[Chimera-users] Question about anomalous Fourier map
Elaine Meng
meng at cgl.ucsf.edu
Wed Jan 11 12:19:13 PST 2023
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
More information about the Chimera-users
mailing list