Symexp - Revision history

Bell: 10 revisions

2014-03-28T03:36:19Z

10 revisions

Speleo3: ARGUMENTS

2011-09-13T07:47:18Z

ARGUMENTS

Hongbo zhu at 09:22, 28 March 2011

2011-03-28T09:22:10Z

Hongbo zhu: /* See Also */

2011-03-28T09:20:59Z

See Also

New page

[[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.

[[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]
</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

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

[[Image:1GVF_assym.png]]

At the PyMOL command prompt type the following: 
<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).

[[Image:1GVF_1A.png]]

<source lang="python">
symexp sym,1GVF,(1GVF),5
</source>
If we color all of the sym* cyan we will produce the following: 

[[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.

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]]

Vinnyrose at 14:27, 20 June 2009

2009-06-20T14:27:40Z

Baker1 at 19:42, 21 November 2008

2008-11-21T19:42:32Z

Baker1 at 19:50, 10 November 2008

2008-11-10T19:50:11Z

Baker1: 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 ...

2008-11-10T19:41:20Z

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 ...

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 [http://www.rcsb.org/pdb/home/home.do PDB] file or equivalent that contains enough information to reproduce the lattice.

=== USAGE ===
symexp name_for_new_objects,asymmetric_name,(asymmetric_name),distance 

* ''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
* ''asymmetric_name'' - this is the name of the loaded asymmetric unit that you wish to reproduce neighboring crystal partners for
* ''(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.
* ''distance'' - in Angstroms; reproduce any other unit that has any part of it falling withing ''distance'' Angstroms from the original asymetric unit

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

add image of 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).

add image of 1GVF_1A

>> symexp sym,1GVF,(1GVF),5 
If we color all of the sym* cyan we will produce the following: 

add image of 1GVF_5A

As you can see, we can begin to understand the crystal environment of our asymmetric unit. 

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.

I will try to learn how to upload pictures soon.
--[[User:Baker1|Baker1]] 13:41, 10 November 2008 (CST)

[[Category:Commands|symexp]]

← Older revision		Revision as of 14:27, 20 June 2009
Line 46:		Line 46:
	--[[User:Baker1\|Baker1]] 13:41, 10 November 2008 (CST)		--[[User:Baker1\|Baker1]] 13:41, 10 November 2008 (CST)

−	[[Category:Commands\|~~symexp~~]]	+	[[Category:Commands\|Symexp]]

@@ 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 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>
 === USAGE ===
 symexp name_for_new_objects,asymmetric_name,(asymmetric_name),distance<br>
-* ''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
+* ''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'' - this is the name of the loaded asymmetric unit that you wish to reproduce neighboring crystal partners for
+* ''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)'' - 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.
+* ''(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'' - in Angstroms; reproduce any other unit that has any part of it falling withing ''distance'' Angstroms from the original asymetric unit
+* ''distance'' (cutoff) - in Angstroms; reproduce any other unit that has any part of it falling withing ''distance'' Angstroms from the original asymmetric unit
@@ Line 31: / Line 41: @@
 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.  I'm not sure how large too large is, but be aware of this.
+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.

← Older revision	Revision as of 03:36, 28 March 2014
(No difference)

@@ Line 3: / Line 3: @@
 [[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 =
+== 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]
+symexp prefix, object, selection, cutoff [, segi]
 </source>
@@ Line 14: / Line 14: @@
 symexp name_for_new_objects,asymmetric_name,(asymmetric_name),distance
 </source>
-= EXAMPLE =
+* '''prefix''' = string: name prefix for new objects
 load any .pdb file into PyMOL (here we use 1GVF).<br>
@@ Line 49: / Line 48: @@
 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 =
+== 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 ?''.
 [[Category:Commands|Symexp]]

@@ Line 15: / Line 15: @@
 load any .pdb file into PyMOL (here we use 1GVF).<br>
-add image of 1GVF
+[[Image:1GVF_assym.png]]
 At the PyMOL command prompt type the following:<br>
@@ Line 21: / Line 21: @@
 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
+[[Image:1GVF_1A.png]]
@@ Line 27: / Line 27: @@
 If we color all of the sym* cyan we will produce the following:<br>
-add image of 1GVF_5A
+[[Image:1GVF_5A.jpeg]]
-As you can see, we can begin to understand the crystal environment of our asymmetric unit.<br>
+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.  I'm not sure how large too large is, but be aware of this.
 --[[User:Baker1|Baker1]] 13:41, 10 November 2008 (CST)
 [[Category:Commands|symexp]]