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 modeller-care@salilab.org
> 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 > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage >