[Chimera-users] Question about anomalous Fourier map

[Elaine Meng]

One thing I forgot to say:  the numerical values shown in the Volume Viewer histogram are not necessarily sigma units, they are the values taken directly from the map file.

So if you want to set a specific sigma (contour at sigma value 1.5, for example), you would need to use a command something like the following, if your map is model #0:

volume #0 sdLevel 1.5
 - or -
volume #0 rmsLevel 1.5

...depending on how you define sigma.  For the difference see explanation here:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#general>

Commands can also set the contour in the same units as shown in the Volume Viewer histogram, although it may be easier just to do it with the GUI.  The command would be something like:

volume #0 level 0.4835

...where you could specify whatever value is appropriate for your data.

I hope this helps,
Elaine

> On Jan 11, 2023, at 4:43 PM, YOSHIWARA Kentaroh via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> 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