Difference between revisions of "Symexp"

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[[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://www.wwpdb.org/documentation/file-format-content/format33/sect8.html#CRYST1 CRYST1 record]) to reproduce the lattice.
  
'''symexp''' is used to reconstruct neighboring asymmetric units from the crystallographic experiment that produced the given structureThis 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>
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[[Symexp]] creates all symmetry related objects for the specified object that occurs within a cutoff about an atom selectionThe new objects are labeled using the prefix provided along with their crystallographic symmetry operation and translation.
  
From the PyMOL developers:
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== USAGE ==
    "'symexp' creates all symmetry related objects for the specified object
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<source lang="python">
    that occurs within a cutoff about an atom selection.  The new objects
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# Expand the ''object'' around its ''selection'' by cutoff Angstroms and
    are labeled using the prefix provided along with their crystallographic
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# prefix the new objects withs ''prefix''.
    symmetry operation and translation."
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symexp prefix, object, selection, cutoff [, segi]
 +
</source>
  
 +
For one protein:
 +
<source lang="python">
 +
symexp name_for_new_objects,asymmetric_name,(asymmetric_name),distance
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</source>
  
=== USAGE ===
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== ARGUMENTS ==
In general:<br>
 
symexp(prefix,object,selection,cutoff)<br>
 
  
For one protein:<br>
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* '''prefix''' = string: name prefix for new objects
symexp name_for_new_objects,asymmetric_name,(asymmetric_name),distance<br>
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* '''object''' = string: name of the object that you wish to reproduce neighboring crystal partners for; the source of the symmetry operators
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* '''selection''' = string: atom selection to measure cutoff distance from
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* '''cutoff''' = float: create all symmetry mates that are within "cutoff" distance from selection (but no more than +/-1 unit cells)
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* '''segi''' = 0/1: if segi=1 then assign to each symmetry mate a unique 4-character segment identifier {default: 0}
  
* ''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
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== EXAMPLE ==
* ''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
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load any .pdb file into PyMOL (here we use 1GVF).<br>
* ''(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
 
* ''distance'' (cutoff) - in Angstroms; reproduce any other unit that has any part of it falling withing ''distance'' Angstroms from the original asymmetric unit
 
  
 
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fetch 1GVF
=== EXAMPLE ===
 
load any .pdb file into PyMOL (here we use 1GVF).<br>
 
  
 
[[Image:1GVF_assym.png]]
 
[[Image:1GVF_assym.png]]
  
 
At the PyMOL command prompt type the following:<br>
 
At the PyMOL command prompt type the following:<br>
>> symexp sym,1GVF,(1GVF),1<br>
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<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).
  
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>> symexp sym,1GVF,(1GVF),5<br>
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<source lang="python">
 +
symexp sym,1GVF,(1GVF),5
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</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]]
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[[Image:1GVF_5A.jpeg|350px]]
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 +
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.
  
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>
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== Naming Scheme ==
  
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.
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The created objects have the following naming scheme:
  
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<prefix>AAXXYYZZ
  
--[[User:Baker1|Baker1]] 13:41, 10 November 2008 (CST)
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* AA: zero-based [https://sourceforge.net/p/pymol/code/HEAD/tree/trunk/pymol/modules/pymol/xray.py#l95 symmetry operator] index, e.g. 00 always corresponds to "x,y,z". A space group like "P 21 21 21" which has 4 symmetry operators will count up to 03
 +
* XX: -1, 0, or 1, this is the unit cell offset from the center of the selection along the x-axis. PyMOL never creates more than 3 unit cells along each axis
 +
* YY: analogous to XX, but along the y-axis
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* ZZ: analogous to XX, but along the z-axis
  
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== See Also ==
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* [http://pdbbeta.rcsb.org/robohelp_f/data_download/biological_unit/pdb_and_mmcif_files_.htm PDB Symmetry Info]
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* [[SuperSym]]
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* [[Supercell]]
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* From within PyMOL, ''help symexp'' and ''symexp ?''.
 
[[Category:Commands|Symexp]]
 
[[Category:Commands|Symexp]]

Latest revision as of 11:48, 20 April 2018

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 (but no more than +/-1 unit cells)
  • 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).

fetch 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.

Naming Scheme

The created objects have the following naming scheme:

<prefix>AAXXYYZZ
  • AA: zero-based symmetry operator index, e.g. 00 always corresponds to "x,y,z". A space group like "P 21 21 21" which has 4 symmetry operators will count up to 03
  • XX: -1, 0, or 1, this is the unit cell offset from the center of the selection along the x-axis. PyMOL never creates more than 3 unit cells along each axis
  • YY: analogous to XX, but along the y-axis
  • ZZ: analogous to XX, but along the z-axis

See Also