BiologicalUnit - Revision history

Cchem: 1 revision

2016-09-19T02:19:30Z

1 revision

Speleo3: assembly

2016-09-01T13:42:48Z

assembly

Pyadmin: 15 revisions

2014-03-28T01:06:26Z

15 revisions

Hongbo zhu: /* See Also */

2012-09-21T10:59:44Z

Zhentg: /* Usage */

2011-09-26T05:06:30Z

Usage

Newacct at 08:07, 19 May 2011

2011-05-19T08:07:05Z

Speleo3: drop cmd.extend calls

2011-03-12T11:48:16Z

drop cmd.extend calls

Speleo3: see also BiologicalUnit/Quat

2011-03-12T11:24:48Z

see also BiologicalUnit/Quat

New page

This script can be used to re-create biological units for proteins. (This was created as a workaround of PyMOL's semi-functioning [[Symexp]] command.) It's also a fun script to play with for learning about symmetry.

<gallery widths=250px heights=250px>
Image:before.png|single unit, before running this program
Image:after.png|after the expansion of the 60 units
Image:1rmv fiber.png|Example creating the biological unit for PDB 1RMV created from fiber diffraction.
</gallery>

= Usage =
<source lang="python">
symMat = readSymmetry("/path/to/some/pdbFile.pdb","pdbFile")
biologicalUnit("mates", "pdbFile", symMat)
</source>

= The Code =
<source lang="python">
#
# Jason Vertrees <Jason-dot-Vertrees-at-schrodinger_dot_com>, 2010.
#
import string
import pymol
from pymol import cmd

def readSymmetry(inFile, verbose=None):
"""
This function will read "inFile" and glean the
symmetry operations, if any, from it.

PARAMS
inFile
(string) path to PDB file

verbose
(boolean) if verbose is not None, print more

RETURNS
matrix
Array of lists. One 16-element list per symmetry operation. Feed this matrix
into manualSymExp in order to make the other symmetry mates in the biological unit
"""
# a remark-350 lines has:
# REMARK 350 BIOMTn TAGn X Y Z Tx
REM, TAG, BIOMT, OPNO, X, Y, Z, TX = range(8)

thePDB = open(inFile, 'rb').readlines()

matrices = []
curTrans = -1

# The transformation is,
# output = U*input + Tx

for l in thePDB:
tokens = string.split(l)
if len(tokens)!=8:
continue
if tokens[REM]=="REMARK" and tokens[TAG]=="350" and tokens[BIOMT].startswith("BIOMT"):
if tokens[OPNO]!=curTrans:
# new transformation matrix
matrices.append([])

matrices[-1].append( map( lambda s: float(s), tokens[X:]))
curTrans = tokens[OPNO]

if verbose!=None:
print "Found %s symmetry operators in %s." % (len(matrices), inFile)
return matrices

def biologicalUnit(prefix, objSel, matrices ):
"""
Manually expands the object in "objSel" by the symmetry operations provided in "matrices" and
prefixes the new objects with "prefix".

PARAMS
prefix
(string) prefix name for new objects

objSel
(string) name of object to expand

matrices
(list of 16-element lists) array of matrices from readSymmetry

RETUNRS
None

SIDE EFFECTS
Creates N new obects each rotated and translated according to the symmetry operators, where N
equals len(matrices).
"""
for m in matrices:
n = cmd.get_unused_name(prefix)
cmd.create(n, objSel)
s1 = "%s + (x*%s + y*%s + z*%s)" % (m[0][3], m[0][0], m[0][1], m[0][2])
s2 = "%s + (x*%s + y*%s + z*%s)" % (m[1][3], m[1][0], m[1][1], m[1][2])
s3 = "%s + (x*%s + y*%s + z*%s)" % (m[2][3], m[2][0], m[2][1], m[2][2])
cmd.alter_state(1, n, "(x,y,z) = (%s, %s, %s)" % (s1, s2, s3) )

cmd.extend("readSymmetry", readSymmetry)
cmd.extend("biologicalUnit", biologicalUnit)
</source>

= Notes =
This is slow compared to [[Symexp]]; use the above for learning, playing and when [[Symexp]] doesn't work as advertised.

= See Also =
*[[BiologicalUnit/Quat]] (alternative implementation)
*[[Symexp]]
*[[SuperSym]]
*[http://pdbbeta.rcsb.org/pdb/static.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html PDB Tutorial Biol. Units]
*[http://en.wikipedia.org/wiki/Fiber_diffraction Wikipedia article]

[[Category:Script_Library]]
[[Category:Math_Scripts]]
[[Category:Structural_Biology_Scripts]]

← Older revision	Revision as of 02:19, 19 September 2016
(No difference)

@@ Line 1: / Line 1: @@
 This script can be used to re-create biological units for proteins.  (This was created as a workaround of PyMOL's semi-functioning [[Symexp]] command.)  It's also a fun script to play with for learning about symmetry.
@@ Line 108: / Line 112: @@
 *[http://www.rcsb.org/pdb/static.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html PDB Tutorial Biol. Units]
 *[http://en.wikipedia.org/wiki/Fiber_diffraction Wikipedia article]
 [[Category:Script_Library]]
 [[Category:Math_Scripts]]
 [[Category:Structural_Biology_Scripts]]

← Older revision	Revision as of 01:06, 28 March 2014
(No difference)

@@ Line 106: / Line 106: @@
 *[[Symexp]]
 *[[SuperSym]]
-*[http://pdbbeta.rcsb.org/pdb/static.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html PDB Tutorial Biol. Units]
+*[http://www.rcsb.org/pdb/static.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html PDB Tutorial Biol. Units]
 *[http://en.wikipedia.org/wiki/Fiber_diffraction Wikipedia article]

@@ Line 9: / Line 9: @@
 = Usage =
 <source lang="python">
 symMat = readSymmetry("/path/to/some/pdbFile.pdb","pdbFile")
 biologicalUnit("mates", "pdbFile", symMat)

@@ Line 18: / Line 18: @@
 # Jason Vertrees <Jason-dot-Vertrees-at-schrodinger_dot_com>, 2010.
+#
 import pymol
 from pymol import cmd
@@ Line 52: / Line 51: @@
    for l in thePDB:
-     tokens = string.split(l)
+     tokens = l.split()
      if len(tokens)!=8:
        continue

@@ Line 97: / Line 97: @@
      s3 = "%s + (x*%s + y*%s + z*%s)" % (m[2][3], m[2][0], m[2][1], m[2][2])
      cmd.alter_state(1, n, "(x,y,z) = (%s, %s, %s)" % (s1, s2, s3) )
 </source>