Difference between revisions of "Label"

From PyMOLWiki
Jump to: navigation, search
(FONT)
m (Examples)
 
(38 intermediate revisions by 12 users not shown)
Line 1: Line 1:
[[Image:Label_pre.png|thumb|PyMol Labels]]
+
[[Image:Pl.png|right|500px]]
===DESCRIPTION===
 
'''label''' labels one or more atoms properties over a selection using the python evaluator with a separate name space for each atom.  The symbols defined in the name space are:
 
*name
 
*resn
 
*resi
 
*chain
 
*q
 
*b
 
*segi
 
*type (ATOM,HETATM)
 
*formal_charge
 
*partial_charge
 
*numeric_type
 
*text_type
 
  
All strings in the expression must be explicitly quoted.  This operation typically takes several seconds per thousand atoms altered.  To clear labels, simply omit the expression or set it to ''.
+
The [[Label]] command controls how PyMOL draws text labels for PyMOL objects.
  
===USAGE===
+
= Details =
  label (selection),expression
+
Labeling is important so there are many options for your fine tuning needs. You can change the [[Label_size|label size]], [[Label_color|label color]], positioning, [[Label_font_id|font]], the [[Label_outline_color|label outline color]] that masks the font and much, much more.
  
 +
You can have PyMOL label atoms by properties or arbitrary strings as you want; you can even use Unicode fonts for special symbols like, <math>\alpha, \beta, \pm, \textrm{\AA}</math>, etc.
  
===SETTINGS===
+
The following gallery shows some examples of how extensible the [[Label]] command is. 
====FONT====
+
<gallery heights="180px" widths="200px" align="center" perrow="3">
There are 10 different scalable fonts.
+
Image:Label_pre.png|Simple label
<source lang="python">set label_font_id, number</source>
+
Image:New_fonts.jpeg|Example showing usage of Unicode fonts for special characters, see [[label_font_id]].
where number is 5 through 14.
+
Image:Font_ex.png|Another example with Unicode fonts
=====UTF8 Fonts=====
+
Image:Label_ex.png|Example label
 +
Image:Ls0.png|Label shadows turned off
 +
Image:Ls2.png|Label shadows turned on
 +
</gallery>
  
[[Image:New_fonts.jpeg|thumb|New fonts in PyMol.  Notice the alpha and beta characters.]]
+
==Built-in Object Properties==
 +
Aside from arbitrary string labels, like "This is the catalytic residue" for an atom/residue you can also use the following built-in molecular properties:
 +
* '''name''', the atom name
 +
* '''resn''', the residue name
 +
*'''resi''', the residue number/identifier
 +
*'''chain''', the chain name
 +
*'''q''', charge
 +
*'''b''', the occupancy/b-factor
 +
*'''segi''', the segment identifier
 +
*'''type''' ''(ATOM,HETATM)'', the type of atom
 +
*'''formal_charge''', the formal charge
 +
*'''partial_charge''', the partial charge
 +
*'''numeric_type''', the numeric type
 +
*'''text_type''', the text type
  
Newer versions support UTF8 fonts; use '''font_label_id''' from above to 15 or 16.  The good news about the UTF8 fonts is that they support the alpha and beta characters. (See iamge.)
+
You can use one of these properties as:
 +
<source lang="python">
 +
# simple example: label residue 22's atoms with their names
 +
label i. 22, name
  
Here's some example code for the image at right:
+
# Label residue #44's alpha carbon with it's residue name, residue number and B-factor.
<source lang="python">
+
label n. CA and i. 44, "(%s, %s, %s)" % (resn, resi, b)
# roman
+
</source>
set label_font_id, 15
 
label 5/CA, "\316\261-Helix"
 
label 10/CA, "\316\262-Sheet"
 
  
# italic
+
See the syntax and examples below for more info.
set label_font_id, 16
 
  
# make bigger
+
=Syntax=
set label_size, 50
+
To use the label command follow this syntax:
 +
<source lang="python">
 +
# labeling syntax
 +
label [ selection[, expression]]
 
</source>
 
</source>
 +
where '''selection''' is some object/selection you want to label and '''expression''' is some string (or set of strings) which PyMOL is to use to label the given selection.
  
====SIZE====
+
We have plenty of examples.  See [[#Examples|the examples]] below.
The font size can be adjusted
 
<source lang="python">set label_size, number</source>
 
where number is the point size (or -number for Angstroms)
 
  
====COLOR====
+
=Settings=
Set a label's color by
+
Here are all the label settings and their general effect. For each label setting, see the respective web page for more details.
  set label_color, color
 
where color is a valid PyMol color.
 
