Opened 9 months ago

Closed 9 months ago

#16639 closed defect (duplicate)

Color key: cannot restore numeric locale

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Depiction Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-6.8.0-51-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.4rc202205290614 (2022-05-29 06:14:06 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.4rc202205290614 (2022-05-29)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open
> /media/hhklab1/500GB/workspace/humanFAS_priynaka/humand_and_FAS_pocket/old/mFAS_simulation_analysis/16jan24_new_500_with_replica_avg/KR/KR_stamp_align_chimerax.cxs
> format session

Log from Tue Apr 23 14:53:14 2024UCSF ChimeraX version: 1.4rc202205290614
(2022-05-29)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open
> /media/hhklab1/500GB/workspace/humanFAS_priynaka/humand_and_FAS_pocket/old/mFAS_simulation_analysis/alignment/KR/KR_stamp_align_chimerax.cxs

Log from Mon Apr 22 15:36:21 2024UCSF ChimeraX version: 1.4rc202205290614
(2022-05-29)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open
> /media/hhklab1/500GB/workspace/humanFAS_priynaka/humand_and_FAS_pocket/old/mFAS_simulation_analysis/alignment/KR/KR_stamp_align_chimerax.cxs

Log from Fri Mar 15 12:05:59 2024UCSF ChimeraX version: 1.4rc202205290614
(2022-05-29)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open
> /media/hhklab1/500GB/workspace/humanFAS_priynaka/humand_and_FAS_pocket/old/mFAS_simulation_analysis/alignment/KR/KR_stamp_align_chimerax.cxs

Log from Fri Feb 23 13:04:41 2024UCSF ChimeraX version: 1.4rc202205290614
(2022-05-29)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open
> /media/hhklab1/500GB/workspace/humanFAS_priynaka/humand_and_FAS_pocket/old/mFAS_simulation_analysis/alignment/KR/KR_stamp_align_chimerax.cxs

Log from Wed Feb 21 03:34:45 2024 Startup Errors  
---  
errors | Bundle 'ChimeraX-DevelExtras' custom initialization failed  
Bundle 'ChimeraX-ISOLDE' custom initialization failed  
warnings | Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 490, in get_module  
m = importlib.import_module(self.package_name)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/importlib/__init__.py", line 127,
in import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
File "<frozen importlib._bootstrap>", line 1030, in _gcd_import  
File "<frozen importlib._bootstrap>", line 1007, in _find_and_load  
File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked  
File "<frozen importlib._bootstrap>", line 680, in _load_unlocked  
File "<frozen importlib._bootstrap_external>", line 850, in exec_module  
File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed  
File "/home/hhklab1/.local/share/ChimeraX/1.4/site-
packages/chimerax/devel_extras/__init__.py", line 26, in <module>  
from . import gui, core  
File "/home/hhklab1/.local/share/ChimeraX/1.4/site-
packages/chimerax/devel_extras/gui.py", line 37, in <module>  
from PyQt5.QtWidgets import (  
ModuleNotFoundError: No module named 'PyQt5'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 364, in initialize  
api = self._get_api(session.logger)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 509, in _get_api  
m = self.get_module()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 492, in get_module  
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-
DevelExtras's module: No module named 'PyQt5'  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 490, in get_module  
m = importlib.import_module(self.package_name)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/importlib/__init__.py", line 127,
in import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
File "<frozen importlib._bootstrap>", line 1030, in _gcd_import  
File "<frozen importlib._bootstrap>", line 1007, in _find_and_load  
File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked  
File "<frozen importlib._bootstrap>", line 680, in _load_unlocked  
File "<frozen importlib._bootstrap_external>", line 850, in exec_module  
File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed  
File "/home/hhklab1/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 51, in <module>  
__version__ = _version()  
File "/home/hhklab1/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 49, in _version  
return pkg_resources.require('ChimeraX-ISOLDE')[0].version  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/pkg_resources/__init__.py", line 891, in require  
needed = self.resolve(parse_requirements(requirements))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/pkg_resources/__init__.py", line 782, in resolve  
raise VersionConflict(dist, req).with_context(dependent_req)  
pkg_resources.ContextualVersionConflict: (ChimeraX-UI 1.2.1
(/home/hhklab1/.local/share/ChimeraX/1.4/site-packages),
Requirement.parse('ChimeraX-UI~=1.10'), {'ChimeraX-SaveCommand'})  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 364, in initialize  
api = self._get_api(session.logger)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 509, in _get_api  
m = self.get_module()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 492, in get_module  
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ISOLDE's
module: (ChimeraX-UI 1.2.1 (/home/hhklab1/.local/share/ChimeraX/1.4/site-
packages), Requirement.parse('ChimeraX-UI~=1.10'), {'ChimeraX-SaveCommand'})  
  
UCSF ChimeraX version: 1.4rc202205290614 (2022-05-29)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /media/hhklab1/500GB/workspace/humanFAS_priynaka/humand_and_FAS_pocket/old/mFAS_simulation_analysis/alignment/MPT/MPT_stamp_alignavpos_hMPT.pdb
> /media/hhklab1/500GB/workspace/humanFAS_priynaka/humand_and_FAS_pocket/old/mFAS_simulation_analysis/alignment/MPT/MPT_stamp_alignavpos_MPT.pdb

Chain information for MPT_stamp_alignavpos_hMPT.pdb #1  
---  
Chain | Description  
A | No description available  
  
Chain information for MPT_stamp_alignavpos_MPT.pdb #2  
---  
Chain | Description  
A | No description available  
  

