[Chimera-users] Need help with fit into segment function

Elaine Meng meng at cgl.ucsf.edu
Mon Oct 28 11:53:38 PDT 2013

Hi Michael,
Chimera's fitting doesn't have options to constrain the fits to make specific residues close to one another.  To do something like that, you may want to look into some other programs, such as mentioned in this recent post:


DOCK development is by a separate group, so you'd probably want to ask them about the download.  (I don't know the answer.) 

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

On Oct 28, 2013, at 11:42 AM, Michael Matho <mmatho at liai.org> wrote:

> Thanks so much Elaine.
> I had figured it out over the week end, but your explanations are spot on.
> I do have another question: I discovered that my map's resolution is too low to embed the molecules accurately (i.e that the interface between molecules corresponds to the known amino acid interface definition, which was determined via other methods (DXMS, X-ray crystallography, alanine scan and mutation analysis).
> Is there a way to guide the embedding process by giving interface definitions as input? I would rather not just do it manually so I can explain my protocol in a manuscript.
> That would be of tremendous help.
> Alternatively, I requested "Dock" software, in order to previously dock the molecules to each other (using the interface as ligand, and then superimposing the whole molecule to the 'ligand').
> The problem is, it said that it worked for OSX but on the download page it doesn't offer OSX as an option, only the source.
> Do I have to download the source or is there another page to download the OSX version?
> Thanks so much,
> Michael

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