[Chimera-users] Fitting structures in biological assembly surfaces

[Elaine Meng]

Hi Ahmad,
It is not clear what you are fitting into what, so I will answer generally.

Unless you are just moving things with the mouse yourself, the surface by itself is not enough to fit.  You can fit atoms to other atoms, or fit atoms to a map (like a density map).  If your surface is actually an isosurface of a map, then you can fit the atoms to the map. 

Fit atoms to atoms:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>

Fit atoms to map: Fit in Map tool or “fitmap” command
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html>

Create a map from atoms (which could be pseudoatoms like a SAXS model):  “molmap” command
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>

Moving by hand:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On May 22, 2018, at 8:35 AM, Ahmad Abdelzaher <underoath006 at gmail.com> wrote:
> 
> Hello,
> I have a structure that generates a surface of the biological assembly. How can I fit this surface with my structures? 
> Regards.