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Today's Topics:
1. Re: [Chimera-users] Opening MTZ files on Mac OS (Elaine Meng)
2. Coloring proteins by Ca rmsd when they have different sequences
(Vorländer)
3. Re: Coloring proteins by Ca rmsd when they have different sequences
(Elaine Meng)
4. Re: Coloring proteins by Ca rmsd when they have different sequences
(Elaine Meng)
5. Extract settings/parameters from a chimerax cxs session file
(alan.cheung@bristol.ac.uk)
----------------------------------------------------------------------
Message: 1
Date: Mon, 3 Jul 2023 19:24:07 -0700
From: Elaine Meng <meng@cgl.ucsf.edu>
Subject: [chimerax-users] Re: [Chimera-users] Opening MTZ files on Mac
OS
To: Natalie Walsh <natalie.walsh@slu.edu>
Cc: "chimera-users@cgl.ucsf.edu" <chimera-users@cgl.ucsf.edu>,
ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>
Message-ID: <56AC7019-083A-43B6-97DE-B674733A0561@cgl.ucsf.edu>
Content-Type: text/plain; charset=us-ascii
Hi Natalie,
This is a ChimeraX question, although sent to the chimera-users list -- although unnecessary this time, for future reference please send chimeraX questions to the chimerax-users@cgl.ucsf.edu list CC'd here (we try not to confuse Chimera users with ChimeraX
answers and vice versa).
The instructions of how to open MTZ files with ChimeraX are here:
<
https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#clipper>
"Opening an MTZ file requires specifying an already-open atomic structure with the structureModel option..." with example command, etc.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco
> On Jul 3, 2023, at 8:52 AM, Natalie Walsh via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
>
> Hello,
>
> I am having troubles opening MTZ maps from PDB on ChimeraX 17.1. on Mac OS. I read somewhere that you need to download the Clipper plug-in. I went ahead and installed that (although I am not sure that I was successful) and am still struggling to open these
files.
>
> Thank you,
> Natalie Walsh
------------------------------
Message: 2
Date: Tue, 4 Jul 2023 14:02:10 +0000
From: Vorländer,Matthias Kopano <matthias.vorlaender@imp.ac.at>
Subject: [chimerax-users] Coloring proteins by Ca rmsd when they have
different sequences
To: "chimerax-users@cgl.ucsf.edu" <chimerax-users@cgl.ucsf.edu>
Message-ID: <3944043A-628C-43CD-8A65-67B361695EDB@imp.ac.at>
Content-Type: multipart/alternative;
boundary="_000_3944043A628C43CD8A6567B361695EDBimpacat_"
Hi all,
I would like to color proteins by the Ca-RMSD after aligning them, and found the Youtube tutorial on how to do this for proteins with identical sequence. However, I would like to compare structures from different species, as for example done in Figure 2 in
this paper
https://www.sciencedirect.com/science/article/pii/S0959440X16302408?via%3Dihub . Is this possible in ChimeraX?
Many thanks,
Matthias
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Message: 3
Date: Tue, 4 Jul 2023 07:53:51 -0700
From: Elaine Meng <meng@cgl.ucsf.edu>
Subject: [chimerax-users] Re: Coloring proteins by Ca rmsd when they
have different sequences
To: "Vorländer,Matthias Kopano" <matthias.vorlaender@imp.ac.at>
Cc: "chimerax-users@cgl.ucsf.edu" <chimerax-users@cgl.ucsf.edu>
Message-ID: <9811BC4E-37D1-464C-81CC-BFD00557806A@cgl.ucsf.edu>
Content-Type: text/plain; charset=utf-8
Hi Matthias,
Yes absolutely. You just need all of the structure chains to be associated with the same sequence window, which might contain a single sequence or a sequence alignment, and then you can show an RMSD histogram above the sequence(s) which is then propagated
as an attribute to the structures for coloring.