> color #1 green

> color #2 dark gray

> color byattribute bfactor
> #1/A:496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,516,517,518,519,520,521,522,523,524,525,526,527,528,529,530,531,532,533,534,535,536,537,538,539,540,541,542,543,544,545,546,547,548,549,550,551,552,553,554,555,556,557,558,559,560,561,562,563,564,565,566,567,568,569,570,571,572,573,574,575,576,577,578,579,580,581,582,583,584,585,586,587,588,589,590,591,592,593,594,595,596,597,598,599,600,601,602,603,604,605,606,607,608,609,610,611,612,613,615,616,617,618,619,620,621,622,623,624,625,626,627,628,629,630,631,632,633,634,635,636,637,638,639,640,641,642,643,644,645,646,647,648,649,650,651,652,653,654,655,656,657,658,660,661,662,664,665,666,667,668,669,670,671,672,673,674,675,676,677,678,679,680,681,682,683,684,685,686,687,688,689,690,691,692,693,694,695,696,697,698,699,700,701,702,703,704,705,706,707,708,709,710,711,712,713,714,715,716,718,719,722,723,724,725,726,727,730,732,733,734,735,736,737,738,739,740,741,742,743,744,745,746,747,748,749,750,751,752,753,754,755,757,758,759,760,761,762,763,764,765,766,767,768,769,770,771,772,773,774,775,776,777,778,779,780,781,782,783,784,785,795,799,800,801,802,803,804,805

4444 atoms, 288 residues, atom bfactor range 0.04 to 0.78  

> color byattribute bfactor
> #2/A:,1315,1316,1317,1318,1319,1320,1321,1322,1323,1324,1325,1326,1327,1328,1329,1330,1331,1333,1334,1335,1336,1337,1338,1339,1340,1341,1342,1343,1344,1345,1346,1347,1348,1350,1351,1352,1353,1354,1355,1356,1357,1358,1359,1360,1361,1362,1363,1364,1378,1379,1380,1381,1382,1383,1384,1385,1386,1387,1388,1389,1390,1391,1392,1393,1394,1395,1396,1397,1398,1399,1400,1401,1402,1403,1404,1405,1406,1407,1408,1411,1412,1413,1414,1415,1416,1417,1418,1419,1420,1421,1422,1423,1424,1425,1427,1428,1429,1430,1431,1432,1433,1434,1435,1436,1437,1438,1439,1440,1441,1442,1443,1444,1445,1446,1447,1448,1449,1450,1451,1452,1459,1461,1462,1463,1464,1465,1466,1467,1473,1475,1479,1480,1481,1482,1483,1484,1485,1486,1489,1490,1492,1493,1494,1495,1496,1497,1498,1499,1500,1501,1502,1504,1505,1506,1507,1508,1509,1510,1511,1512,1513,1514,1515,1517,1518,1519,1521,1522,1523,1524,1530,1531,1533,1534,1535,1536,1537,1538,1539,1540,1541,1542,1543,1544,1545,1546,1547,1548,1549,1550,1551,1552,1553,1554,1555,1556,1557,1558,1559,1560,1561,1562,1563,1564,1565,1566,1567,1568,1570,1573,1574,1575,1576,1577,1578,1579,1580,1581,1582,1583,1584,1587,1592,1593,1626,1627,1628,1629,1630,1631,1632,1633,1634,1635,1636,1637,1638,1639,1640,1641,1642,1643,1644,1645,1646,1647,1648,1649,1659,1660,1661,1662,1663,1664,1665,1666,1667,1668,1671,1672,1673,1674,1675,1676,1677,1678,1679,1680,1681,1682,1687,1688,1691,1692,1693,1694,1695,1696,1697,1698,1699,1700,1701,1702,1703,1704,1706,1708

Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword  

> color byattribute bfactor
> #2/A:1315,1316,1317,1318,1319,1320,1321,1322,1323,1324,1325,1326,1327,1328,1329,1330,1331,1333,1334,1335,1336,1337,1338,1339,1340,1341,1342,1343,1344,1345,1346,1347,1348,1350,1351,1352,1353,1354,1355,1356,1357,1358,1359,1360,1361,1362,1363,1364,1378,1379,1380,1381,1382,1383,1384,1385,1386,1387,1388,1389,1390,1391,1392,1393,1394,1395,1396,1397,1398,1399,1400,1401,1402,1403,1404,1405,1406,1407,1408,1411,1412,1413,1414,1415,1416,1417,1418,1419,1420,1421,1422,1423,1424,1425,1427,1428,1429,1430,1431,1432,1433,1434,1435,1436,1437,1438,1439,1440,1441,1442,1443,1444,1445,1446,1447,1448,1449,1450,1451,1452,1459,1461,1462,1463,1464,1465,1466,1467,1473,1475,1479,1480,1481,1482,1483,1484,1485,1486,1489,1490,1492,1493,1494,1495,1496,1497,1498,1499,1500,1501,1502,1504,1505,1506,1507,1508,1509,1510,1511,1512,1513,1514,1515,1517,1518,1519,1521,1522,1523,1524,1530,1531,1533,1534,1535,1536,1537,1538,1539,1540,1541,1542,1543,1544,1545,1546,1547,1548,1549,1550,1551,1552,1553,1554,1555,1556,1557,1558,1559,1560,1561,1562,1563,1564,1565,1566,1567,1568,1570,1573,1574,1575,1576,1577,1578,1579,1580,1581,1582,1583,1584,1587,1592,1593,1626,1627,1628,1629,1630,1631,1632,1633,1634,1635,1636,1637,1638,1639,1640,1641,1642,1643,1644,1645,1646,1647,1648,1649,1659,1660,1661,1662,1663,1664,1665,1666,1667,1668,1671,1672,1673,1674,1675,1676,1677,1678,1679,1680,1681,1682,1687,1688,1691,1692,1693,1694,1695,1696,1697,1698,1699,1700,1701,1702,1703,1704,1706,1708

