Cchem: 1 revision

2019-03-04T03:58:18Z

1 revision

Speleo3: core command

2019-02-25T10:45:56Z

core command

Pyadmin: 4 revisions

2014-03-28T01:48:51Z

4 revisions

Speleo3: make multi-chain safe and support multiple properties

2011-11-03T12:39:09Z

make multi-chain safe and support multiple properties

New page

= Overview =
[[AlphaToAll]] will expand the alpha-carbon property that you specify to all atoms in the residues. For example, if you set the b-factor column to some different value for all alpha carbons, this script will propagate those values into all the atoms as well.

'''In the example below, notice the color of the sticks.'''

<center>
<gallery heights="200px" widths="400px">
Image:Alphac0.png|The alpha carbon here has a color property that does not match the rest of the residue.
Image:Alphac1.png|This script will fix that, expanding the color attribute to the rest of the atoms.
</gallery>
</center>

= Usage =
<source lang="python">
# expand propertyName in objName on all the alpha carbons
# to every atom, for each residue
alphaToAll objName, propertyName

# Example #1
# For all objects, for each residue, set every atom's b-column value
# to match that residue's alpha carbon's b-column value.
alphaToAll *, b

# Example #2
# For selection 1qox and c. A expand the alpha carbon
# colors to all atoms in the selection
alphaToAll 1qox and c. A, color
</source>

= The Code =
<source lang="python">
from pymol import cmd, CmdException

def alphaToAll(sel, col="b",forceRebuild=False):
"""
alphaToAll -- expand any property of the alpha carbons to all atoms in the residue

PARAMS
sel
The selection or object (include "*" for all objects) to operate on. This will
read the alpha carbon's "COL" property and expand that down to all atoms in the
given residues in sel.

col
Any valid PyMOL property. For example, 'b' or 'q' or 'color', etc.
DEFAULT: b, for B-factor as we most often overwrite that column

forceRebuild
If a color changes, this will rebuild the objects for us. For speed, we
DEFAULT this to False.

RETURNS
None, just epxands the properties as dicsussed above.

NOTES
This script is useful for instances where we update the b-factor column for the
alpha carbons and then want to expand that color to all atoms for smoother looking
images.

AUTHOR:
Jason Vertrees, 2009.

"""
col = '(' + ','.join(col.split()) + ')'
space = {'props': dict()}
cmd.iterate('byca (%s)' % (sel), 'props[model,segi,chain,resi] = ' + col, space=space)
cmd.alter(sel, col + ' = props.get((model,segi,chain,resi), ' + col + ')', space=space)
if forceRebuild != False:
cmd.rebuild(sel)

cmd.extend("alphaToAll", alphaToAll)
</source>

[[Category:Script_Library]]
[[Category:ObjSel_Scripts]]

← Older revision		Revision as of 10:45, 25 February 2019
Line 1:		Line 1:
		+	'' '''alphatoall''' (all lower case) is a core command since PyMOL 1.7.2''
		+
	= Overview =		= Overview =
	[[AlphaToAll]] will expand the alpha-carbon property that you specify to all atoms in the residues. For example, if you set the b-factor column to some different value for all alpha carbons, this script will propagate those values into all the atoms as well.		[[AlphaToAll]] will expand the alpha-carbon property that you specify to all atoms in the residues. For example, if you set the b-factor column to some different value for all alpha carbons, this script will propagate those values into all the atoms as well.

← Older revision	Revision as of 03:58, 4 March 2019
(No difference)

← Older revision	Revision as of 01:48, 28 March 2014
(No difference)

AlphaToAll - Revision history

Cchem: 1 revision

Speleo3: core command

Pyadmin: 4 revisions

Speleo3: make multi-chain safe and support multiple properties