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#15902 closed defect (duplicate)

glDrawBuffer: invalid operation

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

Description

The following bug report has been submitted:
Platform:        Linux-6.8.0-41-generic-x86_64-with-glibc2.39
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6XUX fromDatabase pdb format mmcif

Summary of feedback from opening 6XUX fetched from pdb  
---  
note | Fetching compressed mmCIF 6xux from http://files.rcsb.org/download/6xux.cif  
  
6xux title:  
Crystal structure of Megabody Mb-Nb207-cYgjK_NO [more info...]  
  
Chain information for 6xux #1  
---  
Chain | Description | UniProt  
A | Nanobody,Glucosidase YgjK,Glucosidase YgjK,Nanobody | YGJK_ECOLI 13-309 327-787  
  
Non-standard residues in 6xux #1  
---  
CA — calcium ion  
  
20 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> set bgColor white

> select /A:2-897

7001 atoms, 7190 bonds, 1 pseudobond, 879 residues, 2 models selected  

> select /A:2-897

7001 atoms, 7190 bonds, 1 pseudobond, 879 residues, 2 models selected  

> hide #!1 models

> show #!1 models

> select add #1

7652 atoms, 7190 bonds, 7 pseudobonds, 1530 residues, 3 models selected  

> select subtract #1

Nothing selected  

> open 3w7u fromDatabase pdb format mmcif

Summary of feedback from opening 3w7u fetched from pdb  
---  
notes | Fetching compressed mmCIF 3w7u from http://files.rcsb.org/download/3w7u.cif  
Fetching CCD GLA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/GLA/GLA.cif  
  
3w7u title:  
Escherichia coli K12 YgjK complexed with galactose [more info...]  
  
Chain information for 3w7u #2  
---  
Chain | Description | UniProt  
A B | Uncharacterized protein YgjK | YGJK_ECOLI 1-760  
  
Non-standard residues in 3w7u #2  
---  
CA — calcium ion  
GLA — alpha-D-galactopyranose  
  
3w7u mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
38 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> ui tool show Matchmaker

> matchmaker #!2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6xux, chain A (#1) with 3w7u, chain B (#2), sequence alignment
score = 2385.6  
RMSD between 456 pruned atom pairs is 0.440 angstroms; (across all 526 pairs:
12.662)  
  

> hide #2/b cartoons

> hide #2/a cartoons

> show #2/a cartoons

> show #2/b cartoons

> open 3d3i fromDatabase pdb format mmcif

Summary of feedback from opening 3d3i fetched from pdb  
---  
notes | Fetching compressed mmCIF 3d3i from http://files.rcsb.org/download/3d3i.cif  
Fetching CCD GOL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/GOL/GOL.cif  
  
3d3i title:  
Crystal structural of Escherichia coli K12 YgjK, a glucosidase belonging to
glycoside hydrolase family 63 [more info...]  
  
Chain information for 3d3i #3  
---  
Chain | Description | UniProt  
A B | Uncharacterized protein ygjK | YGJK_ECOLI 0-760  
  
Non-standard residues in 3d3i #3  
---  
CA — calcium ion  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
  
3d3i mmCIF Assemblies  
---  
1| author_defined_assembly  
2| software_defined_assembly  
3| software_defined_assembly  
  

> matchmaker #!3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6xux, chain A (#1) with 3d3i, chain A (#3), sequence alignment
score = 2369.2  
RMSD between 457 pruned atom pairs is 0.323 angstroms; (across all 525 pairs:
12.690)  
  

> open 3w7s fromDatabase pdb format mmcif

Summary of feedback from opening 3w7s fetched from pdb  
---  
notes | Fetching compressed mmCIF 3w7s from http://files.rcsb.org/download/3w7s.cif  
Fetching CCD GLC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/GLC/GLC.cif  
  
3w7s title:  
Escherichia coli K12 YgjK complexed with glucose [more info...]  
  
