Display CCP4 Maps - Revision history

Bell: 1 revision

2015-07-09T20:23:58Z

1 revision

Speleo3: cover "asymmetric unit" instead of "all atoms in PDB file"

2015-06-05T15:19:11Z

cover "asymmetric unit" instead of "all atoms in PDB file"

Pyadmin: 25 revisions

2014-03-28T01:21:21Z

25 revisions

UlfMolich at 09:40, 14 June 2013

2013-06-14T09:40:58Z

Mkhanna at 15:07, 5 April 2010

2010-04-05T15:07:15Z

New page

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 'Fo-Fc map as you wish. CCP4i will create a 2Fo-Fc map by default.
To make a Fo-Fc map, set F1=DELFWT and PHIC=PHDELWT in the task window. 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.''
<pre>
select site, resi 39-50 and resn bct
</pre>

5. To display the map around your selection (''e.g.'', named ''site'') issue a
command similar to this:
<pre>
isomesh map, mymap.map, 2.0, site, carve=1.6
</pre>
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:
<source lang="python">
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
</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:

[[Image:ccp4_map.png|center]]

= 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,
<source lang="python">
unset normalize_ccp4_maps
</source>
'''before''' loading your ccp4 map.

= See Also =
[[normalize_ccp4_maps]]

[[Category:Image_Manipulation|Display CCP4 Maps]]
[[Category:Electron_Density]]
[[Category:Maps]]

Rrowlett at 19:51, 21 October 2009

2009-10-21T19:51:38Z

Rrowlett at 19:51, 21 October 2009

2009-10-21T19:51:12Z

Rrowlett at 12:26, 1 September 2009

2009-09-01T12:26:43Z

New page

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 ''n''Fo-''m''Fc 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.''
<pre>
select site, resi 39-50 and resn bct
</pre>

5. To display the map around your selection (''e.g.'', named ''site'') issue a
command similar to this:
<pre>
isomesh map, mymap.map, 2.0, site, carve=1.6
</pre>
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:
<source lang="python">
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
</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:

[[Image:ccp4_map.png|center]]

= 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,
<source lang="python">
unset normalize_ccp4_maps
</source>
'''before''' loading your ccp4 map.

= See Also =
[[normalize_ccp4_maps]]

[[Category:Image_Manipulation|Display CCP4 Maps]]

Rrowlett at 13:55, 3 April 2009

2009-04-03T13:55:29Z

Rrowlett at 19:34, 16 April 2008

2008-04-16T19:34:06Z

← Older revision	Revision as of 20:23, 9 July 2015
(No difference)

@@ Line 4: / Line 4: @@
 FFT-Create Map'' option under ''Map & Mask Utilities'') You can create a
 simple map or a 'Fo-Fc map as you wish. CCP4i will create a 2Fo-Fc map by default.
-To make a Fo-Fc map, set F1=DELFWT and PHIC=PHDELWT in the task window. Select the option to cover 'all
+To make a Fo-Fc map, set F1=DELFWT and PHIC=PHDELWT in the task window. Select the option to cover ''' 'asymmetric unit' '''. 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

← Older revision	Revision as of 01:21, 28 March 2014
(No difference)

@@ Line 34: / Line 34: @@
 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
+change the contour level and carve parameter to suit. The contour level should be about 1.00 for a 2Fo-Fc map and about 3.00 for a Fo-Fc map. Note: the map object will be named in pymol whatever the filename was minus the .ccp4 extension
 . For a publication quality figure the following are suggestions:

@@ Line 3: / Line 3: @@
 . 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 ''n''Fo-''m''Fc map as you wish. Select the option to cover 'all
+simple map or a 'Fo-Fc map as you wish. CCP4i will create a 2Fo-Fc map by default
 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

@@ Line 18: / Line 18: @@
 extension). An object named ''mymap.map'' will be created by pymol.
-. To display the map around your selection (''e.g.'', named ''site'') issue a
+. Identify a selection about which to display your map, ''e.g.''
 command similar to this:
 <pre>
 isomesh map, mymap.map, 2.0, site, carve=1.6
 </pre>
-This command will create a mesh map object named ''map'' from the object ''mymap.map,''
+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.
+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
 . For a publication quality figure the following are suggestions:
 <source lang="python">
 color grey30, map # sets map to 30% gray