Normalize ccp4 maps - Revision history

Bell: 5 revisions

2015-07-09T20:24:03Z

5 revisions

Speleo3: type cpp -> ccp

2015-06-04T21:09:37Z

type cpp -> ccp

Speleo3: proposed_new_default

2015-06-04T21:04:52Z

proposed_new_default

Speleo3 at 20:37, 4 June 2015

2015-06-04T20:37:32Z

Pyadmin: 1 revision

2014-03-28T02:16:21Z

1 revision

New page

= Overview =
This setting controls whether or not PyMOL normalizes the values in a ccp4 map '''upon loading''. So, if your values are off, ''unset'' this option ''before'' loading your map.

You might need this setting if, when you load maps in other programs (eg. Coot, O) they map properly covers all atoms, but in PyMOL the map does not.

= Syntax =
<source lang="python">
# turn it on
set normalize_ccp4_maps

# turn it off (stop the normalizing)
unset normalize_ccp4_maps
</source>

[[Category:Settings]]
[[Category:Electron_Density]]
[[Category:Maps]]

@@ Line 14: / Line 14: @@
 # load map and normalize data
 set normalize_ccp4_maps, on
-load somemap.cpp4
+load somemap.ccp4
 # load map as-is (without normalization)
 set normalize_ccp4_maps, off
-load somemap.cpp4
+load somemap.ccp4
 </source>

← Older revision		Revision as of 21:04, 4 June 2015
Line 1:		Line 1:
		+	{{proposed_new_default\|off}}
		+
	The [[normalize_ccp4_maps]] settings (default: '''on''') controls whether or not PyMOL normalizes the data from a ccp4 map file '''upon loading'''. The data is shifted and scaled so that mean=0.0 and stdev=1.0.		The [[normalize_ccp4_maps]] settings (default: '''on''') controls whether or not PyMOL normalizes the data from a ccp4 map file '''upon loading'''. The data is shifted and scaled so that mean=0.0 and stdev=1.0.

← Older revision	Revision as of 20:24, 9 July 2015
(No difference)

@@ Line 1: / Line 1: @@
-= Overview =
+The [[normalize_ccp4_maps]] settings (default: '''on''') controls whether or not PyMOL normalizes the data from a ccp4 map file '''upon loading'''. The data is shifted and scaled so that mean=0.0 and stdev=1.0.
-You might need this setting if, when you load maps in other programs (eg. Coot, O) they map properly covers all atoms, but in PyMOL the map does not.
+Normalization is done on the raw data array, not across the unit cell. This means that if the raw data doesn't exactly cover an integral number of asymmetric units, the result will be different than for example when loading the same file into Coot, which normalizes across the cell.
-= Syntax =
+'''Normalization should be turned off before loading, in cases like:'''
 <source lang="python">
-# turn it on
+# load map and normalize data
-set normalize_ccp4_maps
+set normalize_ccp4_maps, on
-# turn it off (stop the normalizing)
+# load map as-is (without normalization)
-unset normalize_ccp4_maps
+set normalize_ccp4_maps, off
 </source>
 [[Category:Settings]]
 [[Category:Electron_Density]]
 [[Category:Maps]]