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

Thu Mar 30 20:29:11 PDT 2023

Hi,

I am looking at pLDDT confidence measure as mentioned in https://alphafold.ebi.ac.uk/faq

  1.  Should I convert pLDDT to B-factors as suggested in https://isolde.cimr.cam.ac.uk/static/isolde/doc/tutorials/alphafold/molecular_replacement/alphafold_mr.html ?

  2.  Why https://scipion-em.github.io/docs/release-3.0.0/docs/user/tutorials/modelBuilding/Alphafold/a010-alphafoldPredictionProtocol.html suggest to use PLDDTs (monomer) or iptm+ptm (multimer) ?

Regards,
Phung Cheng Fei
________________________________
From: Rudy Richardson <rjrich at umich.edu>
Sent: Monday, March 27, 2023 10:30 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

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<mailto: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<mailto:feiphung at hotmail.com>>
Sent: Monday, March 27, 2023 2:43 PM
To: Rudy Richardson <rjrich at umich.edu<mailto:rjrich at umich.edu>>
Cc: chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu> <chimerax-users at cgl.ucsf.edu<mailto: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<mailto:rjrich at umich.edu>>
Sent: Monday, March 27, 2023 12:32 AM
To: Cheng Fei Phung <feiphung at hotmail.com<mailto:feiphung at hotmail.com>>
Cc: chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu> <chimerax-users at cgl.ucsf.edu<mailto: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<mailto: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<mailto: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<mailto:rjrich at umich.edu>>
Sent: Sunday, March 26, 2023 9:20 PM
To: Cheng Fei Phung <feiphung at hotmail.com<mailto:feiphung at hotmail.com>>
Cc: chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu> <chimerax-users at cgl.ucsf.edu<mailto: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<mailto: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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