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

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