[Chimera-users] Cannot dock molecule to targeted region?

[sunyeping]

Hi Tom,

Thank you for your suggestions and instructions. I have tried your method. Yes, the  "Optimize correlation" option in the "Fit in Map" tool can avoid large shit of the molecule. However, the problem with this method is that the final fitted result is determined by the initial position of the antibody molecule. I have no idea how the antibody binds the antigen, and my expectation is to find the correct binding positon of the antibody to the antigen by using the fitting tools of chimera. The only thing I know is that the CDRs face of the antibody should be placed towards the antigen. I have put the coordinations for the antigen (Ag, S.pdb) and the antibody (Ab, 4-8_H3-0175.pdb) at the following link:
          https://drive.google.com/drive/folders/16ELIDsUxiNwRGp9ely2SRn-zjAdHCudH?usp=sharing

Firstly, I fitted the Ag to the map for the ag-ab complex (emd_22158.map), then I put the antibody to target area of the map, and then used Fit in Map tool to fit it and get the complex coordinate fit-in-map_1.pdb. After that, I had another try. I put the Ab at the same initial position in the target area but rotated it by 180 degree around its long axis, then fit it, and get complex coordinate fit-in-map_1.pdb. Both of the two  complex coordinate can also  be found at the above link. In these two complex structures, the heavy chain (H) and light chain (L) of the Ab are totally opposite (a rotation of 180 degree). 
         Maybe you could try to do the fitting and find the most reasonable binding mode of the Ab? One clue is that the CDR3 of the H chain (residue 93-107) should usually be involved in contact with the antigen.

Best regards,
Yeping
------------------------------------------------------------------
From:Tom Goddard <goddard at sonic.net>
Sent At:2020 Aug. 20 (Thu.) 01:15
To:孙业平 <sunyeping at aliyun.com>
Cc:chimera-users <chimera-users at cgl.ucsf.edu>; Greg Pintilie <gregdp at gmail.com>
Subject:Re: [Chimera-users] Cannot dock molecule to targeted region?

Hi Yeping,

  As Greg says Chimera is trying to move your antibody into higher density.  Besides the masking he suggests, another thing you can do is just use the Fit in Map tool (not Fit to Segments), place your anti-body by hand in approximately the correct position using the "Active" checkbuttons in model panel and the mouse, and under options in the Fit in Map tool choose "Optimize correlation" instead of "Optimize overlap".  The default optimize overlap means to move the molecule into the highest density, but optimizing correlation instead moves it to get the best agreement between the shape of the density.  That option will be grayed out until you check "Use map simulated from atoms" since correlation needs a simulated map, and you should enter the approximate resolution of your map.  I don't think Fit to Segments offers that option to optimize correlation.  When you use Fit in Map it just does a local optimization so your initial placement and orientation of the antibody has to be approximately right.

 Tom



On Aug 19, 2020, at 5:13 AM, Greg Pintilie <gregdp at gmail.com> wrote:

Hi Yeping,

It seems that the part of the map you are fitting to has lower values, and the Fit-To-Segments procedure is moving the model (your antibody) towards higher values. To prevent this, there is an option in the Fit To Segments dialog ‘Mask map with region(s) to prevent large drifts’. If you enable this option you should not see the model move outside the region. You may have to press the Options button at the bottom of the dialog first to reveal this option if you don’t see it. Also make sure to try ‘Rotational search’ if the default/faster ‘Align principal axes’ doesn’t seem to find the right fit.

There is also the ‘fitmap’ command in Chimera which does a more global search, perhaps the Chimera team may have some advice on it in this scenario, but I think you have the right idea with segmenting first and then doing the fit - it’s a bit more work but you can target the search better with it.
https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/fitmap.html

Greg


On Aug 19, 2020, at 1:53 AM, 孙业平 <sunyeping at aliyun.com> wrote:
Dear all,

    I am trying to fit an antibody molecule to the cryo-EM density map for an antigen-antibody complex. The related files can be found at the following link
 https://drive.google.com/drive/folders/16ELIDsUxiNwRGp9ely2SRn-zjAdHCudH?usp=sharing.
I first segmented the map ("emd_22158.map") and get the segment map ("emd_22158.seg") in chimera. Then I selected the regions corresponding to the antibody and use the "Fit to segments" tool of chimera to fit the antibody molecule. The "image1.png" shows the inital antibody postion and the expected docking postion in the segmented complex density (indicated by the red arrow). However, the antibody molecule cannot be fitted into the selected target  region after this operation, but moved to the position shown in "image2.png (only the target regions are shown). 
    I have tried to ungoup and regroup the target region to make its overall shape more simial to the antibody, and place the antibody into the region and ajust its orienation, but whatever I tried, the results are the same: the antibody will move to the position shown in "image2.png" after performing the "Fit to segments" action.
    I wonder whether it is impossible to dock the antibody to the expected position with chimera or there is anything wrong with my operation. Could you help me with this issue? I will appreciate any help from you.

Best regards,
Yeping Sun_______________________________________________
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