Difference between revisions of "Display CCP4 Maps"

From PyMOLWiki
Jump to: navigation, search
(User Notes)
Line 9: Line 9:
 
(albeit much larger) map by re-running '''fft''' with a tighter grid spacing.
 
(albeit much larger) map by re-running '''fft''' with a tighter grid spacing.
 
I usually take the default values generated by FFT and double them. You
 
I usually take the default values generated by FFT and double them. You
can change grid spacing under ''Infrequently Used Options''.
+
can change grid spacing under ''Infrequently Used Options''. Alternatively, you can
 +
increase the sampling rate in Pymol in step 3 below.
  
 
2. Open pymol and read in your PDB file. Create a selection about
 
2. Open pymol and read in your PDB file. Create a selection about
Line 16: Line 17:
  
 
3. Open your map in pymol, ''e.g.'' mymap.map.ccp4 (you need the ccp4
 
3. Open your map in pymol, ''e.g.'' mymap.map.ccp4 (you need the ccp4
extension). An object named ''mymap.map'' will be created by pymol.
+
extension). An object named ''mymap.map'' will be created by pymol. To increase the
 +
sampling rate of the map (desirable if you did not do this at the time of map
 +
generation) issue the command '''map_double mymap.map, -1'''
  
 
4. Identify a selection about which to display your map, ''e.g.''
 
4. Identify a selection about which to display your map, ''e.g.''
Line 34: Line 37:
 
6. For a publication quality figure the following are suggestions:
 
6. For a publication quality figure the following are suggestions:
 
<source lang="python">
 
<source lang="python">
color grey30, map # sets map to 30% gray
+
color grey50, map # sets map to 50% gray
 +
set mesh_width, 0.5 # makes meshes thinner for ray-tracing
 
bg_color white #sets background to white
 
bg_color white #sets background to white
set ray_trace_fog, 0 #turns off raytrace fog--optional
+
set ray_trace_fog, 0 # turns off raytrace fog--optional
 
set depth_cue, 0 # turns off depth cueing--optional
 
set depth_cue, 0 # turns off depth cueing--optional
set ray_shadows, off #turns off ray-tracing shadows
+
set ray_shadows, off # turns off ray-tracing shadows
 
ray 1024 1024 # this would create a 1024x1024 pixel ray-traced image
 
ray 1024 1024 # this would create a 1024x1024 pixel ray-traced image
png image.png #output final image
+
png image.png # output final image
 
</source>
 
</source>
 
Labels can be added in GIMP or Photoshop. With these directions you should be able to create an image similar to the following one:
 
Labels can be added in GIMP or Photoshop. With these directions you should be able to create an image similar to the following one:

Revision as of 08:26, 1 September 2009

The following steps can be used to read CCP4-format electron density maps into pymol for the generation of publication-quality images.

1. Use fft to create a map in CCP4. (This task can be run from the Run FFT-Create Map option under Map & Mask Utilities) You can create a simple map or a nFo-mFc map as you wish. Select the option to cover 'all atoms in PDB file'. For pymol to read the map later, you will need to add the file extension .map.ccp4 to the generated map. You may find this map too coarse to make for a pretty diagram. You can generate a nicer (albeit much larger) map by re-running fft with a tighter grid spacing. I usually take the default values generated by FFT and double them. You can change grid spacing under Infrequently Used Options. Alternatively, you can increase the sampling rate in Pymol in step 3 below.

2. Open pymol and read in your PDB file. Create a selection about whatever you want to see the map around. Typically one would display the selection as sticks.

3. Open your map in pymol, e.g. mymap.map.ccp4 (you need the ccp4 extension). An object named mymap.map will be created by pymol. To increase the sampling rate of the map (desirable if you did not do this at the time of map generation) issue the command map_double mymap.map, -1

4. Identify a selection about which to display your map, e.g.

select site, resi 39-50 and resn bct

5. To display the map around your selection (e.g., named site) issue a command similar to this:

isomesh map, mymap.map, 2.0, site, carve=1.6

This command will create a mesh map object named map from the object mymap.map, contoured at 2.0 sigma, around the selection site, within 1.6A of selected atoms. You can change the contour level and carve parameter to suit. Note: the map object will be named in pymol whatever the filename was minus the .ccp4 extension

6. For a publication quality figure the following are suggestions:

color grey50, map # sets map to 50% gray
set mesh_width, 0.5 # makes meshes thinner for ray-tracing
bg_color white #sets background to white
set ray_trace_fog, 0 # turns off raytrace fog--optional
set depth_cue, 0 # turns off depth cueing--optional
set ray_shadows, off # turns off ray-tracing shadows
ray 1024 1024 # this would create a 1024x1024 pixel ray-traced image
png image.png # output final image

Labels can be added in GIMP or Photoshop. With these directions you should be able to create an image similar to the following one:

Ccp4 map.png

User Notes

If the ccp4 maps loaded by PyMOL seem smaller/larger than maps in other programs this might be due to normalization. To stop PyMOL from normalizing a cpp4 map simply unset,

unset normalize_ccp4_maps

before loading your ccp4 map.

See Also

normalize_ccp4_maps