Here are the quick directions to reading CCP4 maps into pymol and
creating nice diagrams:
1. Use fft to create a map in CCP4. (This task can be run from the Run
FFT-Create Map option undere 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 .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'.
2. Open pymol and read in your PDB file. Create a selection about
whatever you want to see the map around. I usually display the selection
3. Open your map in pymol, e.g. mymap.map.ccp4 (you need the ccp4
4. To display the map around your selection (e.g., named 'site') issue a
command similar to this:
isomesh map, mymap.map.ccp4, 2.0, site, carve=1.6
This command will create a mesh object map from mymap.map.ccp4,
countoured at 2.0 sigma, around the
selection 'site', only within 1.6A of selected atoms. You can
change the contour level and carve
parameter to suit.
5. For a publication quality figure than can be labeled in GIMP or
Photoshop, I would further suggest:
* select the map object and change the color to 30% gray
* change the background to white with the command 'bg_color
You should be able to generate a really nice diagram that look something
like the attached image. The operation of CCP4 or pymol is
Roger S. Rowlett
Department of Chemistry
13 Oak Drive
Hamilton, NY 13346
email: [log in to unmask]
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
Sent: Friday, May 11, 2007 12:06 PM
To: [log in to unmask]
Subject: [ccp4bb] quick question...
Good day all,
First off, thank you all so much for your help a
couple days ago! I just have a quick question
regarding the use of CCP4 to generate density maps.
Is there a way to generate a map(s) that can be read
into PyMol? I understand that PyMol can only read CNS
or XPLOR maps, is this correct? Is there a means by
which I can output maps (on a Windows platform) in a
format that can be read by PyMol?
My only option in CCP4 is to create my FFT map in CCP4
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