[chimerax-users] AlphaFold best_model.pdb could not visually overlap the input sequence using matchmaker

[Rudy Richardson]

Yes, there will be mis-matches when attempting to align structures that
cannot be aligned. On a much smaller scale, the problem is akin to trying
to superimpose two optical isomers -- by definition, they are
non-superimposable.

-- RJR


On Mon, Mar 27, 2023 at 10:11 AM Cheng Fei Phung <feiphung at hotmail.com>
wrote:

> Hi Rudy Richardson,
>
> https://i.imgur.com/4V7gjYP.png shows that alphaFold's best_model.pdb and
> the reference 7cr5.pdb have different atoms which makes RMSD calculation to
> be impossible inside Yasara.
>
> I suppose that I will just stick with the ChimeraX for now since Yasara
> could not produce RMSD value in this specific scenario.
>
> Regards,
> Phung Cheng Fei
> ------------------------------
> *From:* Cheng Fei Phung <feiphung at hotmail.com>
> *Sent:* Monday, March 27, 2023 2:43 PM
> *To:* Rudy Richardson <rjrich at umich.edu>
> *Cc:* chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
> *Subject:* Re: [chimerax-users] AlphaFold best_model.pdb could not
> visually overlap the input sequence using matchmaker
>
> Hi Rudy Richardson,
>
> See http://ix.io/4rWg PDB file for the alignment between ChimeraX
> colabFold output and the reference 7cr5 pdb from rcsb.
>
> As seen at the bottom right of https://i.imgur.com/sraWQY4.png , there is
> still quite a structure mismatch which I had highlighted in gold color.
>
> Note:  I have already tried MUSTANG, MMLIGNER, Smith&Waterman, and
> Needleman&Wunsch alignment methods.
>
> Regards,
> Phung Cheng Fei
> ------------------------------
> *From:* Rudy Richardson <rjrich at umich.edu>
> *Sent:* Monday, March 27, 2023 12:32 AM
> *To:* Cheng Fei Phung <feiphung at hotmail.com>
> *Cc:* chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
> *Subject:* Re: [chimerax-users] AlphaFold best_model.pdb could not
> visually overlap the input sequence using matchmaker
>
> PS: I forgot to mention -- if you already have a 3D alignment, you can go
> to Analyze > RMSD of, and choose Objects, Molecules, Residues, or Atoms to
> get corresponding RMSD values. You could also run Analyze > Global distance
> test of, and choose one of the same list of structures. The YASARA
> documentation has explanations of these procedures.
>
> -- RJR
>
> On Sun, Mar 26, 2023 at 12:26 PM Rudy Richardson <rjrich at umich.edu> wrote:
>
> Which version of YASARA do you have? If it is the free viewer, I am not
> sure which features are included. I have purchased a license for
> YASARA-Structure along with WHATIF and the NMR module. In my version at
> least, when I load two structures, I can go to the Analyze > Align menu and
> choose from several 3D alignment programs, e.g., MUSTANG, MM Ligner, or
> Sheba. When the alignment is finished, the data are shown in the console.
>
> -- Rudy
>
>
> On Sun, Mar 26, 2023 at 12:16 PM Cheng Fei Phung <feiphung at hotmail.com>
> wrote:
>
> Hi Rudy Richardson,
>
> I loaded your "3d_align.pdb" file on Yasara which I just installed today
>
> How do you see "RMSD of 1.094 A over 111 aligned residues with 100.0%
> similarity" from https://i.imgur.com/GI0rmEc.png ?
>
> Regards,
> Phung Cheng Fei
>
> ------------------------------
> *From:* Rudy Richardson <rjrich at umich.edu>
> *Sent:* Sunday, March 26, 2023 9:20 PM
> *To:* Cheng Fei Phung <feiphung at hotmail.com>
> *Cc:* chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
> *Subject:* Re: [chimerax-users] AlphaFold best_model.pdb could not
> visually overlap the input sequence using matchmaker
>
> It seems that the problem could be with trying to align each of the entire
> complexes. Predictive models of structures with multiple protein chains can
> have a difficult time with finding the correct interactions between chains.
>
> Have you tried the 3D alignment with each of the corresponding 3 chains? I
> took the A-chain of 7cr5 and did a 3D alignment with the B chain of 4rR0
> using Sheba in Yasara and got a Calpha RMSD of 1.094 A over 111 aligned
> residues with 100.0% similarity. I have attached a PDB file of the aligned
> structures.
>
> Best regards,
>
> R.J. Richardson
>
>
> On Sun, Mar 26, 2023 at 8:38 AM Cheng Fei Phung via ChimeraX-users <
> chimerax-users at 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
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