Command-history deletion bug

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.17134
ChimeraX Version: 0.8 (2018-12-17)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-  
packages\chimerax\core\toolshed\\\\__init__.py", line 338, in __init__  
self.init_available_from_cache(logger)  
File "C:\Program Files\ChimeraX\bin\lib\site-  
packages\chimerax\core\toolshed\\\\__init__.py", line 445, in  
init_available_from_cache  
abc.load_from_cache()  
File "C:\Program Files\ChimeraX\bin\lib\site-  
packages\chimerax\core\toolshed\available.py", line 61, in load_from_cache  
b = _build_bundle(d)  
File "C:\Program Files\ChimeraX\bin\lib\site-  
packages\chimerax\core\toolshed\available.py", line 242, in _build_bundle  
keywords = _extract_extra_keywords(keywords)  
File "C:\Program Files\ChimeraX\bin\lib\site-  
packages\chimerax\core\toolshed\installed.py", line 270, in  
_extract_extra_keywords  
all_kwds = [k.strip() for k in kwds.split(',')]  
AttributeError: 'list' object has no attribute 'split'  
  
UCSF ChimeraX version: 0.8 (2018-12-17)  
How to cite UCSF ChimeraX  

> open "C:/Users/Grosman Lab/Downloads/5c5c_dry.pdb"

Summary of feedback from opening C:/Users/Grosman Lab/Downloads/5c5c_dry.pdb  
---  
warnings | Ignored bad PDB record found on line 100001  
ATOM 186a0 H16Y POPCM 646 64.706 3.804 -1.946 1.00 0.00 MEMB  
  
Ignored bad PDB record found on line 100002  
ATOM 186a1 H16Z POPCM 646 62.931 3.950 -2.003 1.00 0.00 MEMB  
  
Ignored bad PDB record found on line 100003  
ATOM 186a2 N POPCM 647 -62.878 0.815 -20.386 1.00 0.00 MEMB  
  
Ignored bad PDB record found on line 100004  
ATOM 186a3 C12 POPCM 647 -62.972 1.432 -18.981 1.00 0.00 MEMB  
  
Ignored bad PDB record found on line 100005  
ATOM 186a4 H12A POPCM 647 -63.927 1.102 -18.598 1.00 0.00 MEMB  
  
91 messages similar to the above omitted  
Duplicate atom serial number found: 18700  
Duplicate atom serial number found: 18701  
Duplicate atom serial number found: 18702  
Duplicate atom serial number found: 18703  
Duplicate atom serial number found: 18704  
5 messages similar to the above omitted  
Ignored bad PDB record found on line 100107  
ATOM 1870a H7X POPCM 647 -59.422 0.724 -9.432 1.00 0.00 MEMB  
  
Ignored bad PDB record found on line 100108  
ATOM 1870b H7Y POPCM 647 -57.790 1.524 -9.226 1.00 0.00 MEMB  
  
Ignored bad PDB record found on line 100109  
ATOM 1870c C38 POPCM 647 -57.658 -0.402 -8.601 1.00 0.00 MEMB  
  
Ignored bad PDB record found on line 100110  
ATOM 1870d H8X POPCM 647 -56.600 -0.517 -8.919 1.00 0.00 MEMB  
  
Ignored bad PDB record found on line 100111  
ATOM 1870e H8Y POPCM 647 -58.216 -1.362 -8.625 1.00 0.00 MEMB  
  
1 messages similar to the above omitted  
Duplicate atom serial number found: 18710  
Duplicate atom serial number found: 18711  
Duplicate atom serial number found: 18712  
Duplicate atom serial number found: 18713  
Duplicate atom serial number found: 18714  
5 messages similar to the above omitted  
Ignored bad PDB record found on line 100123  
ATOM 1871a H12Y POPCM 647 -57.709 -0.419 -4.249 1.00 0.00 MEMB  
  
Ignored bad PDB record found on line 100124  
ATOM 1871b C313 POPCM 647 -59.769 -1.043 -4.007 1.00 0.00 MEMB  
  
Ignored bad PDB record found on line 100125  
ATOM 1871c H13X POPCM 647 -59.722 -1.525 -5.007 1.00 0.00 MEMB  
  
Ignored bad PDB record found on line 100126  
ATOM 1871d H13Y POPCM 647 -60.726 -0.495 -3.869 1.00 0.00 MEMB  
  
Ignored bad PDB record found on line 100127  
ATOM 1871e C314 POPCM 647 -59.560 -2.052 -2.869 1.00 0.00 MEMB  
  
