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