Atom Specification in Chimera versus Midas
While atom specification
is very similar to that in Midas/MidasPlus, there are some significant
differences, which are summarized below.
The differences in atom specification mainly reflect additions
that do not affect the process of adapting a Midas script
for use in Chimera. However, note that in Chimera, chain IDs are specified
differently and mainchain is not accepted as a specifier.
A few Midas/MidasPlus commands are
unsupported by Chimera.
- The three major levels
in the hierarchy (# for model, : for residue,
and @ for atom) can each have
sub-specifications indicated after "."
(submodel, chain ID, and alternate location indicator, respectively). This
is a major improvement, because:
- When multiple MODEL records appear in a single PDB file,
each MODEL can now be specified independently as a submodel
(for example, #0.2 is the second submodel in model 0). In Midas,
the only way to see one structure at a time is to edit the input file.
- One can specify an entire chain without knowing the starting and
ending residue numbers (for example, :.a specificies all of chain A).
- Atoms in alternate locations can be controlled independently.
- Atoms/bonds that are selected in
the graphics window can be designated with the word
selected, sel, or picked.
- The name of a picked
atom is not echoed in the command line (as in the most recent version of
Midas), but entering a plus sign (+) indicates that the plus sign
should be replaced by the specification string of the next
picked atom (similar to an
older version of Midas).
- Selections previously named and saved with
Select... Name Selection
or the command namesel
can be specified using sel=selection_name or just
- One can use names of entries in the following parts of the
Chimera Select menu:
The same pattern of capitalization and spaces, if any, as shown in the
Select menu should be used.
Where there is ambiguity, the parent menu should be included in the
specification, for example, "IDATM type.H" or "element.H" instead of "H" alone.
One can also use the names of custom amino acid categories defined with
and custom categories for surface calculation defined with the
command msms cat (surfcat).
- The word mainchain is not accepted as an atom specification.
- There are several differences in
property (attribute) descriptor
- In Chimera, property descriptors are termed
attributes and are
defined at the atom,
and model levels. Thus,
the attribute indicator slash ("/") must be preceded by the proper symbol
(#, :, or @) depending on what level is being described. The symbol
does not have to precede the slash immediately (for example,
@ca/color=red indicates red atoms named CA). In Midas, all the
properties are atomic, so the symbol before the slash is not required
unless an atom name is also being used. There are more
attributes in Chimera than in Midas.
- When multiple attributes
at the same level are combined in one statement, they must
be separated with and and/or or to indicate intersection
or union, respectively. In Midas, commas indicate intersection
(and for colors only, union) and multiple occurrences of slash indicate
- Not is indicated for yes/no properties with
!descriptor_name, and for multivalued properties with
descriptor_name!=value. In Midas, ! always
precedes the descriptor_name.
- The operators ~ and !~ can be used instead of
= and !=, respectively, to
indicate that the subsequent string should be treated as a
- The descriptor_name is case-sensitive; the
descriptor value, if any, is case-sensitive if specified
with ==, but not if specified with =.
UCSF Computer Graphics Laboratory / January 2007