4500 atoms, 288 residues, atom bfactor range 0.04 to 0.79  

> color #2 #9a9996 transparency 0

> color byattribute bfactor
> #2/A:1315,1316,1317,1318,1319,1320,1321,1322,1323,1324,1325,1326,1327,1328,1329,1330,1331,1333,1334,1335,1336,1337,1338,1339,1340,1341,1342,1343,1344,1345,1346,1347,1348,1350,1351,1352,1353,1354,1355,1356,1357,1358,1359,1360,1361,1362,1363,1364,1378,1379,1380,1381,1382,1383,1384,1385,1386,1387,1388,1389,1390,1391,1392,1393,1394,1395,1396,1397,1398,1399,1400,1401,1402,1403,1404,1405,1406,1407,1408,1411,1412,1413,1414,1415,1416,1417,1418,1419,1420,1421,1422,1423,1424,1425,1427,1428,1429,1430,1431,1432,1433,1434,1435,1436,1437,1438,1439,1440,1441,1442,1443,1444,1445,1446,1447,1448,1449,1450,1451,1452,1459,1461,1462,1463,1464,1465,1466,1467,1473,1475,1479,1480,1481,1482,1483,1484,1485,1486,1489,1490,1492,1493,1494,1495,1496,1497,1498,1499,1500,1501,1502,1504,1505,1506,1507,1508,1509,1510,1511,1512,1513,1514,1515,1517,1518,1519,1521,1522,1523,1524,1530,1531,1533,1534,1535,1536,1537,1538,1539,1540,1541,1542,1543,1544,1545,1546,1547,1548,1549,1550,1551,1552,1553,1554,1555,1556,1557,1558,1559,1560,1561,1562,1563,1564,1565,1566,1567,1568,1570,1573,1574,1575,1576,1577,1578,1579,1580,1581,1582,1583,1584,1587,1592,1593,1626,1627,1628,1629,1630,1631,1632,1633,1634,1635,1636,1637,1638,1639,1640,1641,1642,1643,1644,1645,1646,1647,1648,1649,1659,1660,1661,1662,1663,1664,1665,1666,1667,1668,1671,1672,1673,1674,1675,1676,1677,1678,1679,1680,1681,1682,1687,1688,1691,1692,1693,1694,1695,1696,1697,1698,1699,1700,1701,1702,1703,1704,1706,1708

4500 atoms, 288 residues, atom bfactor range 0.04 to 0.79  

> color #2 #b5835a transparency 0

> color byattribute bfactor
> #2/A:1315,1316,1317,1318,1319,1320,1321,1322,1323,1324,1325,1326,1327,1328,1329,1330,1331,1333,1334,1335,1336,1337,1338,1339,1340,1341,1342,1343,1344,1345,1346,1347,1348,1350,1351,1352,1353,1354,1355,1356,1357,1358,1359,1360,1361,1362,1363,1364,1378,1379,1380,1381,1382,1383,1384,1385,1386,1387,1388,1389,1390,1391,1392,1393,1394,1395,1396,1397,1398,1399,1400,1401,1402,1403,1404,1405,1406,1407,1408,1411,1412,1413,1414,1415,1416,1417,1418,1419,1420,1421,1422,1423,1424,1425,1427,1428,1429,1430,1431,1432,1433,1434,1435,1436,1437,1438,1439,1440,1441,1442,1443,1444,1445,1446,1447,1448,1449,1450,1451,1452,1459,1461,1462,1463,1464,1465,1466,1467,1473,1475,1479,1480,1481,1482,1483,1484,1485,1486,1489,1490,1492,1493,1494,1495,1496,1497,1498,1499,1500,1501,1502,1504,1505,1506,1507,1508,1509,1510,1511,1512,1513,1514,1515,1517,1518,1519,1521,1522,1523,1524,1530,1531,1533,1534,1535,1536,1537,1538,1539,1540,1541,1542,1543,1544,1545,1546,1547,1548,1549,1550,1551,1552,1553,1554,1555,1556,1557,1558,1559,1560,1561,1562,1563,1564,1565,1566,1567,1568,1570,1573,1574,1575,1576,1577,1578,1579,1580,1581,1582,1583,1584,1587,1592,1593,1626,1627,1628,1629,1630,1631,1632,1633,1634,1635,1636,1637,1638,1639,1640,1641,1642,1643,1644,1645,1646,1647,1648,1649,1659,1660,1661,1662,1663,1664,1665,1666,1667,1668,1671,1672,1673,1674,1675,1676,1677,1678,1679,1680,1681,1682,1687,1688,1691,1692,1693,1694,1695,1696,1697,1698,1699,1700,1701,1702,1703,1704,1706,1708

4500 atoms, 288 residues, atom bfactor range 0.04 to 0.79  

> color #2 #c061cb transparency 0

> color #2 #613583 transparency 0

> color byattribute bfactor
> #1/A:496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,516,517,518,519,520,521,522,523,524,525,526,527,528,529,530,531,532,533,534,535,536,537,538,539,540,541,542,543,544,545,546,547,548,549,550,551,552,553,554,555,556,557,558,559,560,561,562,563,564,565,566,567,568,569,570,571,572,573,574,575,576,577,578,579,580,581,582,583,584,585,586,587,588,589,590,591,592,593,594,595,596,597,598,599,600,601,602,603,604,605,606,607,608,609,610,611,612,613,615,616,617,618,619,620,621,622,623,624,625,626,627,628,629,630,631,632,633,634,635,636,637,638,639,640,641,642,643,644,645,646,647,648,649,650,651,652,653,654,655,656,657,658,660,661,662,664,665,666,667,668,669,670,671,672,673,674,675,676,677,678,679,680,681,682,683,684,685,686,687,688,689,690,691,692,693,694,695,696,697,698,699,700,701,702,703,704,705,706,707,708,709,710,711,712,713,714,715,716,718,719,722,723,724,725,726,727,730,732,733,734,735,736,737,738,739,740,741,742,743,744,745,746,747,748,749,750,751,752,753,754,755,757,758,759,760,761,762,763,764,765,766,767,768,769,770,771,772,773,774,775,776,777,778,779,780,781,782,783,784,785,795,799,800,801,802,803,804,805

