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RasMol FAQ (Frequently Asked Questions) - A
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Is RasMol "Year 2000 (Y2K) compliant"?
RasMol 2.6 and all prior versions are fully Y2K compliant with a single
caveat. RasMol can read and write MDL Mol and Brookhaven PDB files, which
reserve only two characters for the year in a date field. RasMol ignores
these fields and is therefore not affected by Y2K. However programs
reading MDL Mol files generated by RasMol (or any other molecular graphics
program) may suffer if they process the date field.
What is the definitive literature citation for RasMol?
The currently preferred literature reference to RasMol is:
Roger Sayle and E. James Milner-White. "RasMol: Biomolecular graphics
for all", Trends in Biochemical Sciences (TIBS), September
1995, Vol. 20, No. 9, p. 374.
Where can I get more molecule co-ordinate files?
In addition to the three example files that are distributed with RasMol,
the protein crambin (1crn.pdb), the DNA-binding protein CRO (3cro.pdb)
and aspirin (asprin.alc), the major source of data files for RasMol is
the Protein Databank at Brookhaven National Labs. This is the main
repository for all of the world's known 3D xray-crystallography and
nuclear magnetic resonance (NMR) structures of proteins and nucleic
acids. Currently over 7,000 are available at the
Protein Data Bank.
One of the best lists
of sites that hold small molecule co-ordinates (and additional protein
structures) is Eric Martz'z "Molecules Galore!" WWW page at
http://www.umass.edu/microbio/rasmol/whereget.htm
How do I measure distances within RasMol?
There are two ways to measure distances between atoms in version
2.6beta of RasMol. The first is to use the "set picking
distance" command, to set the mouse into interactive distance
measurement mode. Then by clicking on pairs of atoms, RasMol will
report the distance between them on the command line. RasMol also
has similar modes for "set picking angles" and "set picking
torsions". The mouse can be returned to the default mode using
"set picking ident".
The second approach is to use distance monitors. A distance monitor
in RasMol is a graphical dotted line between an arbitrary pair of atoms
optionally labelled by the distance between them. There are two ways
to add a monitor to a molecule. The first is to use "set picking
monitors", similar to set picking distance above. Note that this will
acta as a toggle and selecting the same two atoms again will remove the
monitor. Monitors can also be added from the command line using the
monitor command. This command takes the atom serial numbers of the
two end-point atoms as parameters. All monitors can be turned of using
the command "monitors off".
How do I select residues in a particular chain?
The method for selecting a range of residues in a particular chain has
improved in RasMol version 2.6. It can now be done using the syntax
"select 1-25:a" to select residues 1 to 25 in chain A. Similarly
"select 25:a" and "select :a" will select just residue 25
in chain A and all of chain A respectively.
In RasMol versions prior to v2.6, you'd have to type an atom expression
of the form "select 1-25 and **a" where the final term is a
primitive expression. This primitive expression is a wildcarded form
of the form "cys37a" where the residue name and number are replaced
by the wildcard "*".
Note that care has to be made to ensure that RasMol can determine which
field is being specified. For example, although "select *a" will
select all resiues in chain A, if the chain identifier was a number,
"select **1" would have to be used, as "select *1" denotes
residue 1. To avoid any ambiguity, an optional colon character is now
used to prefix the chain identifier, allowing expressions such as
"cys:a", "cys35:1", "*:1" and even just ":1".
See also the
RasMol Manual.
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