This is a read-only mirror of pymolwiki.org

Difference between revisions of "Symexp"

From PyMOL Wiki
Jump to navigation Jump to search
m (10 revisions)
 
(7 intermediate revisions by 3 users not shown)
Line 1: Line 1:
=== DESCRIPTION ===
+
[[Symexp]] is used to reconstruct neighboring asymmetric units from the crystallographic experiment that produced the given structure.  This is assuming the use of a [http://www.rcsb.org/pdb/home/home.do PDB] file or equivalent that contains enough information ([http://deposit.rcsb.org/adit/docs/pdb_atom_format.html#CRYST1 CRYST1 record]) to reproduce the lattice.
'''symexp''' is used to reconstruct neighboring asymmetric units from the crystallographic experiment that produced the given structure.  This is assuming the use of a [http://www.rcsb.org/pdb/home/home.do PDB] file or equivalent that contains enough information to reproduce the lattice.<br>
 
  
From the PyMOL developers:
+
[[Symexp]] creates all symmetry related objects for the specified object that occurs within a cutoff about an atom selection.  The new objects are labeled using the prefix provided along with their crystallographic symmetry operation and translation.
    "'symexp' creates all symmetry related objects for the specified object
 
    that occurs within a cutoff about an atom selection.  The new objects
 
    are labeled using the prefix provided along with their crystallographic
 
    symmetry operation and translation."
 
  
 +
== USAGE ==
 +
<source lang="python">
 +
# Expand the ''object'' around its ''selection'' by cutoff Angstroms and
 +
# prefix the new objects withs ''prefix''.
 +
symexp prefix, object, selection, cutoff [, segi]
 +
</source>
  
=== USAGE ===
+
For one protein:
In general:<br>
+
<source lang="python">
symexp(prefix,object,selection,cutoff)<br>
+
symexp name_for_new_objects,asymmetric_name,(asymmetric_name),distance
 +
</source>
  
For one protein:<br>
+
== ARGUMENTS ==
symexp name_for_new_objects,asymmetric_name,(asymmetric_name),distance<br>
 
  
* ''name_for_new_objects'' (prefix) - PyMOL will generate a number of new objects corresponding to copies (rotated and translated) of the given asymmetric unit with the given name (prefix) appended with a numerical counter
+
* '''prefix''' = string: name prefix for new objects
* ''asymmetric_name'' (object) - this is the name of the loaded asymmetric unit that you wish to reproduce neighboring crystal partners for; the source of the symmetry operators
+
* '''object''' = string: name of the object that you wish to reproduce neighboring crystal partners for; the source of the symmetry operators
* ''(asymmetric_name)'' (selection) - the same name, but with parentheses around it if you are reproducing a crystal from its asymmetric unit - the source of atom coordinates
+
* '''selection''' = string: atom selection to measure cutoff distance from
* ''distance'' (cutoff) - in Angstroms; reproduce any other unit that has any part of it falling withing ''distance'' Angstroms from the original asymmetric unit
+
* '''cutoff''' = float: create all symmetry mates that are within "cutoff" distance from selection
 +
* '''segi''' = 0/1: if segi=1 then assign to each symmetry mate a unique 4-character segment identifier {default: 0}
  
 
+
== EXAMPLE ==
=== EXAMPLE ===
 
 
load any .pdb file into PyMOL (here we use 1GVF).<br>
 
load any .pdb file into PyMOL (here we use 1GVF).<br>
  
Line 28: Line 29:
  
 
At the PyMOL command prompt type the following:<br>
 
At the PyMOL command prompt type the following:<br>
>> symexp sym,1GVF,(1GVF),1<br>
+
<source lang="python">
 +
symexp sym,1GVF,(1GVF),1
 +
</source>
 
produces three new objects.  We now have four objects corresponding to two biologic units (the functional protein in a cell).
 
produces three new objects.  We now have four objects corresponding to two biologic units (the functional protein in a cell).
  
Line 34: Line 37:
  
  
>> symexp sym,1GVF,(1GVF),5<br>
+
<source lang="python">
 +
symexp sym,1GVF,(1GVF),5
 +
</source>
 
If we color all of the sym* cyan we will produce the following:<br>
 
If we color all of the sym* cyan we will produce the following:<br>
  
[[Image:1GVF_5A.jpeg]]
+
[[Image:1GVF_5A.jpeg|350px]]
 
 
As you can see, we can begin to understand the crystal environment of our asymmetric unit.  Increasing ''distance'' will reveal more of the crystal lattice, but will place in increasing demand on your computer's rendering ability.<br>
 
 
 
NOTE: My PyMOL likes to crash if I ask it to ray trace or make a .png of anything that is too large.  ''Too large'' varies, but (for instance) I was not able to ray trace the above picture using the default settings.  Just making a .png image without the extra visual niceties rarely creates problems.
 
  
 +
As you can see, we can begin to understand the crystal environment of our asymmetric unit.  Increasing ''distance'' will reveal more of the crystal lattice, but will place in increasing demand on your computer's rendering ability.
  
--[[User:Baker1|Baker1]] 13:41, 10 November 2008 (CST)
+
PyMOL is known to exit dramatically (crash) if you provide a scene that is too large or complex.  This is a result of the low-level ''malloc'' function failing.  See [[:Category:Performance]] for workarounds.
  
[[Category:Commands|symexp]]
+
== See Also ==
 +
* [http://pdbbeta.rcsb.org/robohelp_f/data_download/biological_unit/pdb_and_mmcif_files_.htm PDB Symmetry Info]
 +
* [[SuperSym]]
 +
* [[Supercell]]
 +
* From within PyMOL, ''help symexp'' and ''symexp ?''.
 +
[[Category:Commands|Symexp]]

Latest revision as of 03:36, 28 March 2014

Symexp is used to reconstruct neighboring asymmetric units from the crystallographic experiment that produced the given structure. This is assuming the use of a PDB file or equivalent that contains enough information (CRYST1 record) to reproduce the lattice.

Symexp creates all symmetry related objects for the specified object that occurs within a cutoff about an atom selection. The new objects are labeled using the prefix provided along with their crystallographic symmetry operation and translation.

USAGE

# Expand the ''object'' around its ''selection'' by cutoff Angstroms and
# prefix the new objects withs ''prefix''.
symexp prefix, object, selection, cutoff [, segi]

For one protein:

symexp name_for_new_objects,asymmetric_name,(asymmetric_name),distance

ARGUMENTS

  • prefix = string: name prefix for new objects
  • object = string: name of the object that you wish to reproduce neighboring crystal partners for; the source of the symmetry operators
  • selection = string: atom selection to measure cutoff distance from
  • cutoff = float: create all symmetry mates that are within "cutoff" distance from selection
  • segi = 0/1: if segi=1 then assign to each symmetry mate a unique 4-character segment identifier {default: 0}

EXAMPLE

load any .pdb file into PyMOL (here we use 1GVF).

1GVF assym.png

At the PyMOL command prompt type the following:

symexp sym,1GVF,(1GVF),1

produces three new objects. We now have four objects corresponding to two biologic units (the functional protein in a cell).

1GVF 1A.png


symexp sym,1GVF,(1GVF),5

If we color all of the sym* cyan we will produce the following:

1GVF 5A.jpeg

As you can see, we can begin to understand the crystal environment of our asymmetric unit. Increasing distance will reveal more of the crystal lattice, but will place in increasing demand on your computer's rendering ability.

PyMOL is known to exit dramatically (crash) if you provide a scene that is too large or complex. This is a result of the low-level malloc function failing. See Category:Performance for workarounds.

See Also