4444 atoms, 288 residues, atom bfactor range 0.04 to 0.78  

> color byattribute bfactor
> #2/A:1315,1316,1317,1318,1319,1320,1321,1322,1323,1324,1325,1326,1327,1328,1329,1330,1331,1333,1334,1335,1336,1337,1338,1339,1340,1341,1342,1343,1344,1345,1346,1347,1348,1350,1351,1352,1353,1354,1355,1356,1357,1358,1359,1360,1361,1362,1363,1364,1378,1379,1380,1381,1382,1383,1384,1385,1386,1387,1388,1389,1390,1391,1392,1393,1394,1395,1396,1397,1398,1399,1400,1401,1402,1403,1404,1405,1406,1407,1408,1411,1412,1413,1414,1415,1416,1417,1418,1419,1420,1421,1422,1423,1424,1425,1427,1428,1429,1430,1431,1432,1433,1434,1435,1436,1437,1438,1439,1440,1441,1442,1443,1444,1445,1446,1447,1448,1449,1450,1451,1452,1459,1461,1462,1463,1464,1465,1466,1467,1473,1475,1479,1480,1481,1482,1483,1484,1485,1486,1489,1490,1492,1493,1494,1495,1496,1497,1498,1499,1500,1501,1502,1504,1505,1506,1507,1508,1509,1510,1511,1512,1513,1514,1515,1517,1518,1519,1521,1522,1523,1524,1530,1531,1533,1534,1535,1536,1537,1538,1539,1540,1541,1542,1543,1544,1545,1546,1547,1548,1549,1550,1551,1552,1553,1554,1555,1556,1557,1558,1559,1560,1561,1562,1563,1564,1565,1566,1567,1568,1570,1573,1574,1575,1576,1577,1578,1579,1580,1581,1582,1583,1584,1587,1592,1593,1626,1627,1628,1629,1630,1631,1632,1633,1634,1635,1636,1637,1638,1639,1640,1641,1642,1643,1644,1645,1646,1647,1648,1649,1659,1660,1661,1662,1663,1664,1665,1666,1667,1668,1671,1672,1673,1674,1675,1676,1677,1678,1679,1680,1681,1682,1687,1688,1691,1692,1693,1694,1695,1696,1697,1698,1699,1700,1701,1702,1703,1704,1706,1708

4500 atoms, 288 residues, atom bfactor range 0.04 to 0.79  

> color #2 #77767b transparency 0

> color #2 #5e5c64 transparency 0

> color byattribute bfactor
> #2/A:1315,1316,1317,1318,1319,1320,1321,1322,1323,1324,1325,1326,1327,1328,1329,1330,1331,1333,1334,1335,1336,1337,1338,1339,1340,1341,1342,1343,1344,1345,1346,1347,1348,1350,1351,1352,1353,1354,1355,1356,1357,1358,1359,1360,1361,1362,1363,1364,1378,1379,1380,1381,1382,1383,1384,1385,1386,1387,1388,1389,1390,1391,1392,1393,1394,1395,1396,1397,1398,1399,1400,1401,1402,1403,1404,1405,1406,1407,1408,1411,1412,1413,1414,1415,1416,1417,1418,1419,1420,1421,1422,1423,1424,1425,1427,1428,1429,1430,1431,1432,1433,1434,1435,1436,1437,1438,1439,1440,1441,1442,1443,1444,1445,1446,1447,1448,1449,1450,1451,1452,1459,1461,1462,1463,1464,1465,1466,1467,1473,1475,1479,1480,1481,1482,1483,1484,1485,1486,1489,1490,1492,1493,1494,1495,1496,1497,1498,1499,1500,1501,1502,1504,1505,1506,1507,1508,1509,1510,1511,1512,1513,1514,1515,1517,1518,1519,1521,1522,1523,1524,1530,1531,1533,1534,1535,1536,1537,1538,1539,1540,1541,1542,1543,1544,1545,1546,1547,1548,1549,1550,1551,1552,1553,1554,1555,1556,1557,1558,1559,1560,1561,1562,1563,1564,1565,1566,1567,1568,1570,1573,1574,1575,1576,1577,1578,1579,1580,1581,1582,1583,1584,1587,1592,1593,1626,1627,1628,1629,1630,1631,1632,1633,1634,1635,1636,1637,1638,1639,1640,1641,1642,1643,1644,1645,1646,1647,1648,1649,1659,1660,1661,1662,1663,1664,1665,1666,1667,1668,1671,1672,1673,1674,1675,1676,1677,1678,1679,1680,1681,1682,1687,1688,1691,1692,1693,1694,1695,1696,1697,1698,1699,1700,1701,1702,1703,1704,1706,1708

4500 atoms, 288 residues, atom bfactor range 0.04 to 0.79  

> save
> /media/hhklab1/500GB/workspace/humanFAS_priynaka/humand_and_FAS_pocket/old/mFAS_simulation_analysis/alignment/MPT/MPT_stamp_align.cxs

