocol-specific keywo
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SKA has difficulty aligning to mult
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Table 11.8. Keywords syntax for ska
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Chapter 11: Command Syntax ........
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Chapter 11: Command Syntax The foll
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Chapter 11: Command Syntax aligned
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Files Chapter 11: Command Syntax In
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Prime User Manual Chapter 12: Comma
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Table 12.1. Keywords for the seqcon
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Chapter 12: Command-Line Utilities
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Prime User Manual Appendix A: Third
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Prime User Manual Appendix B: Envir
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Prime User Manual Appendix C: File
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Prime User Manual Appendix D: Error
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!UNUSABLE: SEQRES numbering is wron
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Prime User Manual Getting Help Schr
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Getting Help If Maestro fails, an e
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Prime User Manual Glossary Chapter
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Symbols + (plus sign), in Pfam sequ
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K killing jobs ....................
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sequences coloring.................
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