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48 Chapter 6: Fold Recognition Prime 2.1 User Manual Figure 6.4. The Fold Recognition panel with Search results. While it is possible that the top-ranked template will yield good results, it is recommended that multiple templates be used in model building. By default, the top 25 templates are selected. You can select the desired templates using control-click and shift-click. To sort the templates by properties other than rank, click the appropriate column heading. Optionally, if you have not already searched for the family of the query, you can click Find Family to run HMMER/Pfam. The query family name found, with an E-value in parentheses, appears in the Query family name text box. The sequence viewer shows the match between the query and the consensus sequence of the family, as described in Section 3.2.2 on page 20. Ifa
Chapter 6: Fold Recognition potentially meaningful (E-value under 1) family identification is found, it may help you select different or additional seed templates to bring forward to Build Backbone. To view a template colored by secondary structure, click the check box in the V (Visualization) column. The template appears in the sequence viewer, and its secondary structure can be compared to the SSP profile of the query. Note: The query-template “alignments” that can be visualized in this step are provided only as a guide in identifying seed templates. Gaps or other unfavorable features will not affect the quality of the models built using these templates. 6.4 Evaluating Templates To make use of the seed templates to build a model, they must first be evaluated for their suitability for comparative modeling. The evaluation is done with the use of two scripts. The process involves running an alignment for each template, then running the script to do the evaluation. The first step is to export the SSPs in CASP format (or copy them from the working directory so that they have a .casp extension). It is recommended that you use both SSPs. For each template that you want to use, run the alignment script as follows: $SCHRODINGER/run -FROM psp CMAlign.pl target template seqFile sspFiles The arguments for this command are described in Table 6.1. Table 6.1. Arguments for the CMAlign.pl script. Argument Description target Name of the query sequence. template Name of the template, as shown in the Search table of the Fold Recognition step, including any underscore characters. seqFile Target sequence file. sspFiles CASP formatted secondary structure prediction files (.casp), blank-separated. The alignments are stored in the subdirectory CMAlign. Once you have run CMAlign.pl for each of the desired templates, you can run the evaluation script: cd CMAlign $SCHRODINGER/run -FROM psp checkAlign.pl target Prime 2.1 User Manual 49
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Prime User Manual Prime 2.1 User Ma
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Contents Document Conventions .....
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Contents 5.3 Running the Build Stru
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Page 9 and 10: Document Conventions In addition to
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Page 13 and 14: 1.3 Running Schrödinger Software C
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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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