> close session

> open
> /media/hhklab1/500GB/workspace/humanFAS_priynaka/humand_and_FAS_pocket/old/mFAS_simulation_analysis/alignment/MPT/MPT_stamp_alignavpos_hMPT.pdb

Chain information for MPT_stamp_alignavpos_hMPT.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open
> /media/hhklab1/500GB/workspace/humanFAS_priynaka/humand_and_FAS_pocket/old/mFAS_simulation_analysis/alignment/MPT/MPT_stamp_alignavpos_MPT.pdb

Chain information for MPT_stamp_alignavpos_MPT.pdb #2  
---  
Chain | Description  
A | No description available  
  

> close session

> open
> /media/hhklab1/500GB/workspace/humanFAS_priynaka/humand_and_FAS_pocket/old/mFAS_simulation_analysis/alignment/KR/KR_stamp_alignavpos_KR.pdb
> /media/hhklab1/500GB/workspace/humanFAS_priynaka/humand_and_FAS_pocket/old/mFAS_simulation_analysis/alignment/KR/KR_stamp_alignavpos_hKR.pdb

Chain information for KR_stamp_alignavpos_KR.pdb #1  
---  
Chain | Description  
A | No description available  
  
Chain information for KR_stamp_alignavpos_hKR.pdb #2  
---  
Chain | Description  
A | No description available  
  

> close session

> open
> /media/hhklab1/500GB/workspace/humanFAS_priynaka/humand_and_FAS_pocket/old/mFAS_simulation_analysis/alignment/KR/KR_stamp_alignavpos_hKR.pdb

Chain information for KR_stamp_alignavpos_hKR.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open
> /media/hhklab1/500GB/workspace/humanFAS_priynaka/humand_and_FAS_pocket/old/mFAS_simulation_analysis/alignment/KR/KR_stamp_alignavpos_KR.pdb

Chain information for KR_stamp_alignavpos_KR.pdb #2  
---  
Chain | Description  
A | No description available  
  

> color #1 green

> color #2 dark gray

> color #2 #5e5c64 transparency 0

> color #1 #f9f06b transparency 0

> color byattribute bfactor
> #1/A:1894,1895,1896,1897,1898,1899,1900,1901,1902,1903,1904,1905,1906,1907,1908,1909,1911,1912,1913,1914,1915,1916,1917,1918,1919,1921,1923,1924,1925,1926,1927,1928,1929,1930,1931,1932,1933,1934,1935,1936,1937,1938,1939,1940,1941,1942,1943,1944,1945,1946,1947,1948,1949,1950,1951,1952,1953,1954,1955,1956,1957,1958,1959,1960,1961,1962,1963,1964,1965,1966,1967,1968,1969,1970,1971,1972,1973,1974,1975,1976,1977,1978,1982,1983,1984,1986,1987,1988,1989,1990,1991,1992,1993,1994,1995,1996,1997,1998,1999,2000,2001,2002,2003,2004,2005,2006,2007,2008,2009,2010,2011,2012,2013,2014,2016,2017,2018,2019,2020,2021,2022,2023,2026,2027,2031,2032,2033,2034,2035,2036,2037,2038,2039,2040,2041,2042,2043,2044,2045,2046,2047,2048,2050,2051,2052,2053,2054,2055,2056,2057,2058,2059,2060,2061,2062,2063,2064,2065,2066,2067,2068,2072,2073,2074,2075,2076,2077,2078,2079,2081,2082,2083,2084,2085,2086,2087,2088,2089,2090,2091,2092,2093,2094,2095,2096,2097,2098,2099,2100,2101,2102,2103,2104,2105,2106,2107,2108,2109,2110,2111,2112,2113

3092 atoms, 202 residues, atom bfactor range 0.1 to 0.74  

> color byattribute bfactor #2/A:

Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword  

>
> 2105,2106,2108,2109,2110,2111,2112,2113,2114,2115,2116,2117,2118,2119,2120,2121,2122,2123,2124,2125,2126,2127,2128,2129,2130,2131,2132,2133,2134,2135,2136,2137,2138,2139,2140,2141,2142,2143,2147,2149,2150,2151,2152,2153,2154,2155,2156,2157,2158,2159,2160,2161,2162,2163,2164,2165,2166,2167,2168,2169,2170,2171,2172,2173,2174,2188,2191,2192,2193,2194,2195,2196,2197,2198,2199,2200,2201,2202,2206,2207,2208,2209,2210,2211,2212,2213,2214,2215,2216,2217,2218,2219,2220,2221,2222,2223,2224,2225,2226,2227,2228,2229,2230,2231,2232,2233,2234,2235,2236,2237,2240,2244,2246,2247,2248,2249,2250,2251,2252,2253,2259,2261,2262,2263,2264,2266,2267,2268,2269,2270,2271,2272,2273,2274,2275,2276,2277,2278,2279,2280,2281,2282,2283,2284,2287,2288,2290,2291,2292,2293,2294,2295,2296,2297,2298,2299,2300,2301,2302,2303,2304,2305,2306,2307,2309,2312,2313,2314,2315,2318,2319,2320,2321,2322,2323,2324,2325,2326,2327,2328,2329,2330,2331,2332,2333,2334,2335,2336,2338,2340,2343,2347,2348,2350,2351,2352,2353,2354,2355,2356,2360,2361

