Prime User Manual - ISP

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106 Chapter 11: Command Syntax Note that the actual 3D coordinates of the superposed structures are not written out by default You must use ALISTRUCS_OUTFILE to write out the structures. The following input file (align.inp): QUERY_FILE query.pdb TEMPLATE template.pdb ALISTRUCS_OUTFILE superposition.pdb saves the 3D coordinates of the aligned structures in the file superposition.pdb. The following is a sample input file for database creation in dbcreate mode: MODE dbcreate FILELIST filelist.dat DBNAME mydatabase.dat The file filelist.dat contains the file names for the templates, including the path, as follows: /scr/templates/template-1.pdb /scr/templates/template-2.pdb /scr/templates/template-3.pdb /scr/templates/template-4.pdb A minimal input file for a scan is as follows: MODE scan QUERY_FILE query.pdb Running ska with this input file would scan the database supplied with Prime for structural analogs. The output from the structural search contains pairwise alignments between the query structure and every structure in the database (assuming the two structures are sufficiently similar). The results can be analyzed in a more convenient way with the graphical SKA Results Viewer utility, $SCHRODINGER/utilities/SkaResultsViewer. The use of the optional name argument is illustrated next. For the following input file: QUERY_FILE query.pdb 1ctf TEMPLATE 1dd3_A.pdb the output file is as follows: .........+.........+.........+.........+.........+.........+..... 1ctf 1 ceeeeeecc 1dd3_A 1 cchhhhhhhhhhhchhhhhhhhhhhhhhhcccchhhhhhhhhhhhhhhhhhhhhhccceeeeeecc 1ctf 1 ---------------------------------------------------------EFDVILKAA 1dd3_A 1 MTIDEIIEAIEKLTVSELAELVKKLEDKFGVTAAAPVAVAAAPVAGAAAGAAQEEKTEFDVVLKSF Prime 2.1 User Manual
Chapter 11: Command Syntax ..........+.........+.........+.........+.........+.........+. 1ctf 62 ccchhhhhhhhhhhhccchhhhhhhhhhc c eeeeeccchhhhhhhhhhhhhhcceeeee 1dd3_A 67 ccchhhhhhhhhhhhcchhhhhhhhhhhcccccccceeccchhhhhhhhhhhhhhcceeeee 1ctf 62 GANKVAVIKAVRGATGLGLKEAKDLVESA-P--AALKEGVSKDDAEALKKALEEAGAEVEVK 1dd3_A 67 GQNKIQVIKVVREITGLGLKEAKDLVEKAGSPDAVIKSGVSKEEAEEIKKKLEEAGAEVELK RMSD: 0.763733 PSD: 0.024524 Without the name argument for the QUERY_FILE keyword, the output would be .........+.........+.........+.........+.........+.........+..... query 1 ceeeeeecc 1dd3_A 1 cchhhhhhhhhhhchhhhhhhhhhhhhhhcccchhhhhhhhhhhhhhhhhhhhhhccceeeeeecc query 1 ---------------------------------------------------------EFDVILKAA 1dd3_A 1 MTIDEIIEAIEKLTVSELAELVKKLEDKFGVTAAAPVAVAAAPVAGAAAGAAQEEKTEFDVVLKSF ..........+.........+.........+.........+.........+.........+. query 62 ccchhhhhhhhhhhhccchhhhhhhhhhc c eeeeeccchhhhhhhhhhhhhhcceeeee 1dd3_A 67 ccchhhhhhhhhhhhcchhhhhhhhhhhcccccccceeccchhhhhhhhhhhhhhcceeeee query 62 GANKVAVIKAVRGATGLGLKEAKDLVESA-P--AALKEGVSKDDAEALKKALEEAGAEVEVK 1dd3_A 67 GQNKIQVIKVVREITGLGLKEAKDLVEKAGSPDAVIKSGVSKEEAEEIKKKLEEAGAEVELK RMSD: 0.763733 PSD: 0.024524 11.7 ssp—Secondary Structure Prediction The ssp script provides an interface to the secondary structure prediction programs SSPro, which is bundled with Prime, as well as PSIPRED, which is available from a third party. Syntax $SCHRODINGER/ssp [options] jobname By default the input is read from the file jobname.inp and the output is written to jobname.out. Options The standard Job Control command line options listed in Table 11.1 are accepted. There are no options specific to this program. Prime 2.1 User Manual 107
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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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Contents 11.7 ssp—Secondary Struc
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Document Conventions In addition to
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Prime User Manual Chapter 1: Introd
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1.3 Running Schrödinger Software C
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Prime User Manual Chapter 2: Using
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Chapter 2: Using Prime-Structure Pr
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Guide Chapter 2: Using Prime-Struct
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To identify a family for the query
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Table 3.1. Homologs table data Colu
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Chapter 3: Prime-Structure Predicti
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Prime User Manual Chapter 4 Chapter
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4.3 Initial and Imported Alignments
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Chapter 4: Comparative Modeling: Ed
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4.5.2 Align Program Technical Detai
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Prime User Manual Chapter 5 Chapter
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Prime User Manual Chapter 6: Fold R
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Figure 6.2. The Fold Recognition pa
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Figure 6.3. The Fold Recognition-Op
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Chapter 6: Fold Recognition potenti
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Chapter 7: Prime-Refinement If your
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Page 89 and 90: Chapter 9: Docking Covalently Bound
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Page 97 and 98: Table 11.2. Keywords for the blast
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Page 115: Table 11.8. Keywords syntax for ska
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Page 143 and 144: Getting Help If Maestro fails, an e
Page 145 and 146: Prime User Manual Glossary Chapter
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Page 149 and 150: K killing jobs ....................
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