If I recall correctly, the video shows a specialized rarer case. Your case is the more common situation where the structures are homologous and may vary in structure, and you probably want to keep them superimposed.
If the sequences of the structure chains are fairly similar, you may be able to associate all of the structures with the same single sequence. I.e.,
(1) open all of the structures and superimpose them using your preferred method (matchmaker, align, ...)
<
https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html>
<
https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html>
(2) show the sequence of only one of those structures (menu Tools... Sequence... Show Sequence Viewer, choose the chain for which you want to show the sequence)
<
https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html>
(3) use Sequence Viewer context menu (rt-click or Ctrl-click on that window depending on platform) Structure... Associations, add all of the relevant structure chains to the associations of that sequence
<
https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#context>
<
https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#association>
(4) use Sequence Viewer context menu Headers... Calpha RMSD to show RMSD histogram above sequence
<
https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#context>
(4b) in the Sequence Viewer Settings, Headers section, you can choose backbone RMSD instead of Calpha RMSD if you prefer
<
https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#settings>
(5) then all of the associated structure chains get a residue attribute named seq_rmsd, and you can color any/all of them by that attribute using Render by Attribute (in menu under Tools... Depiction) or the "color byattribute" command
<
https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#headers>
<
https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute>
<
https://rbvi.ucsf.edu/chimerax/docs/user/tools/render.html>
(5b) Probably for nice-figure purposes you would only show/color one of the structures. For RMSD calculation purposes during coloring you need to keep the others open and superimposed but they could be hidden, e.g. by unchecking the shown checkboxes in the
Model Panel.
If the structure sequences are very dissimilar, however, and don't associate properly with the sequence in the Sequence Viewer, instead of showing a single sequence you may need to generate a sequence alignment (outside of ChimeraX) of their sequences, and
then open it in ChimeraX and make sure each structure is associated with some sequence in that alignment. Then proceed with (4) - (5) as above.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco
> On Jul 4, 2023, at 7:02 AM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Hi all,
>
> I would like to color proteins by the Ca-RMSD after aligning them, and found the Youtube tutorial on how to do this for proteins with identical sequence. However, I would like to compare structures from different species, as for example done in Figure 2 in
this paper
https://www.sciencedirect.com/science/article/pii/S0959440X16302408?via%3Dihub . Is this possible in ChimeraX?
>
> Many thanks,
> Matthias
------------------------------
Message: 4
Date: Tue, 4 Jul 2023 07:56:51 -0700
From: Elaine Meng <meng@cgl.ucsf.edu>
Subject: [chimerax-users] Re: Coloring proteins by Ca rmsd when they
have different sequences
To: "Vorländer,Matthias Kopano" <matthias.vorlaender@imp.ac.at>
Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>
Message-ID: <51FC214B-81E9-4698-8BDA-20D300158834@cgl.ucsf.edu>
Content-Type: text/plain; charset=us-ascii
> On Jul 4, 2023, at 7:53 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> If I recall correctly, the video shows a specialized rarer case. Your case is the more common situation where the structures are homologous and may vary in structure, and you probably want to keep them superimposed.
I meant to say "...may vary in **sequence**..." !!
Elaine
------------------------------
Message: 5
Date: Tue, 04 Jul 2023 18:42:55 -0000
From: alan.cheung@bristol.ac.uk
Subject: [chimerax-users] Extract settings/parameters from a chimerax
cxs session file
To: chimerax-users@cgl.ucsf.edu
Message-ID:
<168849617579.560673.13097891225723174724@franklin.cgl.ucsf.edu>
Content-Type: text/plain; charset="utf-8"
Hi All - apologies if this has been answered before, couldn't find it with search.
I have a session file with very nicely formatted views/lighting/graphics settings, but i'd like to duplicate them for another (new) session. I can't remember what i set! And it's not in the log.
Is there a way to get ChimeraX to return these values (or indeed, all parameters) for the current session? I imagine this might be useful generally too.
Alan
------------------------------
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