Cyclic protein: Difference between revisions

Latest revision as of 21:22, 16 August 2022

To build a model of a cyclic protein, you must do two things:

Disable the default patching, which would create a C and N terminus.
Use the LINK patching residue in the special_patches routine to link the last and first residues.

For example, the script below builds a cyclic model of 1fdx using 5fd1 as a template (alignment.ali is the example from the Modeller distribution).

⚠️ It is important that you get the residue order correct; the residues must be the last and first residue in the cyclic protein respectively (in the model, not the template). If in doubt, build a regular model first and look at the residue numbers and chain IDs in the final models or .ini file.

from modeller import *
from modeller.automodel import *

log.verbose()
env = Environ()

# Disable default NTER and CTER patching
env.patch_default = False 

class MyModel(AutoModel):
    def special_patches(self, aln):
        # Link between last residue (-1) and first (0) to make chain cyclic:
        self.patch(residue_type='LINK',
                   residues=(self.residues[-1], self.residues[0]))

# Use the new 'MyModel' class rather than 'AutoModel'
a = MyModel(env, alnfile='alignment.ali', knowns='5fd1', sequence='1fdx')

a.starting_model = a.ending_model = 1
a.make()

@@ Line 1: / Line 1: @@
 __NOTOC__
+<!-- ## page was renamed from Cyclic_protein -->
 To build a model of a cyclic protein, you must do two things:
 # Disable the default patching, which would create a C and N terminus.
 # Use the LINK patching residue in the '''special_patches''' routine to link the last and first residues.
-For example, the script below builds a cyclic model of 1fdx using 5fd1 as a template (attachment:alignment.ali is the example from the Modeller distribution).
+For example, the script below builds a cyclic model of 1fdx using 5fd1 as a template ([https://salilab.org/modeller/archive/cyclic-protein-example/alignment.ali alignment.ali] is the example from the Modeller distribution).
-/!\ It is important that you get the numbering of '''residue_ids''' correct; the residue numbers must correspond to the '''last''' and '''first''' residue in the cyclic protein respectively (in the model, not the template). If in doubt, build a regular model first and look at the residue numbers in the final models or `.ini` file.
+⚠️ It is important that you get the residue order correct; the residues must be the '''last''' and '''first''' residue in the cyclic protein respectively (in the model, not the template). If in doubt, build a regular model first and look at the residue numbers and chain IDs in the final models or <code>.ini</code> file.
-<pre><nowiki>#!python
+<syntaxhighlight lang="python">
+from modeller import *
 from modeller.automodel import *
 log.verbose()
-env = environ()
+env = Environ()
 # Disable default NTER and CTER patching
 env.patch_default = False
-class mymodel(automodel):
+class MyModel(AutoModel):
      def special_patches(self, aln):
-         # Link between residues 54 and 1 to make chain cyclic:
+         # Link between last residue (-1) and first (0) to make chain cyclic:
          self.patch(residue_type='LINK',
-                    residues=(self.residues['54'], self.residues['1']))
+                    residues=(self.residues[-1], self.residues[0]))
-# Use the new 'mymodel' class rather than 'automodel'
+# Use the new 'MyModel' class rather than 'AutoModel'
-a = mymodel(env, alnfile='alignment.ali', knowns='5fd1', sequence='1fdx')
+a = MyModel(env, alnfile='alignment.ali', knowns='5fd1', sequence='1fdx')
 a.starting_model = a.ending_model = 1
 a.make()
-</nowiki></pre>
+</syntaxhighlight>
+[[Category:Examples]]