[Chimera-users] how to fit the em density map of crystal
liyaowang2911 at gmail.com
Fri Apr 1 10:11:29 PDT 2016
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
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:
> 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”
> Maybe researchers in this area will have more specific advice.
> I hope this helps,
> 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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