Hi Bala,

One idea is to set the density map contour level so that the surface encloses the expected volume for the molecular assembly. An example of that is in a Chimera tutorial

http://www.cgl.ucsf.edu/chimera/data/tutorials/eman07/chimera-eman-2007.html#part2

Just the data inside the contour level is used for computing correlation coefficients in Chimera (unless "use only data above contour level..." option is turned off). So the contour level has a big effect on the fit correlation coefficients, for example it might vary from 0.5 for a low contour level to 0.9 for a high contour level. It doesn't mean the fits are any different -- they could be in identical positions. But the data used for calculating the correlation is different. People rarely talk about this but basically you can get any correlation value you want. Which contour level is best. There is no obvious answer to that. But the suggestion above to use the level to enclose the right volume is sensible to try.

Tom

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 mail.

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.

Cheers,
Bala

On Wed, Mar 7, 2012 at 7:01 PM, Elaine Meng <meng@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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