Opened 4 years ago

Closed 4 years ago

#5919 closed defect (can't reproduce)

Problem reading cube file: could not convert string to float

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 1.2.1 (2021-05-05 02:17:36 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.1 (2021-05-05)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open D:/UserN/Sahar/Desktop/166_i/166_i_0.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_0.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_0.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_1.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_1.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_1.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_2.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_2.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_2.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_3.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_3.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_3.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_4.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_4.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_4.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_5.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_5.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_5.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_6.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_6.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_6.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_7.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_7.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_7.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_8.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_8.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_8.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_9.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_9.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_9.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_10.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_10.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_10.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_11.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_11.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_11.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_12.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_12.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_12.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_13.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_13.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_13.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_14.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_14.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_14.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_15.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_15.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_15.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_16.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_16.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_16.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_17.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_17.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_17.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_18.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_18.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_18.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_19.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_19.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_19.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_20.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_20.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_20.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_21.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_21.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_21.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i.cube

Opened 166_i.cube as #23, grid size 32,32,32, pixel 0.529, shown at level
-0.0153,0.0153, step 1, values float32  

> volume #23 level -0.01993 level 0.01534

> volume #23 level -0.01993 level 0.0002744

> volume #23 level -0.0002744 level 0.0002744

> volume #23 level -0.0002744 level -0.006432

> volume #23 level 0.007258 level -0.006432

> volume #23 level 0.007258 level -0.006983

> volume #23 level 0.007258 level -9.307e-05

> volume #23 level 0.0002768 level -9.307e-05

> volume #23 level 0.0002768 level -0.0001849

> volume #23 level 0.0002768 level -0.0005524

> volume #23 level 0.0002768 level -0.0003687

> volume #23 level 0.0002768 level -0.004135

> volume #23 level 0.0002768 level -0.002757

> volume #23 level 0.0002768 level -0.0002768

> close session

> open D:/UserN/Sahar/Desktop/166_i/166_i_0.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_0.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_0.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_1.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_1.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_1.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_2.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_2.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_2.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_3.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_3.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_3.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_4.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_4.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_4.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_5.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_5.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_5.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_6.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_6.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_6.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_7.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_7.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_7.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_8.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_8.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_8.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_9.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_9.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_9.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_10.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_10.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_10.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_11.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_11.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_11.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_12.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_12.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_12.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_13.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_13.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_13.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_14.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_14.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_14.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_15.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_15.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_15.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_16.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_16.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_16.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_17.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_17.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_17.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_18.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_18.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_18.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_19.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_19.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_19.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_20.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_20.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_20.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_21.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_21.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_21.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i.cube

Opened 166_i.cube as #23, grid size 32,32,32, pixel 0.529, shown at level
-0.0185,0.0185, step 1, values float32  

> volume #23 level -0.000819 level 0.01846

> volume #23 level -0.000819 level 0.000819

> volume #23 level -0.000819 level 0.00025

> volume #23 level -0.0003638 level 0.00025

> close session

> open D:/UserN/Sahar/Desktop/166_i/166_i_18.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_18.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_18.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_19.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_19.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_19.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_20.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_20.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_20.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_21.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_21.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_21.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_0.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_0.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_0.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_1.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_1.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_1.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_2.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_2.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_2.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_3.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_3.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_3.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_4.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_4.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_4.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_5.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_5.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_5.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_6.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_6.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_6.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_7.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_7.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_7.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_8.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_8.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_8.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_9.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_9.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_9.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_10.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_10.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_10.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_11.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_11.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_11.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_12.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_12.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_12.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_13.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_13.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_13.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_14.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_14.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_14.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_15.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_15.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_15.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_16.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_16.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_16.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_17.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_17.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_17.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i.cube

Opened 166_i.cube as #23, grid size 32,32,32, pixel 0.529, shown at level
2.16e-06,-2.16e-06, step 1, values float32  

