Clipper: density sphere not aligned with structure

[jingjin.fan@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Dear Sir/Madam, there is an issue when I run ISOLDE. I fit the PDB to the map very well, and then I use clipper assoc #5 to #3(also tried to add the maps to working model), but I think the sphere of density doesn't align with the PDB very well. I tried to delet other distracted molecules like HOH, but doesn't help too much. I also tried to use different PDB(1u77, 1u7c, 1u7g,1xqe), the issue still exists. Could you help me with it? Thanks a lot in advanced!

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1u77

1u77 title:  
Crystal Structure of Ammonia Channel AmtB from E. Coli [more info...]  
  
Chain information for 1u77 #1  
---  
Chain | Description | UniProt  
A | Probable ammonium transporter | AMTB_ECOLI 1-385  
  
1u77 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> sym #1 assembly 1

Made 3 copies for 1u77 assembly 1  

> combine #2

Remapping chain ID 'A' in 1u77 #2.2 to 'B'  
Remapping chain ID 'A' in 1u77 #2.3 to 'C'  

> open
> Q:/__BACKUP__/PROJECTS/TEM/img/raw/0578/cryosparc_P109_J40_004_volume_map.mrc

Opened cryosparc_P109_J40_004_volume_map.mrc as #4, grid size 256,256,256,
pixel 0.85, shown at level 0.0789, step 1, values float32  

> hide #!2 models

> view #4 clip false

> select add #3

9126 atoms, 8589 bonds, 1878 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #3,1,0,0,11.599,0,1,0,11.232,0,0,1,47.213

> ui mousemode right "move picked models"

> ui mousemode right "translate selected models"

> view matrix models #3,1,0,0,17.807,0,1,0,3.8859,0,0,1,40.63

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.23836,-0.26733,-0.93366,119.36,-0.95448,-0.11301,0.27603,68.057,-0.1793,0.95696,-0.22822,70.817

> volume flip #4

Opened cryosparc_P109_J40_004_volume_map.mrc z flip as #5, grid size
256,256,256, pixel 0.85, shown at step 1, values float32  

> select subtract #3

Nothing selected  

> select add #5

2 models selected  

> view matrix models
> #5,-0.5163,0.70336,0.48858,37.829,0.76469,0.12176,0.63279,-58.271,0.38559,0.70032,-0.60072,56.199

> select subtract #5

Nothing selected  

> select add #3

9126 atoms, 8589 bonds, 1878 residues, 1 model selected  

> view matrix models
> #3,-0.46807,-0.50519,-0.72504,128.45,-0.70119,-0.287,0.65265,46.275,-0.53781,0.81389,-0.2199,91.155

> ui mousemode right "move picked models"

> view matrix models
> #3,-0.46807,-0.50519,-0.72504,161.86,-0.70119,-0.287,0.65265,112.64,-0.53781,0.81389,-0.2199,142.87

> view matrix models
> #3,-0.46807,-0.50519,-0.72504,169.21,-0.70119,-0.287,0.65265,130.42,-0.53781,0.81389,-0.2199,125.81

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.35641,-0.0017557,-0.93433,158.45,-0.9315,0.07851,0.35518,142.83,0.072731,0.99691,-0.029617,84.861

> ui tool show "Fit in Map"

> fitmap #3 inMap #5

Fit molecule combination (#3) to map cryosparc_P109_J40_004_volume_map.mrc z
flip (#5) using 9126 atoms  
average map value = 0.1157, steps = 124  
shifted from previous position = 10.2  
rotated from previous position = 15.8 degrees  
atoms outside contour = 2873, contour level = 0.078936  
  
Position of combination (#3) relative to cryosparc_P109_J40_004_volume_map.mrc
z flip (#5) coordinates:  
Matrix rotation and translation  
-0.38553584 0.24719127 0.88896489 87.02072801  
-0.46960714 0.77676146 -0.41965553 125.88615831  
-0.79424885 -0.57925651 -0.18338660 168.82570207  
Axis -0.08690821 0.91656763 -0.39032133  
Axis point 115.92265881 0.00000000 78.68783504  
Rotation angle (degrees) 113.33337857  
Shift along axis 41.92409068  
  

> select subtract #3

Nothing selected  

> delete :HOH

> isolde start

> set selectionWidth 4

Done loading forcefield  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  
Removed all altlocs in #3 and reset associated occupancies to 1.  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 48 residues in model #3 to IUPAC-IUB
standards.  

> save Q:/__BACKUP__/PROJECTS/TEM/img/raw/0578/fitting_1u77.cxs

> view #1#3.1,3#2-5#3.2 clip false

> clipper associate #5 toModel #3

Opened cryosparc_P109_J40_004_volume_map.mrc z flip as #3.1.1.1, grid size
256,256,256, pixel 0.85, shown at step 1, values float32  

> ui tool show "Side View"

> isolde sim start #3.2/A-C

Sim termination reason: None  
ISOLDE: stopped sim  

> addh #3.2

Summary of feedback from adding hydrogens to combination #3.2  
---  
warning | Unknown hybridization for atom (SE) of residue type MSE; not adding
hydrogens to it  
notes | Termini for combination (#3.2) chain A determined from SEQRES records  
Termini for combination (#3.2) chain B determined from SEQRES records  
Termini for combination (#3.2) chain C determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: combination #3.2/A ALA
3, combination #3.2/B ALA 3, combination #3.2/C ALA 3  
Chain-final residues that are actual C termini: combination #3.2/A VAL 385,
combination #3.2/B VAL 385, combination #3.2/C VAL 385  
Chain-final residues that are not actual C termini:  
Missing OXT added to C-terminal residue combination #3.2/A VAL 385  
Missing OXT added to C-terminal residue combination #3.2/B VAL 385  
Missing OXT added to C-terminal residue combination #3.2/C VAL 385  
1161 hydrogen bonds  
Adding 'H' to combination #3.2/A ALA 3  
Adding 'H' to combination #3.2/B ALA 3  
Adding 'H' to combination #3.2/C ALA 3  
8670 hydrogens added  
  

> isolde sim start #3.2/A-C

ISOLDE: started sim  




OpenGL version: 3.3.0 - Build 30.0.100.9864
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel

Python: 3.11.2
Locale: en_GB.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

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Model: OptiPlex 7070
OS: Microsoft Windows 10 Enterprise (Build 19045)
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MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-9700 CPU @ 3.00GHz
OSLanguage: en-GB

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[Eric Pettersen]

Reported by Jingjin Fan

[Tristan Croll]

This is a current limitation of Clipper: the map must be in the absolute
reference frame (i.e. not moved from its starting position after opening).
In other words, you should always move the model to fit the map, and not
the other way around.

On Tue, Sep 3, 2024 at 5:16 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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