Register shift: m > k must hold

[csandate@…]

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
Isolde related issue: tried to change register shift for ~4 residues.

Log:
UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/colbysandate/Dropbox (Scripps Research)/KaiC modeling and MS/C2
> models/070720_C2-coot-6FH_IsoldeV3.pdb" format pdb

Chain information for 070720_C2-coot-6FH_IsoldeV3.pdb #1  
---  
Chain | Description  
A D | No description available  
B | No description available  
C F | No description available  
E | No description available  
  

> open "/Users/colbysandate/Dropbox (Scripps Research)/KaiC modeling and
> MS/KaiC_CurrentMapandModel/C2_state/postprocess.mrc"

Opened postprocess.mrc, grid size 192,192,192, pixel 1.15, shown at level
0.0317, step 1, values float32  

> set bgColor white

> isolde start

> set selectionWidth 4

Chain information for 070720_C2-coot-6FH_IsoldeV3.pdb  
---  
Chain | Description  
1.2/A 1.2/D | No description available  
1.2/B | No description available  
1.2/C 1.2/F | No description available  
1.2/E | No description available  
  
Done loading forcefield  

> ui dockable false ISOLDE

> isolde restrain ligands #2

Must specify at least one atomic structure!  

> isolde restrain ligands #1

> addh

Summary of feedback from adding hydrogens to 070720_C2-coot-6FH_IsoldeV3.pdb
#1.2  
---  
warnings | Not adding hydrogens to /A GLU 113 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /A GLN 115 CB because it is missing heavy-atom bond
partners  
notes | No usable SEQRES records for 070720_C2-coot-6FH_IsoldeV3.pdb (#1.2)
chain A; guessing termini instead  
No usable SEQRES records for 070720_C2-coot-6FH_IsoldeV3.pdb (#1.2) chain B;
guessing termini instead  
No usable SEQRES records for 070720_C2-coot-6FH_IsoldeV3.pdb (#1.2) chain C;
guessing termini instead  
No usable SEQRES records for 070720_C2-coot-6FH_IsoldeV3.pdb (#1.2) chain D;
guessing termini instead  
No usable SEQRES records for 070720_C2-coot-6FH_IsoldeV3.pdb (#1.2) chain E;
guessing termini instead  
1 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A GLU 14, /B HIS 15, /C HIS
15, /D GLU 14, /E GLU 14, /F HIS 15  
Chain-initial residues that are not actual N termini: /A MET 449, /B HIS 423,
/C ASP 427, /D MET 449, /E ALA 422, /F ASP 427  
Chain-final residues that are actual C termini: /A SER 473, /B ASP 481, /C ASP
481, /D SER 473, /E ASP 481, /F ASP 481  
Chain-final residues that are not actual C termini: /A GLU 444, /B ALA 418, /C
ALA 422, /D GLU 444, /E ASP 417, /F ALA 422  
2896 hydrogen bonds  
/A GLU 444 is not terminus, removing H atom from 'C'  
/B ALA 418 is not terminus, removing H atom from 'C'  
/C ALA 422 is not terminus, removing H atom from 'C'  
/D GLU 444 is not terminus, removing H atom from 'C'  
/E ASP 417 is not terminus, removing H atom from 'C'  
1 messages similar to the above omitted  
0 hydrogens added  
  

> hide HC

> cview /A:160

> cview /A:150

> graphics silhouettes true

> volume #1.1.1.1 level 0.02406

> cview /A:160

> select #1

44032 atoms, 44404 bonds, 16 pseudobonds, 16 models selected  
Loading residue template for ADP from internal database  
Loading residue template for ATP from internal database  

