[Chimera-users] resolution for volume fitting

Bala subramanian bala.biophysics at gmail.com
Wed Mar 7 13:51:18 PST 2012

Hi Elaine,

Thank you.

I wanted to ask about choosing an optimal threshold level of the volume
data (the experimental map) instead of which i wrote as resolution of the
volume data. I admit that i have not mentioned it clearly in the previous

I tried to fit a structure on to a map and i found that the correlation
value, Avg and Inside in the fit-list changes depending up on the threshold
level of the volume data i chose. So i am not getting how to choose a
correct threshold value of the volume data.


On Wed, Mar 7, 2012 at 7:01 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Bala,
> Since you can't control the resolution of the experimental density map,
> I'm guessing you mean what resolution value to use for the map simulated
> from the atoms that are being fit into the map (simulating a second map
> allows scoring the fit by map-map correlation).
> I believe you would want to use the same or similar value to the
> experimental map's resolution.  In turn, that value should be available
> from the database where you got the map and/or the publication describing
> the map (or if not publicly available, the scientists who did the
> experiment).
> 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 Mar 7, 2012, at 3:22 AM, Bala subramanian wrote:
> > Friends,
> >
> > I am a newbie to fitting molecular structures on a volume map. I would
> appreciate if someone could suggest me some guidelines to choose an optimal
> resolution of the map before fitting.
> >
> > Thanks,
> > Bala
> >
> > --
> > C. Balasubramanian

C. Balasubramanian
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