  
====EXPRESSION====
+
'''[[label_angle_digits]]'''
To set what the label reads (see above)
+
:: sets the number of decimals in angle label.
<source lang="python">label selection, expression</source>
+
'''[[label_distance_digits]]'''
For example
+
:: sets the number of decimals in distance label.
 +
'''[[label_shadow_mode]]'''
 +
:: sets whether or not PyMOL will ray trace shadows for your label text.  Eg: <source lang="python">set label_shadow_mode, 2</source>
 +
'''[[label_color]]'''
 +
:: sets the color of the label text.  Note that you can have labels of different colors for different objects or selections. Some examples:
 
<source lang="python">
 
<source lang="python">
  label all, name
+
# per-object:
label resi 10, b
+
set label_color, color-name, object-name #eg, set label-color, magenta, /protein
 +
 
 +
# per-atom:
 +
set label_color, color-name, selection    #eg, set label-color, marine, /protein/A/A/23/CA
 +
 
 +
# another example
 +
fragment arg
 +
label all, name
 +
set label_color, yellow, arg
 +
set label_color, red, elem c
 
</source>
 
</source>
  
====POSITION====
+
'''[[label_font_id]]'''
To position labels
+
:: sets the font to render your label.  There are 12 different fonts from 5&mdash;16.  Numbers 15 and 16 are special for unicode.  Eg: <source lang="python">set label_font_id, 12</source>. See the [[label_font_id]] page for explicit examples on how to use unicode characters in PyMOL labels.
  edit_mode
+
'''[[label_size]]'''
then
+
:: sets the size of the text.  You can use positive numbers 2, 3, 4, etc for point sizes, or negative numbers for Angstrom-based sizes. Default is 14 points. Labels in Angstrom-size scale with the distance from the front plane, labels in point-size don't.  Eg: <source lang="python">set label_size, -2 #results in a size of 2 Angstroms</source>
ctrl-middle-click-and-drag to position the label in space. (On Windows systems this appears to be ctrl-shift-left-click-and-drag, presumably because the mice lack a true middle button.)
+
'''[[label_digits]]'''
 +
:: sets the number of decimals in label. It affects all digits only if label_distance_digits or label_dihedral_digits or label_angle_digits are set to -1.
 +
'''[[label_outline_color]]'''
 +
:: each label is outlined (so you can do white-on-white labels, for example).  This options sets the color of the label outline.  Eg. <source lang="python">set label_outline_color, orange</source>
 +
'''[[label_dihedral_digits]]'''
 +
:: sets the number of decimals in dihedral label.
 +
'''[[label_position]]'''
 +
:: sets any offset from the original X,Y,Z coordinates for the label. If you like to use the mouse, you can enter [[edit_mode]] and '''ctrl-left_click''' to drag labels around; '''ctrl-shift-left_click''' will let you move the labels in the z-direction. '''"Save labels"-workaround''' If you want to save the position of your labels, the best way might be to create a new object and move the atoms in this object. Since the labels are positioned from the atom positions this is an indirect way of moving the labels and being able to save them.
 +
 
 +
=Examples=
 +
<source lang="python">
 +
#1.
 +
# make a very simple label on the 14th alpha carbon.
 +
label n. CA and i. 14, "This is carbon 14."
  
===EXAMPLES===
+
#2.
label (chain A),chain
+
# make a fake scene label; use this to label entire scenes, not just atoms/bonds.
label (n;ca),"%s-%s" % (resn,resi)
+
pseudoatom foo
label (resi 200),"%1.3f" % partial_charge
+
label foo, "Once upon a time..."
  
The following image was created with
+
#3.
<source lang="python">
+
# make a huge label
 +
set label_size, -5
 +
pseudoatom foo
 +
label foo, "This is large text"
 +
 
 +
#4. Partial Charge
 +
label (chain A),chain
 +
label (n;ca),"%s-%s" % (resn,resi)
 +
label (resi 200),"%1.3f" % partial_charge
 +
 
 +
 
 +
#5. The gallery image above Label_ex.png was created with this code
 +
#  and finally, some labels were moved around in '''edit_mode'''.
 
label (resi 200),"%1.3f" % b
 
label (resi 200),"%1.3f" % b
 
set label_font_id, 10
 
set label_font_id, 10
 
set label_size, 10
 
set label_size, 10
 +
 +
#6. This example shows how to label a selection with the
 +
#  XYZ coordinates of the atoms
 +
from pymol import stored
 +
stored.pos = []
 +
# select the carbon atoms in my hetero atoms to label
 +
select nn, het and e. C
 +
# get the XYZ coordinates and put them into stored.pos
 +
# insert at the front because pop() will read the array in reverse
 +
iterate_state 1, (nn), stored.pos.insert(0,(x,y,z))
 +
# label all N atoms.  You need the pop() function or else
 +
# PyMOL will complain b/c you didn't provide enough coords.
 +
label nn, ("%5.5s, %5.5s, %5.5s") %  stored.pos.pop()
 
</source>
 
</source>
and finally, some labels were moved around in '''edit_mode'''.
 
