Yes - I just had the models opened in the opposite order to you.
Ultimately, it seems to me that the problem here is that you’re asking for something impossible: a good overall structural alignment between two models that are fundamentally different. A rigid body alignment can only rotate and translate one model to overlay the other. If the two models are in very different conformations you have two choices: (a) get a bad overall all-atom alignment, or (b) try to find the biggest piece that *does* align well and just align that. By default MatchMaker takes the latter approach, which is why when you use it on your two models it ends up aligning just the antigen-binding region of the antibody fragment at the expense of everything else - that’s the biggest part of the two models that *can* be aligned well.
If you really want approach (a) you could use MatchMaker with the argument “cutOff None”, in which case it will try to find the best-aligning whole chain and align on that. You can also specify exactly which pair of chains you want to align on, as per the example in my previous email. Ultimately, though, nothing you do here is going to turn a bad AlphaFold prediction into a good one.
— Tristan
On Sun, 26 Mar 2023 at 22:43, Cheng Fei Phung feiphung@hotmail.com wrote:
Hi Tristan Croll,
I presume that you meant "match #2/H to #1/D" and "match #2/L to #1/C" instead?
See https://i.imgur.com/dXCzuIP.png and https://i.imgur.com/VbKhKCd.png
Regards, Phung Cheng Fei
*From:* Tristan Croll tcroll@altoslabs.com *Sent:* Monday, March 27, 2023 1:10 AM
*To:* Cheng Fei Phung feiphung@hotmail.com *Cc:* chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu *Subject:* Re: [chimerax-users] AlphaFold best_model.pdb could not visually overlap the input sequence using matchmaker
... huh. Looking at it again, it seems to me that AlphaFold has predicted the antibody heavy chain in the light chain conformation and vice versa. If you force it to align (predicted heavy) to (experimental light) with "match #2/D to #1/H" then all four antibody domains align reasonably well. Seems like a failure on AlphaFold's part (and one I haven't seen before).
On Sun, Mar 26, 2023 at 1:37 PM Cheng Fei Phung via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi,
I am trying do "matchmaker #2 to #1" between colab output ( best_model.pdb which is pasted here at http://ix.io/4rRO ) and https://www.rcsb.org/structure/7CR5
However, as seen in https://i.imgur.com/gHL8to3.png , there is not really much visual overlapping since the structures are not rotated properly to match each other.
The log for doing matchmaker command is available here at https://i.imgur.com/78h5CLq.png
The colab notebook is also saved as a screenshot here at https://i.imgur.com/LSTdyZe.png
Manually doing "turn z 1 270 model #1 center #1" or similar rotations commands also do not help. Please advise.
Regards, Phung Cheng Fei _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users