Chain information for 3w7s #4  
---  
Chain | Description | UniProt  
A B | Uncharacterized protein YgjK | YGJK_ECOLI 1-760  
  
Non-standard residues in 3w7s #4  
---  
CA — calcium ion  
GLC — alpha-D-glucopyranose  
  
3w7s mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
68 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> matchmaker #!4 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6xux, chain A (#1) with 3w7s, chain A (#4), sequence alignment
score = 2384.8  
RMSD between 458 pruned atom pairs is 0.353 angstroms; (across all 526 pairs:
12.720)  
  

> open 3w7t fromDatabase pdb format mmcif

Summary of feedback from opening 3w7t fetched from pdb  
---  
notes | Fetching compressed mmCIF 3w7t from http://files.rcsb.org/download/3w7t.cif  
Fetching CCD MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif  
  
3w7t title:  
Escherichia coli K12 YgjK complexed with mannose [more info...]  
  
Chain information for 3w7t #5  
---  
Chain | Description | UniProt  
A B | Uncharacterized protein YgjK | YGJK_ECOLI 1-760  
  
Non-standard residues in 3w7t #5  
---  
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)  
CA — calcium ion  
MG — magnesium ion  
  
3w7t mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
202 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> matchmaker #!5 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6xux, chain A (#1) with 3w7t, chain B (#5), sequence alignment
score = 2384.8  
RMSD between 458 pruned atom pairs is 0.377 angstroms; (across all 526 pairs:
12.669)  
  

> hide #!5 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> hide #!1 models

> show #!1 models

> show #!5 models

> show #!4 models

> show #!3 models

> show #!2 models

> open 3w7t fromDatabase pdb format mmcif

3w7t title:  
Escherichia coli K12 YgjK complexed with mannose [more info...]  
  
Chain information for 3w7t #6  
---  
Chain | Description | UniProt  
A B | Uncharacterized protein YgjK | YGJK_ECOLI 1-760  
  
Non-standard residues in 3w7t #6  
---  
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)  
CA — calcium ion  
MG — magnesium ion  
  
3w7t mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
202 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> matchmaker #!6 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6xux, chain A (#1) with 3w7t, chain B (#6), sequence alignment
score = 2384.8  
RMSD between 458 pruned atom pairs is 0.377 angstroms; (across all 526 pairs:
12.669)  
  

> hide #!5 models

> hide #!4 models

> hide #!3 models

> hide #!1 models

> hide #!2 models

> show #!1 models

> show #!5 models

> show #!4 models

> show #!3 models

> show #!2 models

> open 3w7x fromDatabase pdb format mmcif

Summary of feedback from opening 3w7x fetched from pdb  
---  
note | Fetching compressed mmCIF 3w7x from http://files.rcsb.org/download/3w7x.cif  
  
3w7x title:  
Crystal structure of E. coli YgjK D324N complexed with melibiose [more
info...]  
  
Chain information for 3w7x #7  
---  
Chain | Description | UniProt  
A B | Uncharacterized protein YgjK | YGJK_ECOLI 1-760  
  
Non-standard residues in 3w7x #7  
---  
CA — calcium ion  
GLA — alpha-D-galactopyranose (alpha-D-galactose; D-galactose; galactose; α
D-GALACTOSE)  
GLC — alpha-D-glucopyranose (alpha-D-glucose; D-glucose; glucose)  
  
3w7x mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
8 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> matchmaker #!7 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6xux, chain A (#1) with 3w7x, chain A (#7), sequence alignment
score = 2341.7  
RMSD between 456 pruned atom pairs is 0.506 angstroms; (across all 526 pairs:
12.732)  
  

> open 5gw7 fromDatabase pdb format mmcif

Summary of feedback from opening 5gw7 fetched from pdb  
---  
note | Fetching compressed mmCIF 5gw7 from http://files.rcsb.org/download/5gw7.cif  
  
5gw7 title:  
Crystal structure of the glycosynthase mutant E727A of Escherichia coli GH63
glycosidase in complex with glucose and lactose [more info...]  
  