> volume #23 level 2.16e-06 level -0.01138

> volume #23 level -0.0006268 level -0.01138

> volume #23 level -0.0006268 level -0.001651

> volume #23 level -0.007911 level -0.001651

> volume #23 level -0.007911 level -0.0006268

> volume #23 level -0.007911 level -0.0001147

> volume #23 level -0.0001147 level -0.0001147

> volume #23 level -0.0001147 level -8.8e-07

> close session

> open D:/UserN/Sahar/Desktop/166_i/166_i_0.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_0.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_0.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_1.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_1.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_1.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_2.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_2.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_2.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_3.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_3.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_3.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_4.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_4.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_4.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_5.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_5.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_5.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_6.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_6.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_6.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_7.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_7.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_7.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_8.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_8.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_8.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_9.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_9.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_9.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_10.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_10.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_10.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_11.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_11.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_11.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_12.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_12.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_12.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_13.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_13.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_13.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_14.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_14.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_14.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_15.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_15.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_15.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_16.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_16.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_16.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_17.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_17.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_17.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_18.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_18.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_18.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_19.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_19.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_19.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_20.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_20.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_20.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i/166_i_21.mol2

Summary of feedback from opening D:/UserN/Sahar/Desktop/166_i/166_i_21.mol2  
---  
warnings | line 331: bad substructure data  
line 331: ignore unexpected line '1 <1> 1 GROUP 0 **** 0 ROOT'  
  
Opened 166_i_21.mol2 containing 1 structures (154 atoms, 166 bonds)  

> open D:/UserN/Sahar/Desktop/166_i.cube

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\map_data\readarray.py", line 159, in read_float_lines  
values = [float(x) for x in fields]  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\map_data\readarray.py", line 159, in <listcomp>  
values = [float(x) for x in fields]  
ValueError: could not convert string to float: b'[-2.023991756260691e-06,'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\ui\graphics.py", line 51, in event  
if self.handle_drag_and_drop(event):  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\ui\graphics.py", line 116, in handle_drag_and_drop  
mw.dropEvent(event)  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\ui\gui.py", line 552, in dropEvent  
_open_dropped_file(self.session, p)  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\ui\gui.py", line 1812, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 166, in provider_open  
models, status = collated_open(session, None, paths, data_format, _add_models,
log_errors,  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 421, in collated_open  
return func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\map\\__init__.py", line 148, in open  
return open_map(session, path, format=_name, **kw)  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\map\volume.py", line 3589, in open_map  
smodels, smsg = open_grids(session, sgrids, name, **kw)  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\map\volume.py", line 3683, in open_grids  
v.update_drawings()  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\map\volume.py", line 777, in update_drawings  
levels, colors = self.initial_surface_levels()  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\map\volume.py", line 578, in initial_surface_levels  
mstats = self.matrix_value_statistics()  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\map\volume.py", line 1708, in matrix_value_statistics  
matrices = self.displayed_matrices(read_matrix)  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\map\volume.py", line 1743, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\map\volume.py", line 1228, in matrix  
m = self.region_matrix(r, read_matrix)  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\map\volume.py", line 1252, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\map_data\griddata.py", line 302, in matrix  
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\map_data\gaussian\gaussian_grid.py", line 42, in read_matrix  
matrix = self.gc.matrix(self.component_number, progress)  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\map_data\gaussian\gaussian_format.py", line 123, in matrix  
self.matrices = read_text_floats(self.path, self.data_offset, size,  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\map_data\readarray.py", line 121, in read_text_floats  
read_float_lines(f, array, line_format, progress)  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\map_data\readarray.py", line 162, in read_float_lines  
raise SyntaxError(msg)  
File "<string>", line None  
SyntaxError: Bad number format in D:\UserN\Sahar\Desktop\166_i.cube, line  
b'[-2.023991756260691e-06, -2.2979603798872067e-06, -2.600360312645661e-06,
-2.930878531356648e-06, -3.2879944435721872e-06, -3.6686930206119455e-06,
-4.0682087524247615e-06, -4.479842466678192e-06, -4.894898584675912e-06,
-5.3027893301427804e-06, -5.691342724839675e-06, -6.0473323403086255e-06,
-6.357219896043383e-06, -6.608069452559056e-06, -6.788557643316349e-06,
-6.889972769581632e-06, -6.907073308861002e-06, -6.83867236075875e-06,
-6.687837571705336e-06, -6.46164952884207e-06, -6.170537966587619e-06,
-5.827295042688566e-06, -5.445923760712789e-06, -5.040498680317063e-06,
-4.6241917789464e-06, -4.208561114284575e-06, -3.8031348457002427e-06,
-3.415267725921078e-06, -3.0502123985250625e-06, -2.7113350869987363e-06,
-2.4004093332123022e-06]\n'  
  
