Select all residues of the current layer. Use the
"Shift" key to select all residues of each layer.
Deselect all residues of the current layer. Use the
"Shift" key to deselect all residues of each layer.
- Inverse Selection
Simply inverses the selection. Handy if you want to
select all residues but nonpolar ones (for example).
First Select non polar residues, then inverse the
- Extend to other layers
This is typically used when a structural alignement
has been computed. It lets you select some residues in
one layer, and automatically select their counterpart in
other layers. Might be handy to compare active sites of
- Pick on screen
Lets you pick residues you want to select directly
form the screen. All you need to do is click on any atom
of a residue. When you have picked all the residues you
wanted to select, just hit the "esc" key. Note that you
can add the picked residues to the previous selection by
maintaining the "Control" key down while invoking this
Note: This command will only let you select residues of
the current layer. This is useful when two residues of
separate layers are exactly superposed, because only the
residue of the current layer will be selected. No
confusion is possible.
- Group Kind
This submenu lets you select residues by type
(individual amino acid, nucleotide, hetatm, disulphide
This will select Asp and Glu.
This will select Arg Lys and His.
This will select Asn Gln Ser Thr and Tyr
- non Polar
This will select Ala Cys Gly Ile Leu Met Phe Pro Trp
- Helices, Strands, Colis
Select all the corresponding secondary structure
- Visible Groups
Select the residues currently visible. It does take
into account the slab mode, and will not only select
groups that have a show mark in the Control Panel.
- Reconstructed aa
Select residues whose sidechain has been
reconstructed. Remember that incomplete pdb files are
completed upon loading. Usually, reconstructed sidechains
lay at the surface and are highly mobile.
- Neighbours of selected aa
This will let you extend a selection aroud a
previously selection. For example it can be used to
select strands that are forming a beta sheet. First,
select a single beta strand, then invoke this command and
type 4 angstroms. As soon as an atom lays within 4
angstroms of any atom of the current selection, its
corresponding residue will be selected. Then, if you hit
the "return" key, only selected groups will be displayed,
and you will see the contiguous strands.
- Groups close to an other chain
This is useful when you want to focus your attention
on residues at the interface of two chains. Handy to
inspect how dimers or multimers are bound to each other.
- Groups close to an other layer
Some people prefer to have chains loaded in separate
layers, and this will let you do the same as the previous
command. This can also be useful to inspect crystalline
contacts after having built the crystallographic
- accessible aa
Selects residues with more that a certain surface
accessible. See the color by
accessibility menu to get more infos on the subject.
- Groups with same color as
This will let you pick a residue on screen, and wiull
select all residues that have the same color. For
example, lets imagine you want to change all red residues
to yellow. Pick a red residue, then click on the "color"
text of the control Panel header, and pick a yellow color
in the color wheel.
- Iterative Magic Fit
Same as before, but the fitting will be even better,
and the structural alignment will be automatically
updated. Depending on the option you choose in the
dialog, CA or backbone RMS deviation will be minimized.
This is equivalent to several rounds of "Improve Fit".
This will generate a structural alignment for the fitted
molecule, but will also disrupt the structural alignment
of other layers, and you might have to regenerate them.
- aa identical to ref.
Presuppose that a structural alignment has been
computed. Then you can invoke this command to select
residues that are strictly conserved between the current
layer and the refgerence protein (the first loaded).
- aa similar to ref.
Same as before,will select conserved residues. The
PAM200 matrix will be used, and the minimum score needed
to be considered similar can be modified in the
"Alignment" Preferences. Decreasing this stringency value
will increase the number of amino-acids considered as
- non Trans aa
This will select residues whose omega angle (peptidic
bond) is below a certain angle. Typically residues are
trans (around 178 deg.) This lets you select distorted
residues or look at cis residues.
- aa with phi/psi out of core regions
Residues in a peptidic chain can only adopt certain
conformations. This will let you
select residues that lay out of the "core" region (the
region where most of the residue should lay).
- aa with phi/psi out of allowed regions
Same but for allowed regions. Few residues (excetp Gly
that lack a sidechain) should lay in out of the allowed
- aa matching ref. structure
Allows to select residues whose backbone has a rms
deviation to the reference structure inferior or equal to
a certain threshold.
- aa making clashes
Residues with atoms too close to atoms of other
residues will be selected.
- aa making clashes with backbone
Same as before, but only groups with at least one atom
too close to the backbone of an other group will be