Thank you James, Looks like a bundle of exciting tools! While I am waiting for other answers, I am checking the website and I will give it a try. Bien cordialement, Hong On Apr 30, 2022, at 11:13 AM, JAMES MICHAEL S1JJRUdFUiA= <jmkrieger@cnb.csic.es<mailto:jmkrieger@cnb.csic.es>> wrote: ProDy

Dear Elaine, Fabulous! Thank you so much for such detailed instructions along with useful commands. It works perfect for me to align 3D structure using view matrix mod command. I can reproduce the same 3D alignment result as your example. As alignment, I did not manage to make it work either ( what I got was not correct) but I can color them by copying structure alignment to make a Clustal like text file…. But I think your method is much useful:D Super super thanks again for the help and have a great evening. Best, Hong On May 1, 2022, at 12:06 PM, Elaine Meng <meng@cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> wrote: Dear Hong, I broke this down into (A) showing Dali 3D superposition, and (B) showing sequence alignment and RMSD values. (A) showing Dali 3D superposition. Unfortunately the Dali Server <http://ekhidna2.biocenter.helsinki.fi/dali/> does not give anything as convenient as a PDB file! However, you can use the transformation matrix provided by the Dali Server with the ChimeraX "view matrix" command to superimpose the structures. You would not use matchmaker, because Dali already calculated the superposition. You simply want to apply the Dali superposition. Details: (1) I tried the Dali Server with first structure 2gbpA and second structure 2fw0A. Then I got a results page that looks like this: <Screen Shot 2022-05-01 at 9.24.17 AM.png> (2) then I clicked the "Parseable (txt)" link and I got a page that looks like this. (You could also save it as a text file from your web browser). <Screen Shot 2022-05-01 at 9.16.43 AM.png> (3) then I reformatted those 12 numbers in the matrix to use in the ChimeraX "view matrix" command. In ChimeraX, I opened 2gbp (model #1) and 2fw0 (model #2) and then used the following command, which should all be one line even though the email may display as multiple lines: view matrix mod #2,-0.464817,-0.320176,0.825489,65.924568,-0.856265,0.399781,-0.327087,21.951881,-0.225289,-0.858873,-0.459981,18.394049 See help <https://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#matrix> (B) Showing sequence alignment and RMSD values. I couldn't figure out how to get a sequence alignment file that can be used as ChimeraX input from the Dali server either! But it sounds like you were able to do it. If so, you can just open the file in ChimeraX and show the RMSD header and use it for coloring: sequence header rmsd show color byattribute seq_rmsd #2 You need to show the RMSD header in order to be able to color by the seq_rmsd header values. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/sequence.html#header> You can use different coloring if you like: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette-options> Since I couldn't figure out how to get the sequence alignment from Dali, I used ChimeraX for that part too. If it is just a pairwise comparison, actually you can use ChimeraX matchmaker to show the sequence alignment withRMSD header: mm #2 to #1 show true But *after* that matchmaker command, you would then need to use the "view matrix" command from part (A) above, to apply the Dali superposition instead of simply using the matchmaker superposition, if the Dali one is what you want. Then you can color by the seq_rmsd attribute as shown above. If it is >2 structures, then you have to resort to other methods of getting the sequence alignment. One way is to open all of the structures in ChimeraX, then use the "seq align" command to use a web service to make a multiple sequence alignment. This command is a recent feature, so it is not in the version 1.3 release -- you would need to get a new daily build to use it. Example if you want sequence alignment of #1 chain A, #2 chain A, #3 chain B: seq align #1/A #2/A #3/B sequence header rmsd show See "seq align" help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/sequence.html#align> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco On Apr 29, 2022, at 8:14 PM, HONG ZHAN via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Dear all, I am trying to align molecules based on Dali server output. However, I can’t download the superposition results from the Dali server webpage (or anyone know?), but I can generate an alignment file with 2D structural alignment from the Dali server. Is there a way to use matchmaker to superpose molecules based on output alignment from Dali server? How to run structure conservation calculation to color the molecule? If I just give Dali’s alignment file, it still calculate conservation based on sequence not structure. Best, Hong

Thank you James. I will look into ProDy as well. Best, Hong

On May 2, 2022, at 3:43 AM, JAMES MICHAEL S1JJRUdFUiA= <jmkrieger@cnb.csic.es> wrote:

Dear Elaine,

Part (A) sounds great! I didn't realise we could access these matrices so easily.

For (B), there is a list of structural equivalences that you could probably use.