Chain information for 5gw7 #8  
---  
Chain | Description | UniProt  
A B | Glucosidase YgjK | YGJK_ECOLI 1-760  
  
Non-standard residues in 5gw7 #8  
---  
BGC — beta-D-glucopyranose (beta-D-glucose; D-glucose; glucose)  
CA — calcium ion  
GAL — beta-D-galactopyranose (beta-D-galactose; D-galactose; galactose)  
GLC — alpha-D-glucopyranose (alpha-D-glucose; D-glucose; glucose)  
MG — magnesium ion  
  
5gw7 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
49 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> matchmaker #!8 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6xux, chain A (#1) with 5gw7, chain A (#8), sequence alignment
score = 2369.8  
RMSD between 433 pruned atom pairs is 0.812 angstroms; (across all 526 pairs:
12.998)  
  

> open 5CA3 fromDatabase pdb format mmcif

Summary of feedback from opening 5CA3 fetched from pdb  
---  
note | Fetching compressed mmCIF 5ca3 from http://files.rcsb.org/download/5ca3.cif  
  
5ca3 title:  
Crystal structure of the glycosynthase mutant D324N of Escherichia coli GH63
glycosidase in complex with glucose and lactose [more info...]  
  
Chain information for 5ca3 #9  
---  
Chain | Description | UniProt  
A B | Glucosidase YgjK | YGJK_ECOLI 1-760  
  
Non-standard residues in 5ca3 #9  
---  
BGC — beta-D-glucopyranose (beta-D-glucose; D-glucose; glucose)  
CA — calcium ion  
GAL — beta-D-galactopyranose (beta-D-galactose; D-galactose; galactose)  
GLC — alpha-D-glucopyranose (alpha-D-glucose; D-glucose; glucose)  
MG — magnesium ion  
  
5ca3 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  
33 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> matchmaker #!9 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6xux, chain A (#1) with 5ca3, chain B (#9), sequence alignment
score = 2369  
RMSD between 445 pruned atom pairs is 0.571 angstroms; (across all 530 pairs:
13.924)  
  

> hide atoms

> open 7pqq fromDatabase pdb format mmcif

Summary of feedback from opening 7pqq fetched from pdb  
---  
note | Fetching compressed mmCIF 7pqq from http://files.rcsb.org/download/7pqq.cif  
  
7pqq title:  
Structure of thermostabilised human NTCP in complex with Megabody 91 [more
info...]  
  
Chain information for 7pqq #10  
---  
Chain | Description | UniProt  
A | Sodium/bile acid cotransporter | NTCP_HUMAN 3-328  
B | Anti-RON nanobody,Megabody 91,Glucosidase YgjK | YGJK_ECOLI 13-187  
  

> matchmaker #!10 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6xux, chain A (#1) with 7pqq, chain B (#10), sequence alignment
score = 3378.9  
RMSD between 102 pruned atom pairs is 0.854 angstroms; (across all 119 pairs:
2.184)  
  

> hide #!9 models

> show #!9 models

> hide #!9 models

> hide #!8 models

> hide #!7 models

> show #!9 models

> show #!8 models

> show #!7 models

> lighting full

> lighting soft

[Repeated 1 time(s)]

> lighting simple

> lighting soft

> lighting simple

> open 8AFL fromDatabase pdb format mmcif

Summary of feedback from opening 8AFL fetched from pdb  
---  
note | Fetching compressed mmCIF 8afl from http://files.rcsb.org/download/8afl.cif  
  
8afl title:  
Cryo-EM structure of crescentin filaments (wildtype, C1 symmetry and small
box) [more info...]  
  
