VMD supports selection based on the one-letter amino acid
sequence with the sequence
selection keyword. This allows
selections of the form
sequence APD sequence "C..C" (might be used to pick out zinc fingers) sequence AATCGGATUnlike the other string selection commands which take one of three types of strings, all the strings for
sequence
are taken as
regular expressions (though strings with non-alphanumerics must still
be quoted to get past the input parser). The method works by taking
each of the pfrags and nfrags in turn and constructing the one-letter
amino acid sequence. If a regular expression matches any of the
sequence, the atoms in the matching residues are selected. Multiple
matches are allowed, though they cannot overlap. As is usual with
regular expressions, the largest possible match is made, so take care
with expressions like
C.*C
.
Two useful types of selection mechanisms available in VMD
are:
within <number> of <selection>
and same <keyword> as
<selection>
. The first selects all atoms within the specified
distance (in Å) from a selection, including the selection itself.
Therefore, the command:
within 5 of name FE
selects all atoms within 5 Å of atoms named FE. One common use for this command is to limit the region of atoms shown on the screen. Another is to find atoms that may be involved in interactions. For instance:
protein within 5 of nucleic
finds the protein atoms that are nearby nucleic acids. On a cautionary note, the distance search method is not very efficient, making these selections rather slow. Some selections may be sped up by short circuiting.
The same <keyword> as <selection>
finds all the atoms
which have the same `keyword' as the atoms in the selection. This can
be used for selections like
same fragment as resid 35 \end \noindent which finds all the atoms attached to residue id 35. Any keyword can be used, so selections like \begin{verbatim} same resname as (protein within 5 of nucleic)are fine, although weird. The perhaps the most useful keyword for this command is residue, so you can say same residue as ....
ANNMM is an proposed standard for defining how to get molecular data and how to reconstruct a given viewpoint. It contains a simple selection language which has been incorporated directly into VMD ; partially to support the full ANNMM format, and partially to show how extensible VMD s selection language really is. We will not describe the format here (for more information on ANNMM, see ???) but will give a few examples of use.
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