Hi Yumeng,

  It would be useful if ChimeraX could report the per-residue correlation of an atomic model with a map as Phenix can do.  I'll made a feature request for that

https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5897

You can make feature requests yourself using ChimeraX menu entry Help / Report a Bug....  Bugs and feature requests go into our ChimeraX issue tracking database.

  There is a ChimeraX plugin called StrudelScore from the EMDB that gives per-residue fit statistics.  You can get the plugin using ChimeraX menu Tools / More Tools....  There is online documentation here

https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxstrudelscore

and a tutorial

https://ftp.ebi.ac.uk/pub/databases/emdb_vault/strudel_tutorials/introduction_3dstrudel/Introduction_to_3dstrudel.pdf

Also there is a ChimeraX command resfit that lets you look at the fit of each residue in the density, moving a slider to go to the next residue.  It can also make a video, here is an example,

https://www.rbvi.ucsf.edu/chimera/data/sbgrid-apr2017/images/resfit.mp4

https://www.rbvi.ucsf.edu/chimera/data/sbgrid-apr2017/cryomovie.html

and here is resfit command documentation

https://www.cgl.ucsf.edu/chimerax/docs/user/commands/resfit.html

  Tom

Example of resfit command display of residue fit to map.

On Jan 10, 2022, at 3:48 PM, Yumeng Yan <yumeng.yan@cpr.ku.dk> wrote:

Hi Tom, 

Many thanks for your reply. It works follow your suggestion. I can not open ChimeraX in the gui mode while the ChimeraX is installed on a remote cluster and I did not configure it correctly, so bad. Another question, could you add the measure correlation with cc output for each residue in the structure like in Phenix?

Best,
Yumeng

From: Tom Goddard <goddard@sonic.net>
Sent: Tuesday, January 11, 2022 12:38:42 AM
To: Yumeng Yan
Cc: chimerax-users@cgl.ucsf.edu
Subject: Re: [chimerax-users] No cc when using fitmap
 
You don't often get email from goddard@sonic.net. Learn why this is important
Hi Yumeng,

  I would not expect any difference in the correlation coefficient between Windows and Linux or with a large map versus a small map.

  First the command you listed does not do any fitting since you use "shift false rotate false" which does not allow the model to move.

fitmap #2 inMap #1 resolution 4.0 metric correlation shift false rotate false

So I assume you are doing this just to measure the correlation coefficient.  And your output says the correlation coefficient is 0.  That most likely means the atomic model is not located in the map.  Why don't you just do the same steps in gui mode and see what happens -- it should produce exactly the same result as nogui mode.  Also note that the displayed surface level matters because by default fitmap only uses data above the contour level of the displayed surface of the map you are fitting into.  That actually may explain why your large map case did not work, because if you open a large map ChimeraX may initially just show a single plane in gray scale instead of a surface, and with no surface it won't have a surface level.  So to get a predictable result you should use the volume command to show a surface of the full map and set the threshold level you want to use, for example,

    volume #1 style surface region all level 0.2

  I see that ChimeraX does not have the "measure correlation" command that is in the older Chimera program.  I will try to add that.

  Tom




On Jan 10, 2022, at 2:14 PM, Yumeng Yan via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi, 

When I tried to use  fitmap  function ChimeraX in Linux with --nogui option,  I got no CC output when the Cryo-EM map is large(1.6GB) and I think in this situation, the local fit did not work. When the map was cut of a half size, it works. But it works well on Windows. Could you  help me?

Here are the commands:

open ../Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc fit_11.pdb
fitmap #2 inMap #1 resolution 4.0 metric correlation shift false rotate false

Here is the log information:

INFO:
UCSF ChimeraX version: 1.4.dev202201082018 (2022-01-08)
INFO:
© 2016-2021 Regents of the University of California.  All rights reserved.
INFO:
Executing: open .33092SymAndFit.cxc
INFO:
Executing: open ../Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc fit_11.pdb
STATUS:
reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 0%
STATUS:
reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 8%
STATUS:
reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 16%
STATUS:
reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 24%
STATUS:
reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 32%
STATUS:
reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 40%
STATUS:
reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 48%
STATUS:
reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 56%
STATUS:
reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 64%
STATUS:
reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 72%
STATUS:
reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 80%
STATUS:
reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 87%
STATUS:
Done reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc
STATUS:
Computing histogram for Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc
STATUS:
Computing Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc surface, level 0.292
STATUS:
Calculated Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc surface, level 0.292, with 10911480 triangles
INFO:
Opened Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc as #1, grid size 750,750,750, pixel 1.1, shown at level 0.292, step 1, values float32
INFO:
Chain information for fit_11.pdb #2
---
Chain | Description
[F](cxcmd:select /F:2-219 "Select chain") | [No description
available](cxcmd:sequence chain #2/F "Show sequence")


INFO:
Executing: fitmap #2 inMap #1 resolution 8.0 metric correlation shift false rotate false
INFO:
Opened fit_11.pdb map 8 as #3, grid size 40,42,43, pixel 2.67, shown at level 0.0533, step 1, values float32
INFO:
Fit map fit_11.pdb map 8 in map Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc using 2211 points
  correlation = 0, correlation about mean = 0, overlap = 0
  steps = 24, shift = 0, angle = 0 degrees

INFO:
Position of fit_11.pdb map 8 (#3) relative to Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc (#1) coordinates:
  Matrix rotation and translation
     1.00000000   0.00000000   0.00000000   0.00000000
     0.00000000   1.00000000   0.00000000   0.00000000
     0.00000000   0.00000000   1.00000000   0.00000000
  Axis   0.00000000   0.00000000   1.00000000
  Axis point   0.00000000   0.00000000   0.00000000
  Rotation angle (degrees)   0.00000000
  Shift along axis   0.00000000

STATUS:
24 steps, shift 0, rotation 0 degrees, correlation 0.0000


Best wishes, 
Yumeng

Yumeng Yan
Postdoctoral Fellow 

Taylor and Rasmussen Group
University of Copenhagen
Faculty of Health and Medical Sciences
Novo Nordisk Foundation Center for Protein Research

Blegdamsvej 3B, building 6
2200 Copenhagen N
DENMARK


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