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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 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. | |
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| + | = 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] | ||
| + | </source> | ||
| − | = | + | For one protein: |
| − | + | <source lang="python"> | |
| − | + | symexp name_for_new_objects,asymmetric_name,(asymmetric_name),distance | |
| + | </source> | ||
| + | '''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 | ||
| + | '''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 | ||
| + | '''(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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| − | + | = EXAMPLE = | |
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load any .pdb file into PyMOL (here we use 1GVF).<br> | load any .pdb file into PyMOL (here we use 1GVF).<br> | ||
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At the PyMOL command prompt type the following:<br> | At the PyMOL command prompt type the following:<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). | ||
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| − | > | + | <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]] |
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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. |
| + | = See Also = | ||
| + | * [http://pdbbeta.rcsb.org/robohelp_f/data_download/biological_unit/pdb_and_mmcif_files_.htm PDB Symmetry Info] | ||
| + | * [[SuperSym]] | ||
| + | * From within PyMOL, ''help symexp'' and ''symexp ?''. | ||
| + | * [http://deposit.rcsb.org/adit/docs/pdb_atom_format.html#CRYST1 CRYST1 record] in PDB files is used by symexp | ||
[[Category:Commands|Symexp]] | [[Category:Commands|Symexp]] | ||
Revision as of 09:20, 28 March 2011
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 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]
For one protein:
symexp name_for_new_objects,asymmetric_name,(asymmetric_name),distance
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
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
(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
EXAMPLE
load any .pdb file into PyMOL (here we use 1GVF).
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).
symexp sym,1GVF,(1GVF),5
If we color all of the sym* cyan we will produce the following:
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
- PDB Symmetry Info
- SuperSym
- From within PyMOL, help symexp and symexp ?.
- CRYST1 record in PDB files is used by symexp