[Chimera-users] how to fit the em density map of crystal

Elaine Meng meng at cgl.ucsf.edu
Fri Apr 1 10:21:59 PDT 2016

Dear Yaowang,

I don’t know if this is similar to what you want, but there is a symmetric fitting option in the fitmap command. For that you would first have to assign symmetry to the map.

Or, maybe you could try building the larger  multiple-copy atomic structure first with Unit Cell or Multiscale Models tool or the “sym” command, then just fit it as if it were a single structure.  You might need to combine the multiple copies into a single model first (see “combine” command) and then fit that single large model into the map.

However, it is possible that you might not be able to get a good fit no matter what strategy you use, if the map is somehow inconsistent with the crystal structure. 

On Apr 1, 2016, at 10:11 AM, Yaowang Li <liyaowang2911 at gmail.com> wrote:

> Dear Elaine,
> thank you for your suggestion. 
> I want to fit using a peptide structure (a PDB file). It is a crystal's map, so we can see the regular arrangement in this map . Not like the map of single molecule or complex come from the single particle analysis,  it contains many molecules were arranged in a special way. I used the tools of dust, filter, segment, etc. But I did not obtain  a good fit, it is possible that I am not familiar with Chimera.  In addition, the map is not perfect, a part of map is not the exactly same to the another part, but it should be the same based on the space group. 
> Is it possible that I fit one peptide molecule inside first, and then rotate and translate it based on the space group (we have measured the unit cell parameters)? 
> Best Regards,
> Yaowang
> On Fri, Apr 1, 2016 at 6:06 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Dear Yaowang,
> It is unclear whether you want to fit the map with another map or with some atomic structure.  Either way, it can be done with Chimera, but the best strategy is really a question of scientific judgment that depends on both the details of your system and the available information.
> Chimera includes tools for filtering, segmentation, and map-map or map-atoms fitting.   See:
> <http://www.rbvi.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html>
> <http://www.rbvi.ucsf.edu/chimera/videodoc/videodoc.html>
> Several of these features are in the menu under Tools… Volume Data.  Click “Help” on any tool to see its documentation. There are also several commands that do mostly the same things, e.g. “fitmap”
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html>
> Maybe researchers in this area will have more specific advice.
> 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
> On Apr 1, 2016, at 8:51 AM, Yaowang Li <liyaowang2911 at gmail.com> wrote:
> > Dear all,
> >
> > I am thinking about how to fit the EM density map of crystal.
> > cryo-EM images of crystal were collected and reconstructed to a map, but with a poor resolution(around 7A). In this condition, which is the best way to fit the map?
> >
> > Best Regards,
> > Yaowang
> > LIC, Leiden University
> >
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