[Chimera-users] Calculating correlation value between PDB and volume

[Elaine Meng]

Dear Long Gui,
If you turn off both "rotation" and "shift" in the Fit in Map dialog (after showing Options) it is not supposed to move the atoms.  You should probably get a newer version because 1.14 is quite old, but as far as I know that would not change this behavior.  Nevertheless I did the test below in a much newer version, a 1.17 daily build.  The most recent release of Chimera is 1.16 from December 
<https://www.rbvi.ucsf.edu/chimera/download.html>
...and I would expect it to behave the same as in my tests.   Or, you could use ChimeraX instead, which has the same fitting capabilities and options as Chimera, although the command syntax and dialog appearance may be slightly different.

In Chimera 1.17:
I tested this by making a fake example of manually moving atomic model #1 near density calculated from some other model #0, and then entering values in the Fit in Map dialog and clicking the Update button.  This worked correctly for me, meaning that the atomic model #1 did not move from where I put it.  Here is an image of the settings in my dialog:



Alternatively, you can use the "measure correlation" command but only after the simulated map is created (either with the Fit in Map dialog as above, or with "molmap" command), because it requires specifying two maps:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#correlation>

"molmap" command:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.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 Feb 1, 2022, at 10:09 AM, Long Gui via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Dear Chimera-user group,
> I am using Chimera version 1.14. After I have manually place the PDB model in the volume file, I would like to calculate the correlation value between the current position of PDB file and the volume. I have used "Fit dialog" and "use simulated map" but the correlation value only displayed the optimized value after shift and rotation. I have also disabled "rotation" and "shift" but the results were the same.
> 
> Because my volume contains more proteins than the PDB files, the "Fit in map" always place the PDB files into the densities corresponding to other proteins. I just want to have the correlation value between the manually placed PDB and the volume. How could I do this in Chimera? 
> Thanks,
> Long Gui, Ph.D. 

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