Re: [modeller_usage] Model missing residues in a trimer

["Panagiotis L. Kastritis" <>]

Hello 

Thank you for your immediate response. 
it gives an error, saying 'no such residue 1:B'
Here is my alignemnt

>P1;1A2K_b
structureX:1A2K_b:4:A:445 :C::: : 
---KPIWEQIGSSFIQHYYQLFDNDRTQLGAIYIDASCLTWEGQQFQGKAAIVEKLSSLP

FQKIQHSITAQDHQPTPDSCIISMVVGQLKADEDPIMGFHQMFLLKNINDAWVCTNDMFR
LALHNF-
/
---KPIWEQIGSSFIQHYYQLFDNDRTQLGAIYIDASCLTWEGQQFQGKAAIVEKLSSLP
FQKIQHSITAQDHQPTPDSCIISMVVGQLKADEDPIMGFHQMFLLKNINDAWVCTNDMFR
LALHNFG
/

-------QVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIK
FNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLC
GNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMP
ALAPPEVVMDPALAAQYEHDLEV-------------

*
>P1;1A2K_b_fill
sequence:1A2K_b_fill:1:A:470:C::: :
MGDKPIWEQIGSSFIQHYYQLFDNDRTQLGAIYIDASCLTWEGQQFQGKAAIVEKLSSLP
FQKIQHSITAQDHQPTPDSCIISMVVGQLKADEDPIMGFHQMFLLKNINDAWVCTNDMFR
LALHNFG
/
MGDKPIWEQIGSSFIQHYYQLFDNDRTQLGAIYIDASCLTWEGQQFQGKAAIVEKLSSLP

FQKIQHSITAQDHQPTPDSCIISMVVGQLKADEDPIMGFHQMFLLKNINDAWVCTNDMFR
LALHNFG
/
MAAQGEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIK
FNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLC
GNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMP

ALAPPEVVMDPALAAQYEHDLEVAQTTALPDEDDDL
*

and here is my script

from modeller import *
from modeller.automodel import *    # Load the automodel class

log.verbose()
env = environ()

# directories for input atom files

env.io.atom_files_directory = ['.', '../atom_files']

class MyModel(automodel):
    def select_atoms(self):
        return selection(self.residue_range('1:A', '3:A'),
                         self.residue_range('124:A', '124:A'),

                         self.residue_range('1:B', '3:B'),
                         self.residue_range('1:C', '7:C'),
                         self.residue_range('204:C', '216:C'))

a = MyModel(env, alnfile = '1a2k.ali',
            knowns = '1A2K_b', sequence = '1A2K_b_fill')
a.starting_model= 1
a.ending_model  = 1

a.make()

Can you tell me what i am doing wrong? 

Thank you very much for your help 

panagiotis

2009/10/26 Modeller Caretaker <">>

Panagiotis Kastritis wrote:

I would like to ask you how is it possible to model missing residues in a trimer that I have.

The scripts at http://salilab.org/modeller/wiki/Missing%20residues should do the job.

but how can I expand it to more than one chain?

You will need to change your alignment, adding chain breaks ('/' character) where necessary; the first script on that page will write out something suitable. You won't need to change the modeling scripts, unless you explicitly select residue ranges, in which case obviously you will need to change the residue IDs (e.g. to add a chain ID, so '133', '135' might turn into '133:A', '135:A').

       Ben Webb, Modeller Caretaker
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