[Chimera-users] building large size polymer

Elaine Meng meng at cgl.ucsf.edu
Mon May 2 13:56:41 PDT 2011

Hi Hongmin,
Sorry, there is no general polymer-building feature, only for chains of amino acids (Tools... Structure Editing... Build Structure, Start Structure tab, "peptide sequence").

If you have a monomer (or small multimer) of your polymer and know the symmetry operations needed to place additional copies of that structure, you could use the command "sym."  However, it may be difficult to figure out the proper helical or translational symmetry parameters. Also, these copies would not be bonded to each other.

To bond the copies you would have to first put all of them in one model (see command "combine") and then use several "bond" commands, which you would probably want to generate by a script.  So, it might be possible with Chimera, but not very convenient, so you may want to do polymer-building in another program if possible.

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

On May 2, 2011, at 2:23 AM, 윤홍민 wrote:

> Hello I am a student of Korea.(Yonsei Univ)
> I am working on molecular dynamic and use your program for making Mol2 files.
> And now I have tried to make large size polymer that has many monomer.
> I usually use SMILES string for constructing structure.
> In this case, but I could not put the all SMILES strings for constructing.
> Because I have to connet almost 100 monomers.
> Is there a specific fuction or tool for the problem?
> I really appreciate your work.
> Sincerely.
> - Hongmin

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