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

sunyeping sunyeping at aliyun.com
Thu Aug 20 03:23:01 PDT 2020

Hi Greg,
     Thank you for your suggestions and instructions. 
     I have tried your method,and yes,  ‘Mask map with region(s) to prevent large drifts' for the Fit-to-segment can avoid large shift of the antibody molecule. However, I can not get the resonable fitting with the options you suggested yet. I have uploadeded the antibody (Ab, 4-8_H3-0175.pdb) and the antigen (Ag, S.pdb) to the link:

    After fitting the Ag to the map for the Ag-Ab complex (emd_22156.map), I then selected the target region(s) for the Ab and use the Fit-to-segment tool to fit it with the options ‘Align principal axes’ and  ‘Mask map with region(s) to prevent large drifts', and got the complex fit-to-segment_1.pdb. I also tried the option "‘Rotational search’" and got the complex  fit-to-segment_2.pdb. Unfortunately, in both of the two complex structure, there are obvious structural clash bewteen the Ag and the Ab. The  fit-to-segment_1.pdb and  fit-to-segment_2.pdb can also be found at the above link. Then I tried to adjust the size the target area by "ungroup" and "group" functions in the "Segment Map" tool to exclude the area occupied by the Ag in the target region, and get the emd_22156_regrouped.seg (which can be found at the above link). Howeve, when I fitted the Ab to target region this resegmented map, the Ab positions are wrong ( the CDRs face is not facing the Ag). 

    Do you have other suggestions for correct fitting of the Ab molecule?

Best regards,

From:Greg Pintilie <gregdp at gmail.com>
Sent At:2020 Aug. 19 (Wed.) 20:13
To:孙业平 <sunyeping at aliyun.com>
Cc:chimera-users <chimera-users at cgl.ucsf.edu>
Subject:Re: [Chimera-users] Cannot dock molecule to targeted region?

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.


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
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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