> select clear

> select clear

> select A/163

Expected an objects specifier or a keyword  

> select 163/A

Expected an objects specifier or a keyword  

> select 163/a

Expected an objects specifier or a keyword  

> select :163/a

7323 atoms, 7380 bonds, 3 pseudobonds, 3 models selected  

> select clear

> select /A:163

15 atoms, 14 bonds, 1 model selected  

> select /A:157-163

117 atoms, 116 bonds, 1 model selected  

> select clear

> select clear

> cview /A:163

> cview /A:164

> select /A:157-163

117 atoms, 116 bonds, 1 model selected  

> select /A:150-167

312 atoms, 314 bonds, 1 model selected  

> cview /A:164

> cview /A:163

> select clear

> select up

16 atoms, 15 bonds, 1 model selected  

> select up

16 atoms, 15 bonds, 1 model selected  

> select clear

> select clear

> clipper spotlight radius 11.00

> cview /A:163

> cview /A:157-163

> select /A:157-163

117 atoms, 116 bonds, 1 model selected  

> select /A:157-168

215 atoms, 215 bonds, 1 model selected  

> select clear

> select up

16 atoms, 15 bonds, 1 model selected  

> save "/Users/colbysandate/Dropbox (Scripps Research)/KaiC modeling and MS/C2
> models/092220_isolde_rebuild160loop.pdb"

> select /A:157-168

215 atoms, 215 bonds, 1 model selected  

> select /A:159-173

285 atoms, 285 bonds, 1 model selected  

> select clear

> set bgColor black

> select up

19 atoms, 18 bonds, 1 model selected  

> select up

21 atoms, 21 bonds, 1 model selected  

> select clear

> select clear

> select clear

> select up

12 atoms, 11 bonds, 1 model selected  

> select clear

> save "/Users/colbysandate/Dropbox (Scripps Research)/KaiC modeling and MS/C2
> models/092220_isolde_rebuild160loop_1.pdb"

> select clear

> select up

19 atoms, 18 bonds, 1 model selected  

> select up

304 atoms, 304 bonds, 1 model selected  

> select clear

> select up

14 atoms, 13 bonds, 1 model selected  

> select clear

> select up

14 atoms, 13 bonds, 1 model selected  

> select /A:149-151

47 atoms, 47 bonds, 1 model selected  
Traceback (most recent call last):  
File "/Users/colbysandate/Library/Application Support/ChimeraX/1.0/site-
packages/chimerax/isolde/isolde.py", line 1908, in _apply_register_shift  
rs = self._register_shifter = Protein_Register_Shifter(self.session, self,
sel)  
File "/Users/colbysandate/Library/Application Support/ChimeraX/1.0/site-
packages/chimerax/isolde/manipulations/register_shift.py", line 129, in
__init__  
nspl = self.n_spline = interpolate.splprep(ncoords.transpose(), u=u_vals)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/scipy/interpolate/fitpack.py", line 157, in splprep  
quiet)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/scipy/interpolate/_fitpack_impl.py", line 263, in splprep  
raise TypeError('m > k must hold')  
TypeError: m > k must hold  
  
TypeError: m > k must hold  
  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/scipy/interpolate/_fitpack_impl.py", line 263, in splprep  
raise TypeError('m > k must hold')  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-12.10.22
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,2
      Processor Name: Intel Core i7
      Processor Speed: 2.8 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 1037.147.1.0.0 (iBridge: 17.16.16065.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.14.6 (18G6020)
      Kernel Version: Darwin 18.7.0
      Time since boot: 5 days 4:24

Graphics/Displays:

    Intel Iris Plus Graphics 655:

      Chipset Model: Intel Iris Plus Graphics 655
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3ea5
      Revision ID: 0x0001
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
        PHL 277E6:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60 Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: ZQ01621004272
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: DVI or HDMI
          Adapter Firmware Version: 7.55

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

[Eric Pettersen]

Reported by Colby Sandate

[Tristan Croll]

Hmm - thanks for reporting this. The register-shifting tool requires a minimum of four sequential residues selected, but I currently have the minimum selection to make it available set to three. Will fix.

[Tristan Croll]

Sorry... forgot to close this ticket at the time.