building modeller loops refinement

ARMIN HODAEI

4 Apr 2017 4 Apr '17

11:56 a.m.

Dear Chimera Users, I want to use refining loop option to build missing residues for my target protein. First I get the FASTA file structure of protein then I load it into Chimera, after that in the Structure tab I select load structure, then I see the protein. After that Again in the "Structure" tab I select Modeller(loops/refinement). The rest is easy for creating the new structure PDB. But the problem is that I want whole protein to be treated in this refinement, but it only chose one chain, How can I do this for both chains at once? Sincrely, -- Armin Hodaei Department of Physics, Faculty of Arts and Sciences Koc University, Istanbul

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Elaine Meng

4 Apr 4 Apr

3:42 p.m.

Dear Armin, Sorry, the Chimera-Modeller interface does not allow modeling more than one chain. Modeling a multimer or complex of multiple chains requires running Modeller separately. http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mo... Regards, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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On Apr 4, 2017, at 4:56 AM, ARMIN HODAEI wrote:

Dear Chimera Users, I want to use refining loop option to build missing residues for my target protein. First I get the FASTA file structure of protein then I load it into Chimera, after that in the Structure tab I select load structure, then I see the protein. After that Again in the "Structure" tab I select Modeller(loops/refinement). The rest is easy for creating the new structure PDB. But the problem is that I want whole protein to be treated in this refinement, but it only chose one chain, How can I do this for both chains at once? Sincrely, -- Armin Hodaei Department of Physics, Faculty of Arts and Sciences Koc University, Istanbul

ARMIN HODAEI

6 Apr 6 Apr

9:54 a.m.

Dear Elaine, Thank you for your email. So I build missing residues for my both chains separately, is there a way to combine these two chains after that process?? I mean, I have now two chains which they are both the outputs of Modeller, how to create a single PDB out of two processed PDB. Cheers, On Tue, Apr 4, 2017 at 6:42 PM, Elaine Meng wrote:

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Dear Armin, Sorry, the Chimera-Modeller interface does not allow modeling more than one chain. Modeling a multimer or complex of multiple chains requires running Modeller separately.

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ multalignviewer/modeller.html>

Regards, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

...
On Apr 4, 2017, at 4:56 AM, ARMIN HODAEI wrote:

Dear Chimera Users, I want to use refining loop option to build missing residues for my target protein. First I get the FASTA file structure of protein then I load it into Chimera, after that in the Structure tab I select load structure, then I see the protein. After that Again in the "Structure" tab I select Modeller(loops/refinement). The rest is easy for creating the new structure PDB. But the problem is that I want whole protein to be treated in this refinement, but it only chose one chain, How can I do this for both chains at once? Sincrely, -- Armin Hodaei Department of Physics, Faculty of Arts and Sciences Koc University, Istanbul

-- Armin Hodaei Department of Physics, Faculty of Arts and Sciences Koc University, Istanbul

Elaine Meng

3:51 p.m.

Dear Armin, You can either (1) just write a single PDB file that has two models in it, for example with menu: File… Save PDB, and in the resulting dialog make sure both models are highlighted in the “Save models” area, and then at the bottom specify to "Save multiple models in a single file.” http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb - or - (2) combine the two models into a single model before saving to file. Combining can be done with command “combine” or the “copy/combine” function in the right side of the Model Panel (open from Favorites menu). http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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On Apr 6, 2017, at 2:54 AM, ARMIN HODAEI wrote:

Dear Elaine, Thank you for your email. So I build missing residues for my both chains separately, is there a way to combine these two chains after that process?? I mean, I have now two chains which they are both the outputs of Modeller, how to create a single PDB out of two processed PDB. Cheers,

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ARMIN HODAEI
Elaine Meng