Prime User Manual - ISP

Table 3.1. Homologs table data
Column Header Description
Chapter 3: Prime–Structure Prediction: Initial Steps
ID The PDB ID code, including chain name. If a chain name is specified, then
the chain, not the entire protein, is the potential template.
Name Sequence name provided by BLAST.
Score BLAST bit score.
Expect BLAST expectation value.
Identities (%) Percentage of residues that are identical between the sequences.
Positives (%) Percentage of residues that are positive matches according to the similarity
matrix selected in the Options dialog (default matrix is BLOSUM62).
Gaps (%) Percentage of gaps in both query and homolog as returned by BLAST.
Title From the PDB TITLE field.
Compound From the PDB COMPND field.
Source From the PDB SOURCE field.
Experiment From the PDB EXPDTA field. This gives the experimental technique used
to obtain the structure, e.g., X-RAY DIFFRACTION or NMR.
Resolution From the PDB REMARK2 record, where applicable.
Ligands/Cofactors From the PDB HET records: hetID (three alphanumeric characters) and
name for each HET group.
Warning A warning appears in this column for sequences that may be unusable for
model building. See Section D.2.2, for a list of warnings.
3.2.5 Multiple Templates and Structure Alignment
To select more than one template for building, hold down the CTRL key and select another
homolog in the table, or hold down the SHIFT key and select a set of homologs. If more than
one template is selected, they will need to be structurally aligned, that is, rotated to bring them
into a common reference frame, before they can be used in the next step.
• If you have already created a file with structurally aligned multiple templates, import it
using the Import button, as described in Section 3.2.1.
• If you have not yet performed structural alignment on the selected templates, click the
Align Structures button.
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