Unknown command:
2105,2106,2108,2109,2110,2111,2112,2113,2114,2115,2116,2117,2118,2119,2120,2121,2122,2123,2124,2125,2126,2127,2128,2129,2130,2131,2132,2133,2134,2135,2136,2137,2138,2139,2140,2141,2142,2143,2147,2149,2150,2151,2152,2153,2154,2155,2156,2157,2158,2159,2160,2161,2162,2163,2164,2165,2166,2167,2168,2169,2170,2171,2172,2173,2174,2188,2191,2192,2193,2194,2195,2196,2197,2198,2199,2200,2201,2202,2206,2207,2208,2209,2210,2211,2212,2213,2214,2215,2216,2217,2218,2219,2220,2221,2222,2223,2224,2225,2226,2227,2228,2229,2230,2231,2232,2233,2234,2235,2236,2237,2240,2244,2246,2247,2248,2249,2250,2251,2252,2253,2259,2261,2262,2263,2264,2266,2267,2268,2269,2270,2271,2272,2273,2274,2275,2276,2277,2278,2279,2280,2281,2282,2283,2284,2287,2288,2290,2291,2292,2293,2294,2295,2296,2297,2298,2299,2300,2301,2302,2303,2304,2305,2306,2307,2309,2312,2313,2314,2315,2318,2319,2320,2321,2322,2323,2324,2325,2326,2327,2328,2329,2330,2331,2332,2333,2334,2335,2336,2338,2340,2343,2347,2348,2350,2351,2352,2353,2354,2355,2356,2360,2361  

> color byattribute bfactor
> #2/A:2105,2106,2108,2109,2110,2111,2112,2113,2114,2115,2116,2117,2118,2119,2120,2121,2122,2123,2124,2125,2126,2127,2128,2129,2130,2131,2132,2133,2134,2135,2136,2137,2138,2139,2140,2141,2142,2143,2147,2149,2150,2151,2152,2153,2154,2155,2156,2157,2158,2159,2160,2161,2162,2163,2164,2165,2166,2167,2168,2169,2170,2171,2172,2173,2174,2188,2191,2192,2193,2194,2195,2196,2197,2198,2199,2200,2201,2202,2206,2207,2208,2209,2210,2211,2212,2213,2214,2215,2216,2217,2218,2219,2220,2221,2222,2223,2224,2225,2226,2227,2228,2229,2230,2231,2232,2233,2234,2235,2236,2237,2240,2244,2246,2247,2248,2249,2250,2251,2252,2253,2259,2261,2262,2263,2264,2266,2267,2268,2269,2270,2271,2272,2273,2274,2275,2276,2277,2278,2279,2280,2281,2282,2283,2284,2287,2288,2290,2291,2292,2293,2294,2295,2296,2297,2298,2299,2300,2301,2302,2303,2304,2305,2306,2307,2309,2312,2313,2314,2315,2318,2319,2320,2321,2322,2323,2324,2325,2326,2327,2328,2329,2330,2331,2332,2333,2334,2335,2336,2338,2340,2343,2347,2348,2350,2351,2352,2353,2354,2355,2356,2360,2361

2958 atoms, 202 residues, atom bfactor range 0.1 to 0.74  

> color #1 #26a269 transparency 0

> color #1 #f9f06b transparency 0

> color byattribute bfactor
> #2/A:1315,1316,1317,1318,1319,1320,1321,1322,1323,1324,1325,1326,1327,1328,1329,1330,1331,1333,1334,1335,1336,1337,1338,1339,1340,1341,1342,1343,1344,1345,1346,1347,1348,1350,1351,1352,1353,1354,1355,1356,1357,1358,1359,1360,1361,1362,1363,1364,1378,1379,1380,1381,1382,1383,1384,1385,1386,1387,1388,1389,1390,1391,1392,1393,1394,1395,1396,1397,1398,1399,1400,1401,1402,1403,1404,1405,1406,1407,1408,1411,1412,1413,1414,1415,1416,1417,1418,1419,1420,1421,1422,1423,1424,1425,1427,1428,1429,1430,1431,1432,1433,1434,1435,1436,1437,1438,1439,1440,1441,1442,1443,1444,1445,1446,1447,1448,1449,1450,1451,1452,1459,1461,1462,1463,1464,1465,1466,1467,1473,1475,1479,1480,1481,1482,1483,1484,1485,1486,1489,1490,1492,1493,1494,1495,1496,1497,1498,1499,1500,1501,1502,1504,1505,1506,1507,1508,1509,1510,1511,1512,1513,1514,1515,1517,1518,1519,1521,1522,1523,1524,1530,1531,1533,1534,1535,1536,1537,1538,1539,1540,1541,1542,1543,1544,1545,1546,1547,1548,1549,1550,1551,1552,1553,1554,1555,1556,1557,1558,1559,1560,1561,1562,1563,1564,1565,1566,1567,1568,1570,1573,1574,1575,1576,1577,1578,1579,1580,1581,1582,1583,1584,1587,1592,1593,1626,1627,1628,1629,1630,1631,1632,1633,1634,1635,1636,1637,1638,1639,1640,1641,1642,1643,1644,1645,1646,1647,1648,1649,1659,1660,1661,1662,1663,1664,1665,1666,1667,1668,1671,1672,1673,1674,1675,1676,1677,1678,1679,1680,1681,1682,1687,1688,1691,1692,1693,1694,1695,1696,1697,1698,1699,1700,1701,1702,1703,1704,1706,1708