1 messages similar to the above omitted  
Duplicate atom serial number found: 18720  
Duplicate atom serial number found: 18721  
Duplicate atom serial number found: 18722  
Duplicate atom serial number found: 18723  
Duplicate atom serial number found: 18724  
5 messages similar to the above omitted  
Ignored bad PDB record found on line 100139  
ATOM 1872a H12A POPCM 648 51.368 -35.954 -21.031 1.00 0.00 MEMB  
  
Ignored bad PDB record found on line 100140  
ATOM 1872b H12B POPCM 648 52.224 -35.729 -19.621 1.00 0.00 MEMB  
  
Ignored bad PDB record found on line 100141  
ATOM 1872c C13 POPCM 648 50.340 -36.811 -17.931 1.00 0.00 MEMB  
  
Ignored bad PDB record found on line 100142  
ATOM 1872d H13A POPCM 648 49.931 -35.813 -17.887 1.00 0.00 MEMB  
  
Ignored bad PDB record found on line 100143  
ATOM 1872e H13B POPCM 648 49.714 -37.628 -17.605 1.00 0.00 MEMB  
  
1 messages similar to the above omitted  
Duplicate atom serial number found: 18730  
Duplicate atom serial number found: 18731  
Duplicate atom serial number found: 18732  
Duplicate atom serial number found: 18733  
Duplicate atom serial number found: 18734  
5 messages similar to the above omitted  
Ignored bad PDB record found on line 100155  
ATOM 1873a H11B POPCM 648 50.961 -33.776 -20.756 1.00 0.00 MEMB  
  
Ignored bad PDB record found on line 100156  
ATOM 1873b P POPCM 648 50.176 -32.311 -18.439 1.00 0.00 MEMB  
  
Ignored bad PDB record found on line 100157  
ATOM 1873c O13 POPCM 648 50.116 -31.619 -19.739 1.00 0.00 MEMB  
  
Ignored bad PDB record found on line 100158  
ATOM 1873d O14 POPCM 648 50.910 -31.586 -17.348 1.00 0.00 MEMB  
  
Ignored bad PDB record found on line 100159  
ATOM 1873e O12 POPCM 648 50.775 -33.769 -18.674 1.00 0.00 MEMB  
  
1 messages similar to the above omitted  
Duplicate atom serial number found: 18740  
Duplicate atom serial number found: 18741  
Duplicate atom serial number found: 18742  
Duplicate atom serial number found: 18743  
Duplicate atom serial number found: 18744  
5 messages similar to the above omitted  
Ignored bad PDB record found on line 100171  
ATOM 1874a H2S POPCM 648 48.518 -30.611 -14.528 1.00 0.00 MEMB  
  
Ignored bad PDB record found on line 100172  
ATOM 1874b C3 POPCM 648 46.417 -33.503 -16.561 1.00 0.00 MEMB  
  
Ignored bad PDB record found on line 100173  
ATOM 1874c HX POPCM 648 46.265 -34.289 -17.331 1.00 0.00 MEMB  
  
Ignored bad PDB record found on line 100174  
ATOM 1874d HY POPCM 648 45.529 -33.644 -15.910 1.00 0.00 MEMB  
  
Ignored bad PDB record found on line 100175  
ATOM 1874e O31 POPCM 648 47.594 -33.780 -15.873 1.00 0.00 MEMB  
  
1 messages similar to the above omitted  
Duplicate atom serial number found: 18750  
Duplicate atom serial number found: 18751  
Duplicate atom serial number found: 18752  
Duplicate atom serial number found: 18753  
Duplicate atom serial number found: 18754  
5 messages similar to the above omitted  
Ignored bad PDB record found on line 100187  
ATOM 1875a C25 POPCM 648 46.546 -32.994 -11.641 1.00 0.00 MEMB  
  
Ignored bad PDB record found on line 100188  
ATOM 1875b H5R POPCM 648 45.477 -33.109 -11.919 1.00 0.00 MEMB  
  
Ignored bad PDB record found on line 100189  
ATOM 1875c H5S POPCM 648 46.556 -32.248 -10.818 1.00 0.00 MEMB  
  
Ignored bad PDB record found on line 100190  
ATOM 1875d C26 POPCM 648 46.821 -34.424 -11.125 1.00 0.00 MEMB  
  
Ignored bad PDB record found on line 100191  
ATOM 1875e H6R POPCM 648 47.737 -34.342 -10.502 1.00 0.00 MEMB  
  
