No idea. I've never calculated local resolution myself. Some of our users use ResMap for that purpose <https://resmap.sourceforge.net/#> ... but for phenix help specifically, it may be better to ask the phenix community. Elaine
On Oct 6, 2025, at 10:24 AM, Roy Chowdhury, Shatabdi via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Thanks for catching this. So basically, phenix local resolution job is simply passing the input map as output without calculating the values of resolution. Have you ever encountered this issue? I'm running the standard job with unmasked unsharpened half maps, which is quite idiot-proof. Any recommendations for editing parameters would be deeply appreciated.
~ShatabdiFrom: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, October 3, 2025 6:01 PM To: Roy Chowdhury, Shatabdi <Shatabdi.RoyChowdhury@ucsf.edu> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] [Chimera] local resolution map colors !-------------------------------------------------------------------| This Message Is From an External Sender This message came from outside your organization. |-------------------------------------------------------------------!
As far as I can tell, the map you are using for coloring is exactly the same as the original map. If you look at the shapes of the histograms in the Volume Viewer they appear to be the same. So maybe there was some error when you tried to save the local resolution results to a file, or the file is not the one that you think it is.
Of course, if the two maps are the same, when you show an isosurface of one map it is a constant value of the other map (which is the definition of isosurface).
Elaine
On Oct 3, 2025, at 3:04 PM, Roy Chowdhury, Shatabdi via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Thats fair. I hope the new screenshot is more clear. original map used for generating local resolution map is the only one turned on and is now labeled as "original.mrc". Normally this would give me a gradient on the surface for the colors chosen but here, it is just giving me one color.
Thanks for your patience, ~Shatabdi
From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, October 3, 2025 2:45 PM To: Roy Chowdhury, Shatabdi <Shatabdi.RoyChowdhury@ucsf.edu> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [Chimera] local resolution map colors !-------------------------------------------------------------------| This Message Is From an External Sender This message came from outside your organization. |-------------------------------------------------------------------!
I can't tell anything from the image, since I have no idea what your filenames mean.
All I can say (again) is you have to open both the original map and the local resolution map, show the original map as a surface, and use the local resolution map values to color that surface.
Elaine
On Oct 3, 2025, at 2:32 PM, Roy Chowdhury, Shatabdi <Shatabdi.RoyChowdhury@ucsf.edu> wrote:
Hi Elaine,
Thanks for your reply. Attaching the new screenshot here. This shows that the map values are 0.1095 all over. Please let me know if I can give any additional information. ~Shatabdi
From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, October 3, 2025 2:20 PM To: Roy Chowdhury, Shatabdi <Shatabdi.RoyChowdhury@ucsf.edu> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [Chimera] local resolution map colors !-------------------------------------------------------------------| This Message Is From an External Sender This message came from outside your organization. |-------------------------------------------------------------------!
Hi, This question was sent to the commercial licensing address -- for user questions, please use the email address chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> CC'd here to ensure that you get an answer instead of mystified silence.
Is the local resolution map open in addition to the original map? I only see two copies of the same map in the Volume Viewer. Make sure that you open the local resolution map instead of a second copy of the original map.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 3, 2025, at 2:07 PM, Roy Chowdhury, Shatabdi wrote: Hi,
In the past, I've used chimerax to display local resolution on maps using the tools->volume data->surface color function. In a new map, I'm having difficulty with it. I'm attaching screenshots where the phenix local resolution job suggests the resolution range to be 1.27A - 4.6A range which is in agreement with cryosparc. When I load the cctbx_program.ccp4 file on chimerax, it is unable to color the surface and says the surface values are -0.067 - 0.107. Is there something I should be doing differently? Any suggestions would be deeply appreciated.
Thanks!
Shatabdi Roy-Chowdhury, PhD. Cardiovascular Research Institute University of California, San Francisco
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