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Hi Elaine,</div>
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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?</div>
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Thank you,<br>
Kenneth</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Sent:</b> Friday, September 3, 2021 6:52 PM<br>
<b>To:</b> SANDOVAL, KENNETH <K.SANDOVAL1@nuigalway.ie><br>
<b>Cc:</b> Azad, Roksana via Chimera-users <chimera-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [Chimera-users] Copy protein orientation</font>
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Hello Kenneth,<br>
I can't really tell what's going on without having the session file or the atomic coordinates (PDB file) to look at.<br>
<br>
Without that information, my only suggestions are:<br>
(1) make sure you have a reasonably new version of Chimera, say the last production release<br>
(2) try running secondary structure assignment on that model, e.g. if the funny-looking ribbon model is #2, command<br>
<br>
ksdssp #2<br>
<br>
kdssp help:<br>
<<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html</a>><br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D.<br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On Sep 3, 2021, at 6:26 AM, SANDOVAL, KENNETH via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:<br>
><br>
> Hello,<br>
><br>
> 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.<br>
><br>
> 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.<br>
><br>
> Thank you,<br>
> Kenneth<br>
> From: Elaine Meng <meng@cgl.ucsf.edu><br>
> Sent: Tuesday, August 10, 2021 6:00 PM<br>
> To: SANDOVAL, KENNETH <K.SANDOVAL1@nuigalway.ie><br>
> Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu><br>
> Subject: Re: [Chimera-users] Copy protein orientation<br>
><br>
> Hello Kenneth,<br>
> 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.<br>
><br>
> However, given the situation you have now, maybe:<br>
> (1) in session 1, use "matrixget <file-pathname>" to save file with transformation of protein A. See:<br>
> <<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matrixset.html">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matrixset.html</a>><br>
><br>
> (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.<br>
><br>
> (3) in session 2, if protein A is model #0 and protein B is model #1, use command "matrixcopy #0 #1"<br>
> See: <<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html</a>><br>
><br>
> 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.<br>
><br>
> I hope this helps,<br>
> Elaine<br>
> -----<br>
> Elaine C. Meng, Ph.D.<br>
> UCSF Chimera(X) team<br>
> Department of Pharmaceutical Chemistry<br>
> University of California, San Francisco<br>
><br>
> > On Aug 10, 2021, at 9:34 AM, David Gae via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:<br>
> ><br>
> > Dear Kenneth,<br>
> ><br>
> > 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.<br>
> > Then work on the problem from there on. This seems like a possible direction to try?<br>
> ><br>
> > Sincerely,<br>
> > David<br>
> ><br>
> >> On Aug 10, 2021, at 6:47 AM, SANDOVAL, KENNETH via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:<br>
> >><br>
> >> Hello,<br>
> >><br>
> >> 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:<br>
> >><br>
> >> 1) Identify orientation of protein A in session 1<br>
> >> 2) Copy that orientation<br>
> >> 3) Apply that orientation to protein A in session 2<br>
> >> 4) Have protein B in session 2 remain aligned to protein A despite the new orientation<br>
> >><br>
> >> Thank you,<br>
> >> Kenneth Sandoval<br>
> >> _______________________________________________<br>
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> ><br>
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><br>
> <Prot_A_aligned.png><Prot_A.png>_______________________________________________<br>
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