[Chimera-users] the docking confidence score

Yanhe Zhao yanhezhao1990 at gmail.com
Wed Jan 26 16:38:38 PST 2022

Hello there,

Here is continuous question about sequential docking score:

By eyes I can find that models have good fitting to my EM, and the
correlation is 0.8 (I calculate it in two ways: each or all of them). But I
was curious in what range we could consider the docking reliable?

Thanks and cheers,

Elaine Meng <meng at cgl.ucsf.edu> 于2022年1月25日周二 15:18写道:

> Hi Yanhe,
> Chimera does not calculate a single overall score for the sequential
> fitting of multiple structures.
> Sequential fitting just fits one structure locally, then subtracts density
> from where that structure is, then fits the next structure locally, etc.
> So structures are only fit (and scored) one at a time, and it depends what
> order they are in and also their starting positions since they are only fit
> locally.  However, you can keep iterating sequentially through all of the
> structures multiple times to improve the results.
> See sequential fitting help
> <
> https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#sequence
> >
> ...and video
> <https://www.cgl.ucsf.edu/chimera/videodoc/FitSeq/>
> So you have to use your own knowledge of the system both in initially
> placing the structures (although you could do that by a previous fitting
> calculation) and in evaluating the results.
> To get correlations for each of the structures in their current positions
> after sequential fitting, you can use the Fit in Map tool (use the Options
> to turn off rotation and shift if you don't want them to move any more) or
> "measure correlation" command (which will give numbers in the Reply Log
> opened from Favorites menu).
> Maybe you could make a single molmap from all of the structures together
> and then use "measure correlation" to compare it with the original
> experimental map to get an overall correlation.
> <
> https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#correlation>
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>
> Another way to evaluate the results is to look for clashes between the
> atomic structures (e.g. Find Clashes tool or findclash command).
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.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 Jan 25, 2022, at 12:23 PM, Yanhe Zhao via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >
> > Greeting there,
> >
> > I'm doing the sequential fitting to fit 3 models to my map. The question
> is where I can find the docking confidence score?
> >
> > I did try molmap to simulate the map of one model and then use the  "Fit
> in map" to have the correlation readout.
> > But I'm not sure is the correlation good to describe confidence, and
> what I want is the score to describe overall confidence of sequential
> fitting not just one model.
> > So any log file I can find to report the score of docking?
> >
> > Thanks and cheers,
> > Yanhe
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