Chain information for 8afl #11  
---  
Chain | Description | UniProt  
A B E F | Crescentin | A0A8F8EC09_CAUVI 1-457  
C D | Crescentin-specific megabody MB13 |   
  

> matchmaker #!11 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6xux, chain A (#1) with 8afl, chain D (#11), sequence alignment
score = 3256.3  
RMSD between 93 pruned atom pairs is 1.080 angstroms; (across all 109 pairs:
1.805)  
  

> hide #!11 models

> close #11

> hide #!10 models

> show #!10 models

> close #10

> select add #9

13486 atoms, 12531 bonds, 27 pseudobonds, 2814 residues, 2 models selected  

> select add #8

26375 atoms, 25064 bonds, 48 pseudobonds, 5030 residues, 4 models selected  

> select add #7

38727 atoms, 37600 bonds, 60 pseudobonds, 6706 residues, 6 models selected  

> close #8

> close #9

> close #7

> close #6

> close #5

> close #4

> close #3

> close #2

> ui tool show "Model Loops"

No alignments chosen for modeling  
[Repeated 4 time(s)]

> ui tool show "Model Loops"

No alignments chosen for modeling  

> select add #1

7652 atoms, 7190 bonds, 7 pseudobonds, 1530 residues, 3 models selected  
No alignments chosen for modeling  

> show sel atoms

> hide sel atoms

> ui tool show "Model Loops"

No alignments chosen for modeling  
[Repeated 2 time(s)]

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> select /A:309

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:309-357

274 atoms, 280 bonds, 1 pseudobond, 32 residues, 2 models selected  

> select
> /A:3-7,10-11,14-18,35-36,80-84,90-95,97-98,145-146,151-152,155-156,233-234,277-278,285-286,343-347,365-366,382-384,391-404,407-408,412-418,421-427,431-441,444-453,457-465,468-472,475-476,492-496,499-503,508-509,513-514,520-525,530-534,537-544,548-557,620-621,631-632,767-769,782-786,789-796,804-810,817-823,828-831,839-844,849-854,863-870,886-887,891-894

1836 atoms, 1835 bonds, 223 residues, 1 model selected  

> select /A:309-357

274 atoms, 280 bonds, 1 pseudobond, 32 residues, 2 models selected  

> select add #1

7652 atoms, 7190 bonds, 7 pseudobonds, 1530 residues, 3 models selected  

> select subtract #1

Nothing selected  

> select /A:309

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:309-353

237 atoms, 241 bonds, 1 pseudobond, 28 residues, 2 models selected  

> select /A:309-353

237 atoms, 241 bonds, 1 pseudobond, 28 residues, 2 models selected  

> select add #1

7652 atoms, 7190 bonds, 7 pseudobonds, 1530 residues, 3 models selected  

> select subtract #1

Nothing selected  

> select /A:353

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:309-353

237 atoms, 241 bonds, 1 pseudobond, 28 residues, 2 models selected  

> select add #1

7652 atoms, 7190 bonds, 7 pseudobonds, 1530 residues, 3 models selected  

> select subtract #1

Nothing selected  

> select /A:331

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select /A:331

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select clear

[Repeated 1 time(s)]

> modeller refine 1/A:1:all-missing numModels 5 fast false adjacentFlexible 1
> protocol DOPE directory /home/yazdan/work

Webservices job id: IP5G6FCGCQRK0K97  
Modeller job (ID IP5G6FCGCQRK0K97) finished  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6xux, chain A (#1) with chain_A, chain A (#), sequence alignment
score = 4752  
RMSD between 879 pruned atom pairs is 0.045 angstroms; (across all 879 pairs:
0.045)  
  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6xux, chain A (#1) with chain_A, chain A (#), sequence alignment
score = 4752  
RMSD between 879 pruned atom pairs is 0.039 angstroms; (across all 879 pairs:
0.039)  
  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6xux, chain A (#1) with chain_A, chain A (#), sequence alignment
score = 4752  
RMSD between 879 pruned atom pairs is 0.025 angstroms; (across all 879 pairs:
0.025)  
  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6xux, chain A (#1) with chain_A, chain A (#), sequence alignment
score = 4752  
RMSD between 879 pruned atom pairs is 0.040 angstroms; (across all 879 pairs:
0.040)  
  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6xux, chain A (#1) with chain_A, chain A (#), sequence alignment
score = 4752  
RMSD between 879 pruned atom pairs is 0.022 angstroms; (across all 879 pairs:
0.022)  
  
