Re: [Chimera-users] Copy protein orientation

Hello Kenneth, I can't really tell what's going on without having the session file or the atomic coordinates (PDB file) to look at. Without that information, my only suggestions are: (1) make sure you have a reasonably new version of Chimera, say the last production release (2) try running secondary structure assignment on that model, e.g. if the funny-looking ribbon model is #2, command ksdssp #2 kdssp help: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Sep 3, 2021, at 6:26 AM, SANDOVAL, KENNETH via Chimera-users wrote:

Hello,

Thank you for your helpful replies. I apologize for my late response. So following the initial suggestion by David, I have an alignment of protein A with protein B, but with protein B hidden. This is in file prot_A_aligned.png.

However, I am wanting the ribbons of this file to look like those in the image prot_A.png. This is the chimera view for the .pdb file of protein A before alignment with B using TM-align. That is, I want the parts of the protein which are not alpha-helices or beta-sheets to just be in the licorice form. Is this something I can do in chimera? Or is this something that would be integrated into the actual .pdb file which I would have to manually manipulate? I apologize if this is question has an obvious answer.

Thank you, Kenneth From: Elaine Meng Sent: Tuesday, August 10, 2021 6:00 PM To: SANDOVAL, KENNETH Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Copy protein orientation

Hello Kenneth, Similarly to David I was going to say that the better approach would have been to create only a single session with the aligned proteins and simply hide and show model B to make your two figures.

However, given the situation you have now, maybe: (1) in session 1, use "matrixget <file-pathname>" to save file with transformation of protein A. See: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matrixset.html

(2) in session 2, use "matrixset <file-pathname>" to apply the transformation from the file you saved in part 1, assuming protein A has the same model number as in session 1. However, that will probably ignore protein B, so you may need step 3.

(3) in session 2, if protein A is model #0 and protein B is model #1, use command "matrixcopy #0 #1" See: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html

I am not completely sure it will work since it depends on how you got the TM-align alignment in there, but it has at least a chance. Also you may need to adjust the command if you have different model numbers.

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

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On Aug 10, 2021, at 9:34 AM, David Gae via Chimera-users wrote:

Dear Kenneth,

Maybe it be best to put both protein A and B in the same cartisen coordinate system by alignment such as matchmaker program, then save the PDB files. Then work on the problem from there on. This seems like a possible direction to try?

Sincerely, David

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On Aug 10, 2021, at 6:47 AM, SANDOVAL, KENNETH via Chimera-users wrote:

Hello,

I wish to generate two images. The first is of protein A which is in session 1. The second is of protein A aligned with protein B using TM-Align which is in session 2. I wish for the alignment of the second image to be in the same orientation as the first with respect to protein A. Is there a feature which lets me do the following:

1) Identify orientation of protein A in session 1 2) Copy that orientation 3) Apply that orientation to protein A in session 2 4) Have protein B in session 2 remain aligned to protein A despite the new orientation

Thank you, Kenneth Sandoval _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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