To aid in visualization NAMOT2 has several features
NAMOT2 can output in various formats:
- The ability to toggle CPK for
specified atoms using the specifier syntax which can be found in
- The ability to toggle atom color on the
basis of specifiers.
Available colors are:
- usr(this is a user defined color:see
- The ability to set atoms invisible.
- The ability to show the distances being monitored
by dashed lines.
- The ability to set lines thick.
- PPM. PPM is a good standard graphics
format that can be converted to any number of other formats using freely
available programs. We now recommend using TIFF instead of PPM.
- Vector postscript.(EPS) This is suggested
for the best quality wireframe
- Raster postscript.(EPS) This is
suggested for situations where you don't anticipate modifying the image later
with an external program.
- TIFF. TIFF is another raster format like PPM,
but is 1/3 the size of PPM. This format is recommended if you anticipate
processing the image with another program.
See figure 4.1 for the finished image.
- Create a 10 unit helix. This procedure is described in
- Set the color of strand 1 to blue with the command:
set col m1:1:*:* blue
- Set the color of strand 2 to red with the command:
set col m1:2:*:* red
- Choose "CPK" from the Image menu, Choose it again to get
- Selectively set the phosphate atoms on strand 1 to CPK by
set space m1:1:*:P
- Selectively set the phosphate atoms on strand 2 to CPK by
set space m1:2:*:P
- Write text by:
- Determining the x,y position by clicking any mouse button over
where you want the text to start.(example 200,500 )
- Write "This is a test" at position 200, 500 by:
set text 200 500 This is a test
- Write this out as PPM with the command
write ppm test.ppm