AlphaFold best_model.pdb could not visually overlap the input sequence using matchmaker
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
Hi,
There are two main issues I see here. Regarding the overlay: if you look closely you'll see that the variable domains of the antibody (the two domains directly contacting the antigen) actually overlay really well. The other two domains don't, but that's not particularly unusual - if you compare lots of experimental antibody structures you'll see that these naturally "rock" quite a bit relative to the variable domains, so there's no single "true" conformation here.
The second, bigger, issue: AlphaFold (including its variants like ColabFold) is *not* suitable for predicting antibody/antigen complexes (or, for that matter, any complexes where all the components didn't evolve in the same organism). It relies deeply on the use of multiple sequence alignments to glean information on the co-evolution of interacting partners over tens to hundreds of millions of years, and can only correctly make this analysis when all the sequences involved are present in the genomes of each individual organism. Antibody/antigen complexes don't meet either of these criteria, so in almost all cases you can expect its predictions for the antibody/antigen interface to be rubbish.
Best, Tristan
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
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@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
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@umich.edu Sent: Sunday, March 26, 2023 9:20 PM 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
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@cgl.ucsf.edumailto: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.edumailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@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@umich.edu *Sent:* Sunday, March 26, 2023 9:20 PM *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
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@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
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@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@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@umich.edu *Sent:* Sunday, March 26, 2023 9:20 PM *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
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@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
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@umich.edu Sent: Monday, March 27, 2023 12:32 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
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@umich.edumailto:rjrich@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@hotmail.commailto:feiphung@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@umich.edumailto:rjrich@umich.edu> Sent: Sunday, March 26, 2023 9:20 PM To: Cheng Fei Phung <feiphung@hotmail.commailto:feiphung@hotmail.com> Cc: chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edumailto:chimerax-users@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@cgl.ucsf.edumailto: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.edumailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@hotmail.com Sent: Monday, March 27, 2023 2:43 PM To: Rudy Richardson rjrich@umich.edu 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
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@umich.edu Sent: Monday, March 27, 2023 12:32 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
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@umich.edumailto:rjrich@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@hotmail.commailto:feiphung@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@umich.edumailto:rjrich@umich.edu> Sent: Sunday, March 26, 2023 9:20 PM To: Cheng Fei Phung <feiphung@hotmail.commailto:feiphung@hotmail.com> Cc: chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edumailto:chimerax-users@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@cgl.ucsf.edumailto: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.edumailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@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@hotmail.com *Sent:* Monday, March 27, 2023 2:43 PM *To:* Rudy Richardson rjrich@umich.edu *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
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@umich.edu *Sent:* Monday, March 27, 2023 12:32 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
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@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@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@umich.edu *Sent:* Sunday, March 26, 2023 9:20 PM *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
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@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
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/molecula... ?
2. Why https://scipion-em.github.io/docs/release-3.0.0/docs/user/tutorials/modelBui... suggest to use PLDDTs (monomer) or iptm+ptm (multimer) ?
Regards, Phung Cheng Fei ________________________________ From: Rudy Richardson rjrich@umich.edu Sent: Monday, March 27, 2023 10:30 PM 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
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@hotmail.commailto:feiphung@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@hotmail.commailto:feiphung@hotmail.com> Sent: Monday, March 27, 2023 2:43 PM To: Rudy Richardson <rjrich@umich.edumailto:rjrich@umich.edu> Cc: chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edumailto:chimerax-users@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@umich.edumailto:rjrich@umich.edu> Sent: Monday, March 27, 2023 12:32 AM To: Cheng Fei Phung <feiphung@hotmail.commailto:feiphung@hotmail.com> Cc: chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edumailto:chimerax-users@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@umich.edumailto:rjrich@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@hotmail.commailto:feiphung@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@umich.edumailto:rjrich@umich.edu> Sent: Sunday, March 26, 2023 9:20 PM To: Cheng Fei Phung <feiphung@hotmail.commailto:feiphung@hotmail.com> Cc: chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edumailto:chimerax-users@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@cgl.ucsf.edumailto: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.edumailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
... 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
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.edumailto: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.edumailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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
participants (3)
-
Cheng Fei Phung -
Rudy Richardson -
Tristan Croll