No atoms specified  

> color byattribute bfactor
> #1/A:1894,1895,1896,1897,1898,1899,1900,1901,1902,1903,1904,1905,1906,1907,1908,1909,1911,1912,1913,1914,1915,1916,1917,1918,1919,1921,1923,1924,1925,1926,1927,1928,1929,1930,1931,1932,1933,1934,1935,1936,1937,1938,1939,1940,1941,1942,1943,1944,1945,1946,1947,1948,1949,1950,1951,1952,1953,1954,1955,1956,1957,1958,1959,1960,1961,1962,1963,1964,1965,1966,1967,1968,1969,1970,1971,1972,1973,1974,1975,1976,1977,1978,1982,1983,1984,1986,1987,1988,1989,1990,1991,1992,1993,1994,1995,1996,1997,1998,1999,2000,2001,2002,2003,2004,2005,2006,2007,2008,2009,2010,2011,2012,2013,2014,2016,2017,2018,2019,2020,2021,2022,2023,2026,2027,2031,2032,2033,2034,2035,2036,2037,2038,2039,2040,2041,2042,2043,2044,2045,2046,2047,2048,2050,2051,2052,2053,2054,2055,2056,2057,2058,2059,2060,2061,2062,2063,2064,2065,2066,2067,2068,2072,2073,2074,2075,2076,2077,2078,2079,2081,2082,2083,2084,2085,2086,2087,2088,2089,2090,2091,2092,2093,2094,2095,2096,2097,2098,2099,2100,2101,2102,2103,2104,2105,2106,2107,2108,2109,2110,2111,2112,2113

3092 atoms, 202 residues, atom bfactor range 0.1 to 0.74  

> save
> /media/hhklab1/500GB/workspace/humanFAS_priynaka/humand_and_FAS_pocket/old/mFAS_simulation_analysis/alignment/KR/KR_stamp_align_chimerax.cxs

——— End of log from Wed Feb 21 03:34:45 2024 ———

opened ChimeraX session  

> color byattribute bfactor #1/A key true palette 0,green:0.5,white:1,red

> key green:0.0 white:0.5 red:1.0 showTool true

> ui mousemode right "color key"

3590 atoms, 235 residues, atom bfactor range 0 to 0.74  

> color byattribute bfactor #2/A key true palette 0,royalblue:0.5,white:1,red

> key royalblue:0.0 white:0.5 red:1.0 showTool true

4238 atoms, 290 residues, atom bfactor range 0 to 0.74  

> ui mousemode right "move label"

> lighting soft

> graphics silhouettes true

> select #2/A:2253, 2265, 2269

54 atoms, 52 bonds, 3 residues, 1 model selected  

> color sel black

> show sel atoms

> label sel text "{0.name} {0.number}{0.insertion_code}" height 6.5 offset
> 10,18,10

> label sel color black

> label size 80 bgColor white

> select clear

> select #1/A:2021, 2034, 1995

54 atoms, 52 bonds, 3 residues, 1 model selected  

> color sel cyan

> show sel atoms

> label sel text "{0.name} {0.number}{0.insertion_code}" height 6.5 offset
> 10,18,10

> label sel color cyan

> label size 80 bgColor white

> select clear

> save
> /media/hhklab1/500GB/workspace/humanFAS_priynaka/humand_and_FAS_pocket/old/mFAS_simulation_analysis/alignment/KR/KR_stamp_align_chimerax.cxs

——— End of log from Fri Feb 23 13:04:41 2024 ———

opened ChimeraX session  

> label delete

> save
> /media/hhklab1/500GB/workspace/humanFAS_priynaka/humand_and_FAS_pocket/old/mFAS_simulation_analysis/alignment/KR/KR_stamp_align_chimerax.cxs

——— End of log from Fri Mar 15 12:05:59 2024 ———

opened ChimeraX session  
An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.  
  
unsupported locale setting  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/updateloop.py", line 73, in draw_new_frame  
view.draw(check_for_changes = False)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 172, in draw  
draw_overlays(odrawings, r)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1577, in draw_overlays  
_draw_multiple(drawings, r, Drawing.OPAQUE_DRAW_PASS)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1539, in _draw_multiple  
d.draw(renderer, draw_pass)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/color_key/model.py", line 100, in draw  
self._update_graphics(renderer)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/color_key/model.py", line 455, in _update_graphics  
self._update_key_image()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/color_key/model.py", line 458, in _update_key_image  
rgba = self._key_image_rgba()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/color_key/model.py", line 483, in _key_image_rgba  
rect_positions = self._rect_positions(pixels[long_index])  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/color_key/model.py", line 758, in _rect_positions  
locale.setlocale(locale.LC_NUMERIC, local_numeric)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/locale.py", line 610, in setlocale  
return _setlocale(category, locale)  
locale.Error: unsupported locale setting  
  

> graphics restart

> color byattribute bfactor #1/A palette "0,blue:0.37, white:0.74,light gray"

3590 atoms, 235 residues, atom bfactor range 0 to 0.74  

> color byattribute bfactor #2/A palette "0,red:0.37, white:0.74,light gray"

4238 atoms, 290 residues, atom bfactor range 0 to 0.74  

> select #1/A:2021, 2034, 1995

54 atoms, 52 bonds, 3 residues, 1 model selected  

> color sel blue

> select #2/A:2253, 2265, 2269

54 atoms, 52 bonds, 3 residues, 1 model selected  

> color sel red

> select clear

> save
> /media/hhklab1/500GB/workspace/humanFAS_priynaka/humand_and_FAS_pocket/old/mFAS_simulation_analysis/alignment/KR/KR_stamp_align_chimerax.cxs

——— End of log from Mon Apr 22 15:36:21 2024 ———

opened ChimeraX session  
An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.  
  
unsupported locale setting  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/updateloop.py", line 73, in draw_new_frame  
view.draw(check_for_changes = False)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 172, in draw  
draw_overlays(odrawings, r)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1577, in draw_overlays  
_draw_multiple(drawings, r, Drawing.OPAQUE_DRAW_PASS)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1539, in _draw_multiple  
d.draw(renderer, draw_pass)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/color_key/model.py", line 100, in draw  
self._update_graphics(renderer)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/color_key/model.py", line 455, in _update_graphics  
self._update_key_image()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/color_key/model.py", line 458, in _update_key_image  
rgba = self._key_image_rgba()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/color_key/model.py", line 483, in _key_image_rgba  
rect_positions = self._rect_positions(pixels[long_index])  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/color_key/model.py", line 758, in _rect_positions  
locale.setlocale(locale.LC_NUMERIC, local_numeric)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/locale.py", line 610, in setlocale  
return _setlocale(category, locale)  
locale.Error: unsupported locale setting  
  

