Zero residues - Revision history

Bell: 8 revisions

2014-03-28T04:07:14Z

8 revisions

Speleo3: added chains argument

2013-01-26T11:06:45Z

added chains argument

Warren: /* CODE */

2009-05-12T17:10:09Z

CODE

New page

== 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 ==
<source lang="python">
zero_residues 1AFK
zero_residues *

# make the first residue's number, 30.
zero_residues 1AFK, 30
</source>

== 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 ==
<source lang="python">
import pymol

def zero_residues(sel1,offset=0):
"""
PURPOSE: renumbers the residues so that the first one is zero, or offset .
USAGE: zero_residues protName # first residue is 0
USAGE: zero_residues protName, 5 # first residue is 5
EXAMPLE: zero_residues *
"""
offset = int(offset)

# variable to store the offset
stored.first = None
# get the names of the proteins in the selection
names = cmd.get_names(selection=sel1)

# for each name shown
for p in names:
# get this offset
cmd.iterate("first %s and polymer and n. CA" % p,"stored.first=resi")
# don't waste time if we don't have to
if ( 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.sort()

# let pymol know about the function
cmd.extend("zero_residues", zero_residues)
</source>

[[Category:Script_Library|Zero Residues]]
[[Category:ObjSel_Scripts]]

← Older revision	Revision as of 04:07, 28 March 2014
(No difference)

@@ Line 19: / Line 19: @@
 == CODE ==
 <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
-        USAGE: zero_residues protName, 5 # first residue is 5
+    Renumbers the residues so that the first one is zero, or offset
-        EXAMPLE: zero_residues *
          """
          offset = int(offset)
@@ Line 33: / Line 43: @@
          stored.first = None
          # get the names of the proteins in the selection
-         names = cmd.get_names(selection=sel1)
          # for each name shown
          for p in names:
                  # 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
-                 if ( stored.first == offset ):
+                 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.sort()
 # let pymol know about the function