Difference between revisions of "Zero residues"

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(OVERVIEW)
(added chains argument)
 
(4 intermediate revisions by 2 users not shown)
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zero_residues 1AFK
 
zero_residues 1AFK
 
zero_residues *
 
zero_residues *
 +
 +
# make the first residue's number, 30.
 +
zero_residues 1AFK, 30
 
</source>
 
</source>
  
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== CODE ==
 
== CODE ==
 
<source lang="python">
 
<source lang="python">
import pymol
+
from pymol import cmd, stored
  
def zero_residues(sel1,offset=0):
+
def zero_residues(sel1,offset=0,chains=0):
 
         """
 
         """
        PURPOSE: renumbers the residues so that the first one is zero, or offset           .
+
DESCRIPTION
        USAGE: zero_residues protName   # first residue is 0
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        USAGE: zero_residues protName, 5 # first residue is 5
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    Renumbers the residues so that the first one is zero, or offset
        EXAMPLE: zero_residues *
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 +
USAGE
 +
 
 +
    zero_residues selection [, offset [, chains ]]
 +
 
 +
EXAMPLES
 +
 
 +
    zero_residues protName           # first residue is 0
 +
    zero_residues protName, 5         # first residue is 5
 +
    zero_residues protName, chains=1  # each chain starts at 0
 +
    zero_residues *
 
         """
 
         """
 
         offset = int(offset)
 
         offset = int(offset)
Line 30: Line 43:
 
         stored.first = None
 
         stored.first = None
 
         # get the names of the proteins in the selection
 
         # get the names of the proteins in the selection
         names = cmd.get_names(sel1)
+
 
 +
         names = ['(model %s and (%s))' % (p, sel1)
 +
                        for p in cmd.get_object_list('(' + sel1 + ')')]
 +
 
 +
        if int (chains):
 +
                names = ['(%s and chain %s)' % (p, chain)
 +
                                for p in names
 +
                                for chain in cmd.get_chains(p)]
  
 
         # for each name shown
 
         # for each name shown
 
         for p in names:
 
         for p in names:
 
                 # get this offset
 
                 # get this offset
                 cmd.iterate("first %s and polymer and n. CA" % p,"stored.first=resi")
+
                 ok = cmd.iterate("first %s and polymer and n. CA" % p,"stored.first=resv")
 
                 # don't waste time if we don't have to
 
                 # don't waste time if we don't have to
                 if ( stored.first == offset ):
+
                 if not ok or stored.first == offset:
 
                         continue;
 
                         continue;
 
                 # reassign the residue numbers
 
                 # reassign the residue numbers
 
                 cmd.alter("%s" % p, "resi=str(int(resi)-%s)" % str(int(stored.first)-offset))
 
                 cmd.alter("%s" % p, "resi=str(int(resi)-%s)" % str(int(stored.first)-offset))
 
                 # update pymol
 
                 # update pymol
                cmd.sort()
+
 
 +
        cmd.rebuild()
  
 
# let pymol know about the function
 
# let pymol know about the function
Line 48: Line 69:
 
</source>
 
</source>
  
[[Category:Script_Library]]
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[[Category:Script_Library|Zero Residues]]
 +
[[Category:ObjSel_Scripts]]

Latest revision as of 06:06, 26 January 2013

OVERVIEW

This script will renumber all the residues such that the first one is numbered 0. This is often helpful when dealing with alignments.

Ordering from Sequence End

If you want to change numbering based off the last residue's number in the sequence, just replace first in the code with last.

EXAMPLE

zero_residues 1AFK
zero_residues *

# make the first residue's number, 30.
zero_residues 1AFK, 30

INSTALL

Copy the source code below, to "zero_residues.py" and then simply run the file. The command, "zero_residues" will now be defined and can be used as in the examples above.

CODE

from pymol import cmd, stored

def zero_residues(sel1,offset=0,chains=0):
        """
DESCRIPTION

    Renumbers the residues so that the first one is zero, or offset

USAGE

    zero_residues selection [, offset [, chains ]]

EXAMPLES

    zero_residues protName            # first residue is 0
    zero_residues protName, 5         # first residue is 5
    zero_residues protName, chains=1  # each chain starts at 0
    zero_residues *
        """
        offset = int(offset)

        # variable to store the offset
        stored.first = None
        # get the names of the proteins in the selection

        names = ['(model %s and (%s))' % (p, sel1)
                        for p in cmd.get_object_list('(' + sel1 + ')')]

        if int (chains):
                names = ['(%s and chain %s)' % (p, chain)
                                for p in names
                                for chain in cmd.get_chains(p)]

        # for each name shown
        for p in names:
                # get this offset
                ok = cmd.iterate("first %s and polymer and n. CA" % p,"stored.first=resv")
                # don't waste time if we don't have to
                if not ok or stored.first == offset:
                        continue;
                # reassign the residue numbers
                cmd.alter("%s" % p, "resi=str(int(resi)-%s)" % str(int(stored.first)-offset))
                # update pymol

        cmd.rebuild()

# let pymol know about the function
cmd.extend("zero_residues", zero_residues)