Rasmol
Rasmol is a program for visualising protein structures in pdb
format.
The program is intuitive and easy to use.
You start the program by typing
rasmol pdb_file
(you can also start it without any pdb_file and then open the file
with File/Open)
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Mouse button
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Left
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Middle
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Right
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-
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Rotate x,y
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Translate
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Translate
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Shift
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Resize
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Rotate z
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Rotate z
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- You can select certain atoms by writing
select list_of_atoms
e.g. residue_numbers or residue_names or within a distance of a
certain residue:
select within(5.0,residue_number) (note that you have to
include the decimal point)
Select an atom:
select *.CA (all CA atoms)
Then you can change the colour of these by for example
colour red
Or you can change way of display by selecting something under
Display or by
wireframe 0.1 (a line intermediate between wireframe and
sticks)
wireframe off (hides the selected amino acids; c.f. restrict)
The command restrict works almost as select, but it
hides all amino acids not selected by restrict
e.g. restrict within (4.0,ASP302.CG) (not
restrict within (4.0,302.CG)
- You can measure bond lengths, angles, or torsions by writing:
set picking bond
set picking angle
set picking torsion
Then you pick two, three, or four atoms by the left mouse button.
- You can show the name or numbers of the atoms by
label %a (name)
label %i (number)
select *.CA
label %n%r (residue name and number)
If you have residues with numbers in the name, you need to put it inside square brackets [0YA].
- You change the colour of the background by
colour background white
- If you want to do the same action for several molecules, you
can write the rasmol commands in a script file and then invoke
it by:
script rasmol_script_file
- The direction of the axes are as expected: x is horizontal, y
is vertical.
- When reading in several file, rasmol unfortunately do not use the
same coordinate system. The only way to get them in the same system is
to catenate the files before reading them in as a single file.
The new version on Linux cannot write any figures
at all.
The old version on Mac can write ps figures.
The new version on Windows can write all supported file formats.
The quality of the figures is poor (except vector ps, but I have not
found any program that can read and convert these files (not gimp or
preview).
It does not help at all to read in ps figures in gimp with high
resolution and strong antialiasing.
The quality can be somewhat improved by using full screen and make
the molecules as large as possible.
The newest Windows version also give somewhat improved images.
Rasmol run on Kebnekaise and Tetralith
only through ThinLinc.
For Kebnekaise, you then need to login on kebnekaise-tl.hpc2n.umu.se
Rasmol on Aurora:
There is now a
rasmol module available on Aurora for viewing structures by my
request to the Lunarc support (i.e. that does not require mounting
the filesystem to view molecules locally).
You need a
desktop/machine acting as X11-server.
To run the module you can login from an existing ssh terminal
session and load it as:
ssh -X aurora.lunarc.lu.se
module load rasmol/.2.7.5.2
Martin 21/11-17
A complete manual and further information are available in: http://openrasmol.org/ and
http://www.umass.edu/microbio/rasmol/ .
The current version of the program is 2.6 (sgi) and 2.7.1.1
(linux).
To run it on the linux mashines, you need to have 24 or 32 colour
bits.
The program is found in:
/usr/local/bin/rasmol (garm, 32 bit)
/usr/local/bin/rasmol (signe; 8-bit)
/sw/rasmol/RasMol26/rasmol (ask/lif, 32 bit)
/home/bio/Bin/rasmol (husmodern; 32-bit