Associated chain_A chain A to chain A with 0 mismatches  
[Repeated 4 time(s)] Chain information for chain_A  
---  
Chain | Description  
2.1/A 2.2/A 2.3/A 2.4/A 2.5/A | No description available  
  

> hide #2.5 models

> hide #2.4 models

> hide #2.3 models

> hide #2.2 models

> hide #2.1 models

> show #2.3 models

> hide #2.3 models

> show #2.3 models

> hide #2.3 models

> select clear

[Repeated 1 time(s)]

> select #1/A:897

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select clear

[Repeated 1 time(s)]

> select #1/A:2

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #1/A:2

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select clear

> show #2.3 models

> show #2.5 models

> show #2.4 models

> hide #2.4 models

> hide #2.5 models

> select #2.3/A:907

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #2.3/A:907

6 atoms, 5 bonds, 1 residue, 1 model selected  

> hide #!2 models

> select add #2

39145 atoms, 36865 bonds, 7790 residues, 6 models selected  

> select subtract #2

Nothing selected  

> hide #2.3 models

> show #2.3 models

> hide #2.3 models

> hide #!2 models

> open 5CA3 format mmcif fromDatabase pdb

5ca3 title:  
Crystal structure of the glycosynthase mutant D324N of Escherichia coli GH63
glycosidase in complex with glucose and lactose [more info...]  
  
Chain information for 5ca3 #3  
---  
Chain | Description | UniProt  
A B | Glucosidase YgjK | YGJK_ECOLI 1-760  
  
Non-standard residues in 5ca3 #3  
---  
BGC — beta-D-glucopyranose (beta-D-glucose; D-glucose; glucose)  
CA — calcium ion  
GAL — beta-D-galactopyranose (beta-D-galactose; D-galactose; galactose)  
GLC — alpha-D-glucopyranose (alpha-D-glucose; D-glucose; glucose)  
MG — magnesium ion  
  
5ca3 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  
33 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> matchmaker #!3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6xux, chain A (#1) with 5ca3, chain B (#3), sequence alignment
score = 2369  
RMSD between 445 pruned atom pairs is 0.571 angstroms; (across all 530 pairs:
13.924)  
  

> select #2.1/A:1,310-326,898-907 #2.2/A:1,310-326,898-907
> #2.3/A:1,310-326,898-907 #2.4/A:1,310-326,898-907 #2.5/A:1,310-326,898-907

885 atoms, 905 bonds, 140 residues, 5 models selected  

> hide #!3 models

> close #3

> show #2.1 models

> select add #2

39145 atoms, 36865 bonds, 7790 residues, 6 models selected  

> select subtract #2

Nothing selected  

> hide #2.1 models

> show #2.1 models

> show #2.2 models

> hide #2.1 models

> hide #2.2 models

> show #2.3 models

> show #2.4 models

> hide #2.3 models

> show #2.3 models

> show #2.5 models

> hide #2.4 models

> hide #2.3 models

> show #2.1 models

> hide #2.5 models

> show #2.2 models

> hide #2.1 models

> show #2.5 models

> hide #2.2 models

> show #2.4 models

> hide #2.5 models

> show #2.5 models

> hide #2.4 models

> select clear

Drag select of 4 residues  

> select clear

Drag select of 9 residues  

> select add #2.5/A:319

50 atoms, 3 bonds, 10 residues, 1 model selected  

> select add #2.5/A:316

54 atoms, 6 bonds, 11 residues, 1 model selected  

> select add #2.5/A:321

58 atoms, 9 bonds, 12 residues, 1 model selected  

> select add #2.5/A:320

64 atoms, 14 bonds, 13 residues, 1 model selected  
Drag select of 2 residues  
Drag select of 6 residues  

