[Chimera-users] Copy protein orientation

[SANDOVAL, KENNETH]

Hi Elaine,

Thank you for your answer. I attempted to use the ksdssp command, but it doesn't appear to be doing anything. I have attached the two pdb files. I am wanting the structures of the two proteins in F791140.pdb to be like that of the one in A791140.pdb. Do you have advice on how to do this?

Thank you,
Kenneth
________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Friday, September 3, 2021 6:52 PM
To: SANDOVAL, KENNETH <K.SANDOVAL1 at nuigalway.ie>
Cc: Azad, Roksana via Chimera-users <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Copy protein orientation

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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 <chimera-users at cgl.ucsf.edu> 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 <meng at cgl.ucsf.edu>
> Sent: Tuesday, August 10, 2021 6:00 PM
> To: SANDOVAL, KENNETH <K.SANDOVAL1 at nuigalway.ie>
> Cc: chimera-users at cgl.ucsf.edu <chimera-users at 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
>
> > On Aug 10, 2021, at 9:34 AM, David Gae via Chimera-users <chimera-users at cgl.ucsf.edu> 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
> >
> >> On Aug 10, 2021, at 6:47 AM, SANDOVAL, KENNETH via Chimera-users <chimera-users at cgl.ucsf.edu> 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
> >> _______________________________________________
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> <Prot_A_aligned.png><Prot_A.png>_______________________________________________
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