[Chimera-users] Question about anomalous Fourier map

[YOSHIWARA Kentaroh]

Dear Elaine C. Meng,

Thank you for replying to me about the sigma level.
I got about the way to change the contour level using Volume Viewer tool ("regulate the contour level" meant "change the sigma level.")
Also, I will think about install of ChimeraX.

Sincerely,
Yoshiwara, K.

-------------------------------------------------------------------
Kentaro Yoshiwara
Department of Bioscience, Graduate School of Agriculture, Ehime University
3-5-7 Tarumi, Matsuyama, Ehime 790-8566, Japan
Mail：i652020m at mails.cc.ehime-u.ac.jp


-----Original Message-----
From: Elaine Meng <meng at cgl.ucsf.edu> 
Sent: Thursday, January 12, 2023 5:19 AM
To: YOSHIWARA Kentaroh <i652020m at mails.cc.ehime-u.ac.jp>
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Question about anomalous Fourier map

[meng at cgl.ucsf.edu からのメールを受け取る頻度は高くありません。これが問題である可能性の理由については、https://aka.ms/LearnAboutSenderIdentification をご覧ください。]

Dear Yoshiwara, K,
I do not understand "not able to regulate the contoured sigma level."  When you open a map, it will automatically show the Volume Viewer tool.  This tool shows a histogram of the values with a vertical bar at the contour level.  You can just drag the vertical bar to the left or the right to change the contour level (the threshold).

Chimera Volume Viewer:
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html>

Surface or mesh contour level in that tool:
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#dispsurf>

Maybe interesting: using our newer program ChimeraX with the Clipper plugin (available from ChimeraX toolshed, e.g. ChimeraX menu: Tools... More tools) allows opening mtz files directly:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#clipper>

If you want to try that, here is the download page for ChimeraX:
<https://www.rbvi.ucsf.edu/chimerax/download.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 Jan 11, 2023, at 3:16 AM, YOSHIWARA Kentaroh via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>
> Dear Developer,
>
> I want to have a figure of a zinc atom with the anomalous Fourier map, and I generated the pdb and mtz files from Phenix. refine.
> Then I converted .mtz into .ccp4 using CCP4i FFT and opened it in UCSF Chimera1.16.
> While meshes derived from the .ccp4 file were observed, I was not able to regulate the contoured sigma level.
> Actually, I was able to get a figure with a Fourier map using Pymol.
> Although the scale of the mesh looks the same between the figures from Chimera and Pymol, the values of the sigma level were completely different.
> Would you suggest to me how to have a figure of a zinc atom with the anomalous Fourier map?
>
> Sincerely,
> Yoshiwara, K.
>
> -------------------------------------------------------------------
> Kentaro Yoshiwara
> Department of Bioscience, Graduate School of Agriculture, Ehime University
> 3-5-7 Tarumi, Matsuyama, Ehime 790-8566, Japan
> Mail：i652020m at mails.cc.ehime-u.ac.jp