> graphics restart

> lighting soft

> color byattribute bfactor #2/A palette "0,red:0.37, white:0.74,black"

4238 atoms, 290 residues, atom bfactor range 0 to 0.74  

> color byattribute bfactor #2/A palette "0,red:0.37, white:0.74,black"

4238 atoms, 290 residues, atom bfactor range 0 to 0.74  

> color byattribute bfactor #1/A palette "0,blue:0.37, white:0.74,black"

3590 atoms, 235 residues, atom bfactor range 0 to 0.74  

> ui mousemode right "color key"

> key royalblue:0.0 white:0. red:1.0

> key royalblue:0.0 white:0 red:1.0

> key royalblue:0.0 white:00 red:1.0

> key #0000df:0.0 white:00 red:1.0

> key #0000df:0.0 white:00 black:1.0

> key #0000df:0.0 white:00 black:0

> key #0000df:0.0 white:00 black:0.

> key #0000df:0.0 white:00 black:0.7

> key #0000df:0.0 white:00 black:0.72

> key #0000df:0.0 white:0 black:0.72

> key #0000df:0.0 white:0/ black:0.72

> key #0000df:0.0 white:0 black:0.72

> key #0000df:0.0 white:0. black:0.72

> key #0000df:0.0 white:0.3 black:0.72

> key #0000df:0.0 white:0.37 black:0.72

> key #0000df:0.0 white:0.37 black:0.7

> key #0000df:0.0 white:0.37 black:0.74

> ui mousemode right translate

> ui mousemode right "color key"

> key fontSize 28

> key ticks true

> ui mousemode right translate

> ui mousemode right "color key"

> key bold true

> ui mousemode right translate

> save
> /media/hhklab1/500GB/workspace/humanFAS_priynaka/humand_and_FAS_pocket/old/mFAS_simulation_analysis/alignment/KR/KR_stamo_align.png
> width 800 height 800 supersample 3

> save
> /media/hhklab1/500GB/workspace/humanFAS_priynaka/humand_and_FAS_pocket/old/mFAS_simulation_analysis/alignment/KR/KR_stamo_align.tif
> width 800 height 800 supersample 3

> save
> /media/hhklab1/500GB/workspace/humanFAS_priynaka/humand_and_FAS_pocket/old/mFAS_simulation_analysis/alignment/KR/KR_stamp_align_chimerax.cxs

——— End of log from Tue Apr 23 14:53:14 2024 ———

opened ChimeraX session  
An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.  
  
unsupported locale setting  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/updateloop.py", line 73, in draw_new_frame  
view.draw(check_for_changes = False)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 172, in draw  
draw_overlays(odrawings, r)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1577, in draw_overlays  
_draw_multiple(drawings, r, Drawing.OPAQUE_DRAW_PASS)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1539, in _draw_multiple  
d.draw(renderer, draw_pass)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/color_key/model.py", line 100, in draw  
self._update_graphics(renderer)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/color_key/model.py", line 455, in _update_graphics  
self._update_key_image()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/color_key/model.py", line 458, in _update_key_image  
rgba = self._key_image_rgba()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/color_key/model.py", line 483, in _key_image_rgba  
rect_positions = self._rect_positions(pixels[long_index])  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/color_key/model.py", line 758, in _rect_positions  
locale.setlocale(locale.LC_NUMERIC, local_numeric)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/locale.py", line 610, in setlocale  
return _setlocale(category, locale)  
locale.Error: unsupported locale setting  
  




OpenGL version: 4.6 (Core Profile) Mesa 22.2.5-0ubuntu0.1~22.04.3
OpenGL renderer: RENOIR (renoir, LLVM 15.0.7, DRM 3.57, 6.8.0-51-generic)
OpenGL vendor: AMD

Python: 3.9.11
Locale: en_IN.ISO8859-1
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Micro-Star International Co., Ltd.
Model: MS-7C56
OS: Ubuntu 22.04 jammy
Architecture: 64bit ELF
Virtual Machine: none
CPU: 16 AMD Ryzen 7 5700G with Radeon Graphics
Cache Size: 512 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            27Gi       4.6Gi        18Gi       112Mi       4.3Gi        22Gi
	Swap:          2.0Gi       134Mi       1.9Gi

Graphics:
	30:00.0 VGA compatible controller [0300]: Advanced Micro Devices, Inc. [AMD/ATI] Cezanne [1002:1638] (rev c8)	
	Subsystem: Advanced Micro Devices, Inc. [AMD/ATI] Cezanne [1002:1636]	
	Kernel driver in use: amdgpu

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2022.5.18.1
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-ArtiaX: 0.3
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.18.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4rc202205290614
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-Cytoscape: 0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-DevelExtras: 0.4.1
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.4
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    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-NIHPresets: 1.1.9
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBImages: 1.1
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-Phenix: 0.3
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RMF: 0.11
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-TestManager: 0.3
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.1
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-XMAS: 1.1.2
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    distro: 1.6.0
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    MolecularDynamicsViewer: 1.4
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.0.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    Send2Trash: 1.8.0
    SEQCROW: 1.5.10
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 9 months ago

Component: Unassigned → Depiction
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Color key: cannot restore numeric locale

comment:2 by Eric Pettersen, 9 months ago

Resolution: → duplicate
Status: accepted → closed

Duplicate of #10105

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