> select add #2.5/A:322

78 atoms, 17 bonds, 16 residues, 1 model selected  

> select add #2.5/A:323

82 atoms, 20 bonds, 17 residues, 1 model selected  

> select add #2.5/A:327

90 atoms, 27 bonds, 18 residues, 1 model selected  

> hide #!1 models

> hide #2.5 models

> show #2.5 models

> select add #2.5/A:321

94 atoms, 27 bonds, 19 residues, 1 model selected  

> set bgColor black

> set bgColor transparent

> select subtract #2.5/A:315

88 atoms, 27 bonds, 18 residues, 1 model selected  

> select add #2.5/A:315

94 atoms, 32 bonds, 19 residues, 1 model selected  

> save /home/yazdan/work/chimera/2.5.pdb models #2.5 selectedOnly true

> select add #2.5/A:1

103 atoms, 40 bonds, 20 residues, 1 model selected  

> save /home/yazdan/work/chimera/2.5.pdb models #2.5 selectedOnly true

> set bgColor white

> set bgColor #ffffff00

> open /home/yazdan/work/chimera/MB6xux-coot-0.pdb

Summary of feedback from opening /home/yazdan/work/chimera/MB6xux-coot-0.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
98 messages similar to the above omitted  
  
Chain information for MB6xux-coot-0.pdb #3  
---  
Chain | Description  
A | No description available  
  
20 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide #2.5 models

> show #!1 models

> select clear

[Repeated 6 time(s)]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.  
  
GLError(  
err = 1282,  
description = b'invalid operation',  
baseOperation = glDrawBuffer,  
cArguments = (GL_BACK,)  
)  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 84, in draw_new_frame  
view.draw(check_for_changes = False)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 188, in draw  
self._draw_scene(camera, drawings)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 273, in _draw_scene  
draw_highlight_outline(r, highlight_drawings, color = self._highlight_color,  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1625, in draw_highlight_outline  
r.outline.finish_rendering_outline(color=color, pixel_width=pixel_width)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1927, in finish_rendering_outline  
r.pop_framebuffer()  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 764, in pop_framebuffer  
fb.activate()  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 2313, in activate  
GL.glDrawBuffer(self._draw_buffer)  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1282,  
description = b'invalid operation',  
baseOperation = glDrawBuffer,  
cArguments = (GL_BACK,)  
)  
  




OpenGL version: 3.3.0 NVIDIA 550.107.02
OpenGL renderer: NVIDIA GeForce RTX 4070 SUPER/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: ASUSTeK COMPUTER INC.
Model: ROG STRIX G16CHR_G16CHR
OS: Ubuntu 24.04 Noble Numbat
Architecture: 64bit ELF
Virtual Machine: none
CPU: 28 Intel(R) Core(TM) i7-14700KF
Cache Size: 33792 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            31Gi        10Gi        14Gi       442Mi       7.8Gi        21Gi
	Swap:          8.0Gi          0B       8.0Gi

Graphics:
	0000:01:00.0 VGA compatible controller [0300]: NVIDIA Corporation AD104 [GeForce RTX 4070 SUPER] [10de:2783] (rev a1)	
	DeviceName: VGA	
	Subsystem: ASUSTeK Computer Inc. Device [1043:895c]

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2024.6.2
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    distro: 1.9.0
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11

Change History (2)

comment:1 by Eric Pettersen, 14 months ago

Component:	Unassigned → Graphics
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → glDrawBuffer: invalid operation

comment:2 by Tom Goddard, 14 months ago

Resolution:	→ duplicate
Status:	assigned → closed

Never figured this OpenGL but out, only happens on Linux. Possibly related to the OpenGL context being invalidated.

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