1 messages similar to the above omitted  
Duplicate atom serial number found: 18760  
Duplicate atom serial number found: 18761  
Duplicate atom serial number found: 18762  
Duplicate atom serial number found: 18763  
Duplicate atom serial number found: 18764  
5 messages similar to the above omitted  
Ignored bad PDB record found on line 100203  
ATOM 1876a C211 POPCM 648 46.032 -37.959 -7.406 1.00 0.00 MEMB  
  
Ignored bad PDB record found on line 100204  
ATOM 1876b H11R POPCM 648 46.031 -39.063 -7.280 1.00 0.00 MEMB  
  
Ignored bad PDB record found on line 100205  
ATOM 1876c H11S POPCM 648 45.035 -37.759 -7.854 1.00 0.00 MEMB  
  
Ignored bad PDB record found on line 100206  
ATOM 1876d C212 POPCM 648 46.089 -37.215 -6.055 1.00 0.00 MEMB  
  
Ignored bad PDB record found on line 100207  
ATOM 1876e H12R POPCM 648 47.007 -37.320 -5.438 1.00 0.00 MEMB  
  
1 messages similar to the above omitted  
Duplicate atom serial number found: 18770  
Duplicate atom serial number found: 18771  
Duplicate atom serial number found: 18772  
Duplicate atom serial number found: 18773  
Duplicate atom serial number found: 18774  
5 messages similar to the above omitted  
Ignored bad PDB record found on line 100219  
ATOM 1877a H16R POPCM 648 46.683 -32.283 -6.159 1.00 0.00 MEMB  
  
Ignored bad PDB record found on line 100220  
ATOM 1877b H16S POPCM 648 47.611 -33.373 -5.191 1.00 0.00 MEMB  
  
Ignored bad PDB record found on line 100221  
ATOM 1877c C217 POPCM 648 46.944 -31.589 -4.117 1.00 0.00 MEMB  
  
Ignored bad PDB record found on line 100222  
ATOM 1877d H17R POPCM 648 46.036 -30.956 -4.214 1.00 0.00 MEMB  
  
Ignored bad PDB record found on line 100223  
ATOM 1877e H17S POPCM 648 47.735 -31.035 -4.666 1.00 0.00 MEMB  
  
1 messages similar to the above omitted  

[a lot of this went on]

Duplicate atom serial number found: 22900  
Duplicate atom serial number found: 22901  
Duplicate atom serial number found: 22902  
Duplicate atom serial number found: 22903  
Duplicate atom serial number found: 22904  
5 messages similar to the above omitted  
Ignored bad PDB record found on line 141579  
ATOM 2290a CLA CLA I 826 -28.245 -49.648 86.886 1.00 0.00 ION1CL  
  
Ignored bad PDB record found on line 141580  
ATOM 2290b CLA CLA I 827 42.915 36.295 149.406 1.00 0.00 ION1CL  
  
Ignored bad PDB record found on line 141581  
ATOM 2290c CLA CLA I 828 28.728 1.069 -35.403 1.00 0.00 ION1CL  
  
Ignored bad PDB record found on line 141582  
ATOM 2290d CLA CLA I 829 34.495 30.525 95.196 1.00 0.00 ION1CL  
  
Ignored bad PDB record found on line 141583  
ATOM 2290e CLA CLA I 830 59.512 14.302 123.499 1.00 0.00 ION1CL  
  
1 messages similar to the above omitted  
Duplicate atom serial number found: 22910  
Duplicate atom serial number found: 22911  
Duplicate atom serial number found: 22912  
Duplicate atom serial number found: 22913  
Duplicate atom serial number found: 22914  
5 messages similar to the above omitted  
Ignored bad PDB record found on line 141595  
ATOM 2291a CLA CLA I 842 31.955 -4.812 131.599 1.00 0.00 ION1CL  
  
Ignored bad PDB record found on line 141596  
ATOM 2291b CLA CLA I 843 -34.514 -24.959 -35.104 1.00 0.00 ION1CL  
  
Ignored bad PDB record found on line 141597  
ATOM 2291c CLA CLA I 844 15.364 -51.514 79.666 1.00 0.00 ION1CL  
  
Ignored bad PDB record found on line 141598  
ATOM 2291d CLA CLA I 845 -1.951 -15.859 135.441 1.00 0.00 ION1CL  
  
Ignored bad PDB record found on line 141599  
ATOM 2291e CLA CLA I 846 34.464 -73.054 101.242 1.00 0.00 ION1CL  
  
