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

[Rudy Richardson]

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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