[chimerax-users] No cc when using fitmap

[Yumeng Yan]

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

yumeng.yan at cpr.ku.dk<mailto:yumeng.yan at cpr.ku.dk>

[1638361915486]
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