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110 Chapter 11: Command Syntax Table 11.11. Keywords for the sta program. Keyword syntax Description QUERY_NAME name Name of the query sequence. QUERY_FILE filename File name of the query sequence in FASTA format. FORMAT string Alignment file format. Default is Maestro. Set to dev for plain text format—see page 111 for an example. BGNRES n The first residue of the query that is used in alignment. Default: 1. ENDRES n The last residue of the query sequence that is used. Default: the last residue of the original query sequence. PREDSS[_i] filename Secondary structure prediction file of the query sequence, in CASP format. One occurrence of this keyword is required for each file, and there must be at least one SSP file specified. If only one prediction is used, the keyword is PREDSS; if more predictions are used, the keyword is suffixed with an index i, starting from zero: PREDSS_0, PREDSS_1, and so on. For an example of CASP format, see page 93. TEMPLATE_PDB filename Filename of the template structure, in PDB format. MODE string Optional. Needed in the input file only when there are user-specified constraints. In that case, the value is set to user. PAIR pair-list Optional. User-specified residue pairing, used only when MODE is set to user. All the residue pairs can be added after the keyword in one or multiple lines. For example, the following lines pair residue 12, 20, 60 from the query sequence with residue 15, 24, 65 from the template. MODE user PAIR 12 15 20 24 PAIR 60 65 GAP gap-list Optional. User-specified gaps, used only when MODE is set to user. Can be used with or without PAIR. Gaps are specified by the residues in either query (P) or template (T) that are aligned with them. For example, the following opens gaps against query residue 10, 11, template residue 34 and 35. MODE user GAP P10 P11 T34 T35 • Template PDB file—Template structure file, in PDB format. The sequence used for the template is taken from SEQRES lines in the PDB file. If SEQRES is not found in the PDB file, the template sequence is then taken from ATOM records. • Output alignment file—File named jobname.out containing pairwise alignment between the query and the template. By default, the alignment is in Maestro format. To generate plain text format, include FORMAT dev in the command input file. In plain text format, Prime 2.1 User Manual
Chapter 11: Command Syntax aligned residues from the query and the template are placed on top of each other—see below for an example. • Log file—File named jobname.logcontaining progress of the sta program, including warnings and error messages. Return Value and Errors sta returns 0 for success and non-zero for failure. In case of failure, check the log file for details, and search for ERROR. To further analyze the failure, use the -DEBUG option when you run sta. Examples Below is an example input file, where query_seq.fasta stores the query sequence in FASTA format. QUERY_NAME query QUERY_FILE query_seq.fasta PREDSS_0 query-ssp1.casp PREDSS_1 query-ssp2.casp PREDSS_3 query-ssp3.casp BGNRES 1 ENDRES 149 TEMPLATE_PDB pdb1vpe.ent Below is an example of the plain text format for output alignment files. This format is generated when you include ALIFORMAT dev in the command input file. probe length=70======tmplt_T0281_d1dq3a2 length=79 TotalScore= 42 SEQ= -4 SSTR= 102 SEQID= 0.061538 nali= 65 probe bgnRes=1 endRes=70 template bgnRes=3 endRes=75 ProbeAA: ..MWMPPRPEEVARKLRRLGFVERMAKGGHRLYTHPDGRIVVVPFH...SGELP....KG ProbeSS: LLLLLLHHHHHHHHHHLLLEEEEELLLEEEEELLLLLEEEeLLL LLLLL HH Fold AA: GNFGLPLNFNAFKEWASEYGVEFKTNGSQTIAIIND...ERISLGQWHTRNRVSKAVLVK Fold SS: LLLEELLLHHHHHHHHHLLLLEEEEELLEEEEEELL EEEELLLHHHHLLEEHHHHHH ProbeAA: TFKRILRDAGLTEEEFHNL.... ProbeSS: HHHHHHHHhLLLHHHHHLL Fold AA: MLRKLYEATK.DEEVKRMLHLIE Fold SS: HHHHHHHHHL LHHHHHHHHHHL The file contains header information at the top, then in the alignment section, the query sequence (ProbeAA), query composite secondary structure (ProbeSS), template sequence (Fold AA) and template secondary structure (Fold SS) are given. Gaps are denoted by periods in the sequences and by spaces in the secondary structures. Prime 2.1 User Manual 111
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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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Chapter 2: Using Prime-Structure Pr
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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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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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7.2 Using the Refinement Panel Chap
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2. Click New Membrane (Auto-Place).
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Page 143 and 144: Getting Help If Maestro fails, an e
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