[[Image:Label_ex.png|thumb|Labels.]]
 
  
===Users Comments===
+
= User Comments =
====Labels Using ID Numbers====
+
==Labels Using ID Numbers==
 
The following commnent,
 
The following commnent,
label SELECTION, " %s" % ID  
+
<source lang="python">
 +
label SELECTION, " %s" % ID  
 +
</source>
 
labels the SELECTION with atom ID numbers.
 
labels the SELECTION with atom ID numbers.
  
 
You can make more complicated selections/lables such as
 
You can make more complicated selections/lables such as
label SELECTION, " %s:%s %s" % (resi, resn, name)
+
<source lang="python">
 +
label SELECTION, " %s:%s %s" % (resi, resn, name)
 +
</source>
 
which will give you something like "GLU:139 CG"
 
which will give you something like "GLU:139 CG"
  
====Labels Using One Letter Abbreviations====
+
==Labels Using One Letter Abbreviations==
 
* First, Add this to your $HOME/.pymolrc  file:
 
* First, Add this to your $HOME/.pymolrc  file:
 
<source lang="python">
 
<source lang="python">
Line 106: Line 160:
 
</source>
 
</source>
  
*. Second, instead of:
+
* Second, instead of:
label n. ca, resn
+
<source lang="python">
 +
label n. ca, resn
 +
</source>
 
use:
 
use:
label n. ca, one_letter[resn]
+
<source lang="python">
 +
label n. ca, one_letter[resn]
 +
</source>
 +
or: ( to get something like D85)
 +
<source lang="python">
 +
label n. ca, "%s%s" %(one_letter[resn],resi)
 +
</source>
 +
 
 +
==Labels and defer_builds_mode==
 +
If You have a weak video card, You might want to set
 +
<source lang="python">
 +
set defer_builds_mode, 5
 +
</source>
 +
It helps a lot but breaks labels rendering. You can use
 +
<source lang="python">
 +
set defer_builds_mode, 4
 +
</source>
 +
instead.
 +
 
 +
=See Also=
 +
[[:Category:Labeling]]
 +
 
 +
All the settings posted above.
  
[[Category:Commands|label]]
+
[[Category:Labeling|Label]]
 +
[[Category:Commands|Label]]

Latest revision as of 18:09, 23 January 2017

Pl.png

The Label command controls how PyMOL draws text labels for PyMOL objects.

Details

Labeling is important so there are many options for your fine tuning needs. You can change the label size, label color, positioning, font, the label outline color that masks the font and much, much more.

You can have PyMOL label atoms by properties or arbitrary strings as you want; you can even use Unicode fonts for special symbols like, , etc.

The following gallery shows some examples of how extensible the Label command is.

Built-in Object Properties

Aside from arbitrary string labels, like "This is the catalytic residue" for an atom/residue you can also use the following built-in molecular properties:

  • name, the atom name
  • resn, the residue name
  • resi, the residue number/identifier
  • chain, the chain name
  • q, charge
  • b, the occupancy/b-factor
  • segi, the segment identifier
  • type (ATOM,HETATM), the type of atom
  • formal_charge, the formal charge
  • partial_charge, the partial charge
  • numeric_type, the numeric type
  • text_type, the text type

You can use one of these properties as:

# simple example: label residue 22's atoms with their names
label i. 22, name

# Label residue #44's alpha carbon with it's residue name, residue number and B-factor.
label n. CA and i. 44, "(%s, %s, %s)" % (resn, resi, b)

See the syntax and examples below for more info.

Syntax

To use the label command follow this syntax:

# labeling syntax
label [ selection[, expression]]

where selection is some object/selection you want to label and expression is some string (or set of strings) which PyMOL is to use to label the given selection.

We have plenty of examples. See the examples below.