In your example of 2gbp-A and 2fw0-A, there is just one entry:

# Structural equivalences 1: 2gbp-A 2fw0-A 2 - 306 <=> 1 - 305 (ASP 2 - PHE 306 <=> ASP 2 - PHE 306 )

For a more complicated case that I made with 3h5v-A and 3qel-A (http://ekhidna2.biocenter.helsinki.fi/barcosel/tmp//ESTfGn3xaNs//3h5vA.txt), we get many more:

# Structural equivalences 1: 3h5v-A 3qel-A 1 - 11 <=> 2 - 12 (SER 3 - PRO 13 <=> PRO 24 - SER 34 ) 1: 3h5v-A 3qel-A 18 - 25 <=> 16 - 23 (TYR 20 - MET 27 <=> HIS 38 - ALA 45 ) 1: 3h5v-A 3qel-A 26 - 32 <=> 25 - 31 (VAL 28 - GLU 34 <=> ASN 47 - HIS 53 ) . . .

1: 3h5v-A 3qel-A 371 - 376 <=> 342 - 347 (LYS 373 - LEU 378 <=> TYR 392 - ASP 397 )

ProDy can parse something similar for searches against the whole PDB, but I don't know if the format is similar enough for that to be helpful. Maybe I can let you know later.

Best wishes James

Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> escribió:

...

Dear Hong, I broke this down into (A) showing Dali 3D superposition, and (B) showing sequence alignment and RMSD values.

(A) showing Dali 3D superposition. Unfortunately the Dali Server <http://ekhidna2.biocenter.helsinki.fi/dali/> does not give anything as convenient as a PDB file!

However, you can use the transformation matrix provided by the Dali Server with the ChimeraX "view matrix" command to superimpose the structures. You would not use matchmaker, because Dali already calculated the superposition. You simply want to apply the Dali superposition.

Details:

(1) I tried the Dali Server with first structure 2gbpA and second structure 2fw0A. Then I got a results page that looks like this:

(2) then I clicked the "Parseable (txt)" link and I got a page that looks like this. (You could also save it as a text file from your web browser).

(3) then I reformatted those 12 numbers in the matrix to use in the ChimeraX "view matrix" command. In ChimeraX, I opened 2gbp (model #1) and 2fw0 (model #2) and then used the following command, which should all be one line even though the email may display as multiple lines:

view matrix mod #2,-0.464817,-0.320176,0.825489,65.924568,-0.856265,0.399781,-0.327087,21.951881,-0.225289,-0.858873,-0.459981,18.394049

See help <https://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#matrix>

(B) Showing sequence alignment and RMSD values.

I couldn't figure out how to get a sequence alignment file that can be used as ChimeraX input from the Dali server either! But it sounds like you were able to do it. If so, you can just open the file in ChimeraX and show the RMSD header and use it for coloring:

sequence header rmsd show color byattribute seq_rmsd #2

You need to show the RMSD header in order to be able to color by the seq_rmsd header values. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/sequence.html#header>

You can use different coloring if you like: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette-options>

Since I couldn't figure out how to get the sequence alignment from Dali, I used ChimeraX for that part too. If it is just a pairwise comparison, actually you can use ChimeraX matchmaker to show the sequence alignment withRMSD header:

mm #2 to #1 show true

But *after* that matchmaker command, you would then need to use the "view matrix" command from part (A) above, to apply the Dali superposition instead of simply using the matchmaker superposition, if the Dali one is what you want. Then you can color by the seq_rmsd attribute as shown above.

If it is >2 structures, then you have to resort to other methods of getting the sequence alignment. One way is to open all of the structures in ChimeraX, then use the "seq align" command to use a web service to make a multiple sequence alignment. This command is a recent feature, so it is not in the version 1.3 release -- you would need to get a new daily build to use it. Example if you want sequence alignment of #1 chain A, #2 chain A, #3 chain B:

seq align #1/A #2/A #3/B sequence header rmsd show

See "seq align" help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/sequence.html#align>

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

...

...

On Apr 29, 2022, at 8:14 PM, HONG ZHAN via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear all, I am trying to align molecules based on Dali server output. However, I can’t download the superposition results from the Dali server webpage (or anyone know?), but I can generate an alignment file with 2D structural alignment from the Dali server. Is there a way to use matchmaker to superpose molecules based on output alignment from Dali server? How to run structure conservation calculation to color the molecule? If I just give Dali’s alignment file, it still calculate conservation based on sequence not structure. Best, Hong