File "", line None  
SyntaxError: Bad number format in D:\UserN\Sahar\Desktop\166_i.cube, line  
b'[-2.023991756260691e-06, -2.2979603798872067e-06, -2.600360312645661e-06,
-2.930878531356648e-06, -3.2879944435721872e-06, -3.6686930206119455e-06,
-4.0682087524247615e-06, -4.479842466678192e-06, -4.894898584675912e-06,
-5.3027893301427804e-06, -5.691342724839675e-06, -6.0473323403086255e-06,
-6.357219896043383e-06, -6.608069452559056e-06, -6.788557643316349e-06,
-6.889972769581632e-06, -6.907073308861002e-06, -6.83867236075875e-06,
-6.687837571705336e-06, -6.46164952884207e-06, -6.170537966587619e-06,
-5.827295042688566e-06, -5.445923760712789e-06, -5.040498680317063e-06,
-4.6241917789464e-06, -4.208561114284575e-06, -3.8031348457002427e-06,
-3.415267725921078e-06, -3.0502123985250625e-06, -2.7113350869987363e-06,
-2.4004093332123022e-06]\n'  
  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\map_data\readarray.py", line 162, in read_float_lines  
raise SyntaxError(msg)  
  
See log for complete Python traceback.  
  

> open D:/UserN/Sahar/Desktop/166_i.cube

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\map_data\readarray.py", line 159, in read_float_lines  
values = [float(x) for x in fields]  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\map_data\readarray.py", line 159, in <listcomp>  
values = [float(x) for x in fields]  
ValueError: could not convert string to float: b'[-2.023991756260691e-06,'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\ui\graphics.py", line 51, in event  
if self.handle_drag_and_drop(event):  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\ui\graphics.py", line 116, in handle_drag_and_drop  
mw.dropEvent(event)  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\ui\gui.py", line 552, in dropEvent  
_open_dropped_file(self.session, p)  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\ui\gui.py", line 1812, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 166, in provider_open  
models, status = collated_open(session, None, paths, data_format, _add_models,
log_errors,  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 421, in collated_open  
return func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\map\\__init__.py", line 148, in open  
return open_map(session, path, format=_name, **kw)  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\map\volume.py", line 3589, in open_map  
smodels, smsg = open_grids(session, sgrids, name, **kw)  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\map\volume.py", line 3683, in open_grids  
v.update_drawings()  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\map\volume.py", line 777, in update_drawings  
levels, colors = self.initial_surface_levels()  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\map\volume.py", line 578, in initial_surface_levels  
mstats = self.matrix_value_statistics()  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\map\volume.py", line 1708, in matrix_value_statistics  
matrices = self.displayed_matrices(read_matrix)  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\map\volume.py", line 1743, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\map\volume.py", line 1228, in matrix  
m = self.region_matrix(r, read_matrix)  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\map\volume.py", line 1252, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\map_data\griddata.py", line 302, in matrix  
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\map_data\gaussian\gaussian_grid.py", line 42, in read_matrix  
matrix = self.gc.matrix(self.component_number, progress)  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\map_data\gaussian\gaussian_format.py", line 123, in matrix  
self.matrices = read_text_floats(self.path, self.data_offset, size,  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\map_data\readarray.py", line 121, in read_text_floats  
read_float_lines(f, array, line_format, progress)  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\map_data\readarray.py", line 162, in read_float_lines  
raise SyntaxError(msg)  
File "<string>", line None  
SyntaxError: Bad number format in D:\UserN\Sahar\Desktop\166_i.cube, line  
b'[-2.023991756260691e-06, -2.2979603798872067e-06, -2.600360312645661e-06,
-2.930878531356648e-06, -3.2879944435721872e-06, -3.6686930206119455e-06,
-4.0682087524247615e-06, -4.479842466678192e-06, -4.894898584675912e-06,
-5.3027893301427804e-06, -5.691342724839675e-06, -6.0473323403086255e-06,
-6.357219896043383e-06, -6.608069452559056e-06, -6.788557643316349e-06,
-6.889972769581632e-06, -6.907073308861002e-06, -6.83867236075875e-06,
-6.687837571705336e-06, -6.46164952884207e-06, -6.170537966587619e-06,
-5.827295042688566e-06, -5.445923760712789e-06, -5.040498680317063e-06,
-4.6241917789464e-06, -4.208561114284575e-06, -3.8031348457002427e-06,
-3.415267725921078e-06, -3.0502123985250625e-06, -2.7113350869987363e-06,
-2.4004093332123022e-06]\n'  
  