Settings

Here are all the label settings and their general effect. For each label setting, see the respective web page for more details.

label_angle_digits

sets the number of decimals in angle label.

label_distance_digits

sets the number of decimals in distance label.

label_shadow_mode

sets whether or not PyMOL will ray trace shadows for your label text. Eg:
set label_shadow_mode, 2

label_color

sets the color of the label text. Note that you can have labels of different colors for different objects or selections. Some examples:
# per-object:
set label_color, color-name, object-name  #eg, set label-color, magenta, /protein

# per-atom:
set label_color, color-name, selection    #eg, set label-color, marine, /protein/A/A/23/CA

# another example
fragment arg
label all, name
set label_color, yellow, arg
set label_color, red, elem c

label_font_id

sets the font to render your label. There are 12 different fonts from 5—16. Numbers 15 and 16 are special for unicode. Eg:
set label_font_id, 12
. See the label_font_id page for explicit examples on how to use unicode characters in PyMOL labels.

label_size

sets the size of the text. You can use positive numbers 2, 3, 4, etc for point sizes, or negative numbers for Angstrom-based sizes. Default is 14 points. Labels in Angstrom-size scale with the distance from the front plane, labels in point-size don't. Eg:
set label_size, -2  #results in a size of 2 Angstroms

label_digits

sets the number of decimals in label. It affects all digits only if label_distance_digits or label_dihedral_digits or label_angle_digits are set to -1.

label_outline_color

each label is outlined (so you can do white-on-white labels, for example). This options sets the color of the label outline. Eg.
set label_outline_color, orange

label_dihedral_digits

sets the number of decimals in dihedral label.

label_position

sets any offset from the original X,Y,Z coordinates for the label. If you like to use the mouse, you can enter edit_mode and ctrl-left_click to drag labels around; ctrl-shift-left_click will let you move the labels in the z-direction. "Save labels"-workaround If you want to save the position of your labels, the best way might be to create a new object and move the atoms in this object. Since the labels are positioned from the atom positions this is an indirect way of moving the labels and being able to save them.

Examples

#1.
# make a very simple label on the 14th alpha carbon.
label n. CA and i. 14, "This is carbon 14."

#2.
# make a fake scene label; use this to label entire scenes, not just atoms/bonds.
pseudoatom foo
label foo, "Once upon a time..."

#3.
# make a huge label
set label_size, -5
pseudoatom foo
label foo, "This is large text"

#4. Partial Charge
label (chain A),chain
label (n;ca),"%s-%s" % (resn,resi)
label (resi 200),"%1.3f" % partial_charge


#5. The gallery image above Label_ex.png was created with this code
#   and finally, some labels were moved around in '''edit_mode'''.
label (resi 200),"%1.3f" % b
set label_font_id, 10
set label_size, 10

#6. This example shows how to label a selection with the 
#   XYZ coordinates of the atoms 
from pymol import stored
stored.pos = []
# select the carbon atoms in my hetero atoms to label
select nn, het and e. C
# get the XYZ coordinates and put them into stored.pos
# insert at the front because pop() will read the array in reverse
iterate_state 1, (nn), stored.pos.insert(0,(x,y,z))
# label all N atoms.  You need the pop() function or else
# PyMOL will complain b/c you didn't provide enough coords.
label nn, ("%5.5s, %5.5s, %5.5s") %  stored.pos.pop()

User Comments

Labels Using ID Numbers

The following commnent,

label SELECTION, " %s" % ID

labels the SELECTION with atom ID numbers.

You can make more complicated selections/lables such as

label SELECTION, " %s:%s %s" % (resi, resn, name)

which will give you something like "GLU:139 CG"

Labels Using One Letter Abbreviations

  • First, Add this to your $HOME/.pymolrc file:
# start $HOME/.pymolrc modification
one_letter ={'VAL':'V', 'ILE':'I', 'LEU':'L', 'GLU':'E', 'GLN':'Q', \
'ASP':'D', 'ASN':'N', 'HIS':'H', 'TRP':'W', 'PHE':'F', 'TYR':'Y',    \
'ARG':'R', 'LYS':'K', 'SER':'S', 'THR':'T', 'MET':'M', 'ALA':'A',    \
'GLY':'G', 'PRO':'P', 'CYS':'C'}
# end modification
  • Second, instead of:
label n. ca, resn

use:

label n. ca, one_letter[resn]

or: ( to get something like D85)

label n. ca, "%s%s" %(one_letter[resn],resi)

Labels and defer_builds_mode

If You have a weak video card, You might want to set

set defer_builds_mode, 5

It helps a lot but breaks labels rendering. You can use

set defer_builds_mode, 4

instead.

See Also

Category:Labeling

All the settings posted above.