[chimerax-users] MCCOY - coloring a map by local resolution - Rnd 2

[Tom Goddard]

Hi Bill,

  I made a video showing how to color a cryoEM map by local resolution.

	https://youtu.be/2EDZQs7lGNs <https://youtu.be/2EDZQs7lGNs>

  Tom



> On Apr 14, 2021, at 10:53 AM, McCoy, William <mccoyw at wustl.edu> wrote:
> 
> Got it! Now it works. Thanks!
> 
> Bill
> 
> William H. McCoy IV, MD, PhD
> Research Instructor in Medicine
> Department of Medicine, Division of Dermatology
> Washington University School of Medicine
> Saint Louis, MO 63110
> 
> The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone at (314) 540-1512 or by return email.
> From: Elaine Meng <meng at cgl.ucsf.edu <mailto:meng at cgl.ucsf.edu>>
> Sent: Wednesday, April 14, 2021 9:57 AM
> To: McCoy, William <mccoyw at wustl.edu <mailto:mccoyw at wustl.edu>>
> Cc: chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu> <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>>
> Subject: Re: [chimerax-users] MCCOY - coloring a map by local resolution - Rnd 2
>  
> * External Email - Caution *
> 
> Hi Bill,
> You need to get a newer version of ChimeraX (1.2 daily build).
> 
> Version 1.1 (and 1.1.1) are from August 2020, but the  "Surface Color" tool was added in March 2021, according to the change log:
> 
> <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog>>
> 
> This change log is a link near the top of the download page.  Also in that page, go to the daily builds section to get the current daily build.
> <https://www.rbvi.ucsf.edu/chimerax/download.html <https://www.rbvi.ucsf.edu/chimerax/download.html>>
> <https://www.rbvi.ucsf.edu/chimerax/download.html#daily <https://www.rbvi.ucsf.edu/chimerax/download.html#daily>>
> 
> 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 13, 2021, at 6:26 PM, McCoy, William <mccoyw at wustl.edu> wrote:
> >
> > Dear Elaine and other Chimera support staff,
> >
> > Thank you for your explanation. Unfortunately, my problem is that I cannot find the tool "Surface Color" in ChimeraX-1.1.1. Here is a screenshot of what I see when I look for it with both .mrc files loaded. From the hyperlink that you provided (https://rbvi.ucsf.edu/chimerax/docs/user/tools/surfacecolor.html <https://rbvi.ucsf.edu/chimerax/docs/user/tools/surfacecolor.html>), it appears that I could also access "Surface Color" from "Depiction" within tools, but I also cannot find "Depiction" as an option. Is there somewhere else that I should be looking for the "Surface Color" tool? Thanks ahead of time for the help.
> >
> > Sincerely,
> > Bill McCoy
> >
> > William H. McCoy IV, MD, PhD
> > Research Instructor in Medicine
> > Department of Medicine, Division of Dermatology
> > Washington University School of Medicine
> > Saint Louis, MO 63110
> >
> > The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone at (314) 540-1512 or by return email.
> >
> > From: Elaine Meng <meng at cgl.ucsf.edu>
> > Sent: Tuesday, April 13, 2021 6:47 PM
> > To: McCoy, William <mccoyw at wustl.edu>
> > Cc: Elaine Meng <meng at cgl.ucsf.edu>
> > Subject: Re: [chimerax-users] coloring a map by local resolution
> >
> > * External Email - Caution *
> >
> > I just sent the question to the whole list already, right above my response (below), so you didn't need to do it.... the reason I gave the address is for your future reference and future correspondence.  The moderator is deleting the duplicate question so that people don't have to read the same exact question again.
> >
> > Elaine
> >
> > > On Apr 13, 2021, at 4:40 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > >
> > >
> > >> On Apr 13, 2021, at 4:17 PM, William.H.McCOy.IV at cgl.ucsf.edu wrote:
> > >>
> > >> I can't get the following from relion 3.1 to work: The output is a file called LocalRes/polished/relion_locres.mrc that may be used in UCSF chimera to color the Postprocess/polished/postprocess.mrc map according to local resolution.  # This is done using Tools -> Volume data -> Surface color, and then select by volume data value and browse to the resmap file.
> > >
> > > Dear William,
> > > We have a mailing list that is recommended for asking questions, chimerax-users at cgl.ucsf.edu (CC'd on this message).
> > > <https://www.rbvi.ucsf.edu/chimerax/docs/contact.html <https://www.rbvi.ucsf.edu/chimerax/docs/contact.html>>
> > >
> > > Coloring by local resolution is a fairly common task and I don't know of any reason it wouldn't work.  It is not clear what you mean by not working.  If you are more specific with your question, we can give more targeted answers.
> > >
> > > First you have to open both mrc files in ChimeraX.  Say you opened the map that you want to show as a surface as model #1 and the map with locres values for coloring as model #2.  Then in Volume Viewer, you can adjust the isosurface level of map #1 and hide the isosurface of map #2 (or you can hide it using Model Panel, same thing).   In Surface Color you would choose the (already open) models: the surface to color is model #1, you want to color it by "volume data value," and the map with values to use for coloring is #2.  You can see the help for the tool by clicking its Help button, or view the copy on our website here:
> > >
> > > <https://rbvi.ucsf.edu/chimerax/docs/user/tools/surfacecolor.html <https://rbvi.ucsf.edu/chimerax/docs/user/tools/surfacecolor.html>>
> > >
> > > I hope this helps,
> > > Elaine
> > > -----
> > > Elaine C. Meng, Ph.D.
> > > UCSF Chimera(X) team
> > > Department of Pharmaceutical Chemistry
> > > University of California, San Francisco
> 
>  
> The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
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