With Chime, you can use the select commands described here only on web pages which have a command line slot. Most pages which have a command line slot will also have a separate message slot or box. (Most Chime pages on the web don't have a command line slot. However, Chime version 2, unlike RasMol, has an extensive set of select commands on its menu.)

RasMol always has a white command-line window. (On Windows systems, it starts out minimized -- look for it on the task bar in Win95 to open it.) Position the command line window so that even when RasMol's black graphics window is on top, you can see a few lines of the white window below the bottom of the black window. Make sure you can see the bottom of the command-line window since this is where the action occurs.

Select vs. Restrict

Restrict commands select, but hide atoms not selected. All expressions which can be used in select commands can also be used in restrict commands. The command

Atom serial numbers. Every atom in PDB file has a serial number. To find out an atom's serial number, click on it. The serial number is the first number in the report. You can select, for example:

atomno = 131     a single atom atomno = 217, atomno = 1426     two atoms atomno >= 195 and atomno <= 277     a range of atom serial numbers

Rarely, you may get a PDB file lacking atom serial numbers. This will cause bizzare behavior in RasMol and Chime! To fix this, load the PDB file, then save it back to disk from RasMol with the command "save pdb filename", or from Chime with the menu File, Save Molecule As. This will insert serial numbers, but unfortunately will lose all remarks and have other possibly unwanted effects. For complete details, and other methods for adding serial numbers, see the PDB Tools page.

Element names. Type the full element name, not the 2-character symbol. You can select, for example:

magnesium iron, sulfur

Atom PDB names. PDB files name each atom in a standardized way (up to 4 characters). Alpha-carbons are CA, beta-carbons CB, and so forth through CG, CD, CE, CZ, CH (gamma, delta, epsilon, zeta, eta). Other examples are N7 (7th nitrogen in a residue), O2P (second oxygen on a phosphorus), OE2 (second oxygen on an epsilon carbon), HD1 (1st hydrogen on a delta carbon). To find out an atom's PDB name, click on it. Its name is reported as the first word following "Atom:". You can select, for example:

*.cg     all carbons in gamma position lys.cg     all lysine gamma-carbons :a.cg     all gamma-carbons in chain A lys:a.cg     all lysine gamma-carbons in chain A 27-42:a.cg     gamma-carbons in chain A residues 27 through 42 *.h?     all hydrogens with 2-character names *.h???     all hydrogens

Group/Residue names. RasMol uses the broad term group to designate residues or other chemical groups. Here, we'll use the terms group and residue interchangeably.

Each residue in the PDB file is given a name of 1-3 characters in length. All amino acids use the standard 3-letter abbreviations ALA, ASN, ASP, etc. DNA and RNA nucleotides are given residue names A, T, U, G, and C. Other common residue names are HOH (water), NAG (N-acetyl glucosamine), and so forth. Uncommon ligands or moieties may be given nonstandard 3-character residue names. To find out the name of a residue, click on it: the residue name is the word after "Group:" or "Hetero:" in the message report.

Some residue names may contain digits, such as SO3 or PO4. These must be enclosed in square brackets in order to be recognized in select commands, for example "select [so3]".

Calcium or other metals are commonly given 2-character residue names the same as their element symbols, e.g. CA, MN, MG, ZN, etc. Note that in the case of calcium, "select ca" (the "residue" calcium) gives different results from "select *.ca" (all alpha carbons plus calcium). Confusingly, the atom names for both are CA. So in this case, to select only alpha carbons, "select protein and *.ca".

You can select, for example:

lys     all lysines lys:a     all lysines in chain A (lys, arg) and :b     lysines or arginines in chain B a     all adenylate residues in all chains c:d     all cytidylate residues in chain D [po3]     all phosphate residues

Group/Residue numbers Each residue is give a residue number (not to be confused with the serial numbers of the atoms within the residue). Residues numbers are unique within each chain, and within hetero residues. Thus, "select 1" will select residue 1 in each chain plus hetero residue 1. To find out the number of a residue, click on it. The second number in the report is the residue number. You can select, for example:

32     residue 32 in each chain + hetero residue 32 19-32     residues 19-32 in each chain + hetero residues 19-32 19-32 and not hetero     residues 19-32 in each chain 19-32 and hetero     hetero residues 19-32 19-32:y     residues 19-32 in chain Y asp47     aspartates at residue position 47 in all chains having Asp47

Chains. Each polymer chain (polypeptide, nucleic acid, carbohydrate, etc.) has a single character name (letter or digit). In a select command, this character must be prefixed with a colon or an asterisk to signify that the letter represents a chain. Most ATOM records in the PDB file are members of a chain; sometimes all. Whether or not ligands of a chain are given the same letter as the chain to which they bind, a different chain letter, or no chain letter, varies. HETATM (hetero) atom records are considered to be a "chain" only in the sense that they are all assigned the same color by the "color chain" command. To find out what chain an atom belongs to, click on it. You could select:

:d     all atoms in chain D *d     all atoms in chain D :d, :e     all atoms in chains D or E glu:2     all glutamates in chain 2

Predefined terms. Chime and RasMol predefine the following terms which can be used in select commands. The Venn diagram below, kindly contributed by Kurt Giles, is an excellent overview. Below the diagram is a table listing all the terms, hyperlinked to the RasMol Reference Manual -- if you click on these, be patient, it will take while to download (it is 160K bytes). Below the table is a summary of the definitions of the terms which aren't obvious.

Summary definitions of predefined terms (equivalent expressions understood by Chime/Rasmol are in regular print; explanations are in italics):

User-defined terms. You can define arbitrary terms to represent groups of atoms, and then use the terms you have defined in select or restrict commands. The general form for the define command is:

select within(4.5, :h or :l) and :p and not hetero
define neighbors selected

select neighbors and backbone
color [128,0,128] # dark magenta
# select hydrophobic side chains, color gray
select neighbors and not backbone and hydrophobic
color [180,180,180] # gray
# select polar side chains, color magenta
select neighbors and not (backbone or hydrophobic)
color magenta

Within specified distance. The "select within" command is one of the most powerful in RasMol. The format is

The semi-automated Noncovalent Bond Finder exploits the select within command as its core operation.

Further Information

The above examples include the commonly needed cases, but not all cases recognized by Chime and RasMol. To learn more about the select commands and command language in RasMol and Chime, consult these documents:

• RasMol Quick Start (for complete novices).
• What can you learn about a protein/DNA molecule with RasMol? (Detailed tutorials on basic commands.)
• RasMol Reference Manual.