File "", line None  
SyntaxError: Bad number format in D:\UserN\Sahar\Desktop\166_i.cube, line  
b'[-2.023991756260691e-06, -2.2979603798872067e-06, -2.600360312645661e-06,
-2.930878531356648e-06, -3.2879944435721872e-06, -3.6686930206119455e-06,
-4.0682087524247615e-06, -4.479842466678192e-06, -4.894898584675912e-06,
-5.3027893301427804e-06, -5.691342724839675e-06, -6.0473323403086255e-06,
-6.357219896043383e-06, -6.608069452559056e-06, -6.788557643316349e-06,
-6.889972769581632e-06, -6.907073308861002e-06, -6.83867236075875e-06,
-6.687837571705336e-06, -6.46164952884207e-06, -6.170537966587619e-06,
-5.827295042688566e-06, -5.445923760712789e-06, -5.040498680317063e-06,
-4.6241917789464e-06, -4.208561114284575e-06, -3.8031348457002427e-06,
-3.415267725921078e-06, -3.0502123985250625e-06, -2.7113350869987363e-06,
-2.4004093332123022e-06]\n'  
  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\map_data\readarray.py", line 162, in read_float_lines  
raise SyntaxError(msg)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 27.20.100.8682
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel
Manufacturer: ASUSTeK COMPUTER INC.
Model: X510UAR
OS: Microsoft Windows 10 Home (Build 18363)
Memory: 8,471,212,032
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-8550U CPU @ 1.80GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.4.1
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.3
    ChimeraX-AtomicLibrary: 3.1.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.2
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.3
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.7
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 1.1.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pywin32: 228
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (3)

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Problem reading cube file: could not convert string to float

comment:2 by Tom Goddard, 4 years ago

Seems the cube file is not a file of the correct format. It seems to have an array of numbers but there is a leading square bracket as if it were a Python or JSON list.

> open D:/UserN/Sahar/Desktop/166_i.cube

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\map_data\readarray.py", line 159, in read_float_lines  
values = [float(x) for x in fields]  
File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-
packages\chimerax\map_data\readarray.py", line 159, in <listcomp>  
values = [float(x) for x in fields]  
ValueError: could not convert string to float: b'[-2.023991756260691e-06,'

The error came from a file drag and drop and gave more info

SyntaxError: Bad number format in D:\UserN\Sahar\Desktop\166_i.cube, line  
b'[-2.023991756260691e-06, -2.2979603798872067e-06, -2.600360312645661e-06,
-2.930878531356648e-06, -3.2879944435721872e-06, -3.6686930206119455e-06,
-4.0682087524247615e-06, -4.479842466678192e-06, -4.894898584675912e-06,
-5.3027893301427804e-06, -5.691342724839675e-06, -6.0473323403086255e-06,
-6.357219896043383e-06, -6.608069452559056e-06, -6.788557643316349e-06,
-6.889972769581632e-06, -6.907073308861002e-06, -6.83867236075875e-06,
-6.687837571705336e-06, -6.46164952884207e-06, -6.170537966587619e-06,
-5.827295042688566e-06, -5.445923760712789e-06, -5.040498680317063e-06,
-4.6241917789464e-06, -4.208561114284575e-06, -3.8031348457002427e-06,
-3.415267725921078e-06, -3.0502123985250625e-06, -2.7113350869987363e-06,
-2.4004093332123022e-06]\n'

But earlier opening the same file works fine

> open D:/UserN/Sahar/Desktop/166_i.cube

Opened 166_i.cube as #23, grid size 32,32,32, pixel 0.529, shown at level
-0.0153,0.0153, step 1, values float32


comment:3 by Tom Goddard, 4 years ago

Resolution: → can't reproduce
Status: assigned → closed

All I can guess is the user overwrote the file so it was no longer in cube format.

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