Hi Qing,

As you observed, different programs report different correlation values. You can get any correlation value you want by changing the region over which the correlation is computed, or the formula for the correlation, or the resolution of the simulated map.

First Chimera 1.5 or newer reports two correlation values: the correlation about the mean and the correlation about 0.   It is typical for EM maps to report the correlation about zero which is usually much higher. If you use the old Chimera 1.4 it only reports the lower correlation about mean. Formulas for these two correlation values are given in the Chimera manual.

Next you need to choose the region over which the correlation is calculated. Your approach of setting the simulated map contour level so the enclosed volume is what is expected is good. Make sure you list the simulated map first in the measure correlation command since the first volume determines the region for the computation.

Lastly, the simulated map resolution should match the map resolution. There are different definitions of resolution used by the EM community -- it is controversial. In any case you want the simulated map to match the level of detail seen in the experimental map. If it doesn't match then you will get lower correlation.   You may need to try a range of resolutions. The molmap documentation describes the different options for how the resolution value is used to make the simulated map.

Unfortunately reported correlation values in publications rarely describe all the above choices so the values are not very meaningful or reproducible.

    Tom

-------- Original Message --------
Subject: Re: [Chimera-users] CC calculation
From: Qing Xie
To: Tom Goddard
Date: 1/26/12 11:31 AM

Hi, Tom,

Thanks for your help!

I'm helping to model a structure (.pdb) into a EM density map.... This is my first time using Chimera. I got a CC of ~0.87 after refining the structure against the EM map using Rsref in CNS. I was suggested to cross-check the CC by using Chimera since Chimera is more popular in EM community.

I calculated the simulated map following your email, but the CC varies a lot by choosing different contour level for the EM map (#0). The EM map's range is from -0.12 to 0.17 (sigma 0.013), while the simulated map's range is from 0 to 2.64 (sigma 0.20). After I tried to claculate the volumes and then matchs the volume of (#0) to (#1), CC is only ~0.63.

I also tried CCP4 overlapmap and it gave me a CC of ~0.73.

Do you have any other suggestions?

Thank you very much!

Qing

Tom Goddard wrote:

If the PDB (#1) is already fit to the map (#0) you could create a simulated map for the pdb then measure its correlation with the experimental map:

    molmap #1 12.5
    measure correlation #2 #1

The 12.5 in the molmap command is the resolution for the simulated map which should match the experimental map. By default the correlation will be measured within the displayed contour level of the first map given in the command.

The commands are described in the Chimera User's Guide.

http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/molmap.html
http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/measure.html#correlation

   Tom

Hi,

Can anyone help me with calculating correlation coefficient from a .pdb model to a .mrc map?

Thank you!

Qing