Structure Window : Select Commands
Pick structures
This dialog allows you to manually select which parts of which structures are
visible. You will see a hierarchical list of all structures (for example, "1BML"),
biopolymer chains in each structure (such as "1BML_C"), and domains
in each chain (like "1BML_C d2"). You can turn each part on and off
by clicking any line to select or deselect that part of the structure - a highlighted
line means that part is visible. (On the Macintosh, you'll need to hold down the
Meta key when clicking.) Because the assembly is hierarchical, if you turn of
a chain, all domains in that chain will also be turned off. Similarly, if you
turn on a domain, the chain that contains that domain will also be turned on.
Show everything
Makes all parts of all structures visible.
Show aligned chains
Shows only chains that contain residues that are in aligned blocks of the current
alignment.
Show aligned domains
Shows only domains that contain residues that are in aligned blocks of the current
alignment. This is convenient to trim down the display when several multi-domain
and/or multi-chain PDB structures are represented in the alignment.
Show aligned residues
Shows only residues that are in aligned blocks of the current alignment. This
is useful for examining the conserved structural core of an alignment.
Unaligned residues
Shows unaligned residues. There are two choices: show all unaligned residues,
or show unaligned residues only in aligned domains. The latter is particularly
useful for examining unconserved loop regions of the structural core.
Show selected domains
Shows only domains that contain selected residues.
Show selected residues
Shows only selected (highlighted) residues.
Select by distance
These functions allow you to highlight residues based on distance between atoms. To use this feature, first select
any number of residues (or solvent or heterogen molecules) in either the structure
or sequence window. Then do Select by Distance and enter a distance cutoff. This will
add
highlights to all biopolymer residues (or all molecules, including heterogens
and solvents) that contain any atom within this distance from any atom in the initially selected
set of residues, based on center-to-center separation. The options checkboxes allow you to choose what types of residues will be selected, and the other option lets you select only residues that are on different molecules from the
initially selected residues (for focussing on intermolecular contacts).
Toggle chain
Brings up a dialog containing all chains of all molecules in the strucure. Selecting one or more chains will cause highlights on every residue of these chains to be toggled on/off.
Select molecule
Select a molecule by either the single-character PDB chain code, or the MMDB molecule integer ID. For individual structures only.