1 messages similar to the above omitted  
Duplicate atom serial number found: 22920  
Duplicate atom serial number found: 22921  
Duplicate atom serial number found: 22922  
Duplicate atom serial number found: 22923  
Duplicate atom serial number found: 22924  
5 messages similar to the above omitted  
Ignored bad PDB record found on line 141611  
ATOM 2292a CLA CLA I 858 -84.885 -4.760 38.052 1.00 0.00 ION1CL  
  
Ignored bad PDB record found on line 141612  
ATOM 2292b CLA CLA I 859 -85.353 -83.368 118.373 1.00 0.00 ION1CL  
  
Ignored bad PDB record found on line 141613  
ATOM 2292c CLA CLA I 860 61.687 -38.192 106.217 1.00 0.00 ION1CL  
  
Ignored bad PDB record found on line 141614  
ATOM 2292d CLA CLA I 861 73.900 11.961 35.491 1.00 0.00 ION1CL  
  
Ignored bad PDB record found on line 141615  
ATOM 2292e CLA CLA I 862 63.621 -24.088 116.577 1.00 0.00 ION1CL  
  
1 messages similar to the above omitted  
Duplicate atom serial number found: 22930  
Duplicate atom serial number found: 22931  
Duplicate atom serial number found: 22932  
Duplicate atom serial number found: 22933  
Duplicate atom serial number found: 22934  
5 messages similar to the above omitted  
Ignored bad PDB record found on line 141627  
ATOM 2293a CLA CLA I 874 19.128 62.098 154.194 1.00 0.00 ION1CL  
  
Ignored bad PDB record found on line 141628  
ATOM 2293b CLA CLA I 875 51.115 30.575 57.720 1.00 0.00 ION1CL  
  
Ignored bad PDB record found on line 141629  
ATOM 2293c CLA CLA I 876 87.650 -59.185 49.976 1.00 0.00 ION1CL  
  
Ignored bad PDB record found on line 141630  
ATOM 2293d CLA CLA I 877 -70.094 -21.815 110.397 1.00 0.00 ION1CL  
  
Ignored bad PDB record found on line 141631  
ATOM 2293e CLA CLA I 878 46.942 -42.734 71.881 1.00 0.00 ION1CL  
  
1 messages similar to the above omitted  
Duplicate atom serial number found: 22940  
Duplicate atom serial number found: 22941  
Duplicate atom serial number found: 22942  
Duplicate atom serial number found: 22943  
Duplicate atom serial number found: 22944  
5 messages similar to the above omitted  
Ignored bad PDB record found on line 141643  
ATOM 2294a CLA CLA I 890 45.037 -31.260 -35.906 1.00 0.00 ION1CL  
  
Ignored bad PDB record found on line 141644  
ATOM 2294b CLA CLA I 891 21.955 23.927 148.630 1.00 0.00 ION1CL  
  
Ignored bad PDB record found on line 141645  
ATOM 2294c CLA CLA I 892 48.142 -74.638 60.450 1.00 0.00 ION1CL  
  
Ignored bad PDB record found on line 141646  
ATOM 2294d CLA CLA I 893 -28.840 47.048 82.150 1.00 0.00 ION1CL  
  
Ignored bad PDB record found on line 141647  
ATOM 2294e CLA CLA I 894 -84.885 -70.180 38.051 1.00 0.00 ION1CL  
  
1 messages similar to the above omitted  
Duplicate atom serial number found: 22950  
  
Chain information for 5c5c_dry.pdb #1  
---  
Chain | Description  
A B C D E | No description available  
  

> hide selAtoms ribbons

> show selAtoms ribbons

> hide selAtoms

> show selAtoms

> select /A

4991 atoms, 5060 bonds selected  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 334, in <lambda>  
but.clicked.connect(lambda arg, txt=but_name: self.button_clicked(txt))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 421, in button_clicked  
if self.typed_only and not h[1]:  
NameError: name 'h' is not defined  
  
NameError: name 'h' is not defined  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 421, in button_clicked  
if self.typed_only and not h[1]:  
  
See log for complete Python traceback.  
  

> hide selAtoms

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 334, in <lambda>  
but.clicked.connect(lambda arg, txt=but_name: self.button_clicked(txt))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 421, in button_clicked  
if self.typed_only and not h[1]:  
NameError: name 'h' is not defined  
  
NameError: name 'h' is not defined  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 421, in button_clicked  
if self.typed_only and not h[1]:  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 388.13
OpenGL renderer: GeForce GTX 1060 3GB/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Eric Pettersen]

Fixed back in December