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(New page: === 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 ...)
 
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=== DESCRIPTION ===
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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://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.
 
  
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[[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 ===
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== USAGE ==
symexp name_for_new_objects,asymmetric_name,(asymmetric_name),distance<br>
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<source lang="python">
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# Expand the ''object'' around its ''selection'' by cutoff Angstroms and
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# prefix the new objects withs ''prefix''.
 +
symexp prefix, object, selection, cutoff [, segi]
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</source>
  
* ''name_for_new_objects'' - PyMOL will generate a number of new objects corresponding to copies (rotated and translated) of the given asymmetric unit with the given name appended with a numerical counter
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For one protein:
* ''asymmetric_name'' - this is the name of the loaded asymmetric unit that you wish to reproduce neighboring crystal partners for
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<source lang="python">
* ''(asymmetric_name)'' - the same name, but with parantheses around it - my guess is that the first is the source of atom coordinates and this is the source of the symmetry operators, but that is only a guess.
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symexp name_for_new_objects,asymmetric_name,(asymmetric_name),distance
* ''distance'' - in Angstroms; reproduce any other unit that has any part of it falling withing ''distance'' Angstroms from the original asymetric unit
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</source>
  
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== ARGUMENTS ==
  
=== EXAMPLE ===
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* '''prefix''' = string: name prefix for new objects
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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
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* '''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).<br>
 
load any .pdb file into PyMOL (here we use 1GVF).<br>
  
add image of 1GVF
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[[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).
  
add image of 1GVF_1A
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[[Image:1GVF_1A.png]]
  
  
>> 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>
  
add image of 1GVF_5A
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[[Image:1GVF_5A.jpeg|350px]]
 
 
As you can see, we can begin to understand the crystal environment of our asymmetric unit.<br>
 
 
 
NOTE: My PyMOL likes to crash if I ask it to ray trace or make a .png of anything that is too large.  I'm not sure how large too large is, but be aware of this.
 
  
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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.
  
I will try to learn how to upload pictures soon.
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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.
--[[User:Baker1|Baker1]] 13:41, 10 November 2008 (CST)
 
  
[[Category:Commands|symexp]]
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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]]

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