Blast results problem

[antosuk@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 1.0 (2020-05-07)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.0rc202005070439 (2020-05-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  
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> toolshed show "Modeller Comparative"

> ui dockable false "Modeller Comparative"

> ui autostart true "Modeller Comparative"

> ui autostart false "Modeller Comparative"

No alignments chosen for modeling  

> open D:\install\Modeller10.0\bin\ssb\TdTBovine_SSB.B99990001.pdb format pdb

Chain information for TdTBovine_SSB.B99990001.pdb #1  
---  
Chain | Description  
A | No description available  
  

> select #1

5436 atoms, 5551 bonds, 1 model selected  

> close

No such database 'C'  
No such database 'C'  
No such database 'C'  
No such database 'C'  

> open "D:\ASP\MOD Fus\RaptorX_TdTBovine_EcSSB\613261.all_in_one\RRR.pdb"
> format pdb

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

> toolshed show "Blast Protein"

> blastprotein #1 database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 name
> bp1

Web Service: BlastProtein2 is a Python wrapper that calls blastp to search nr
or pdb for sequences similar to the given protein sequence  
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service  
Opal job id: appBlastProtein2Service1613543738368-1488103089  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appBlastProtein2Service1613543738368-1488103089  
stdout.txt = standard output  
stderr.txt = standard error  
BlastProtein finished.  

Fetching BLAST PDB info using URL:  
https://www.rcsb.org/pdb/rest/describePDB?structureId=d,f,p,4pgy,7dep,k,5xgt,7d8j,h,b,e,a,g,5yyu,c,i,m  
Failed HTTP Error 404: Not Found  
  

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\ui\gui.py", line 603, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\blastprotein\job.py", line 104, in on_finish  
self.tool.job_finished(self, p, self._params())  
File "C:\Program Files\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\blastprotein\tool.py", line 281, in job_finished  
self._show_results(job.atomspec, blast_results)  
File "C:\Program Files\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\blastprotein\tool.py", line 323, in _show_results  
self._add_pdbinfo(pdb_chains)  
File "C:\Program Files\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\blastprotein\tool.py", line 342, in _add_pdbinfo  
for k, v in data[chain_id].items():  
KeyError: 'A'  
  
KeyError: 'A'  
  
File "C:\Program Files\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\blastprotein\tool.py", line 342, in _add_pdbinfo  
for k, v in data[chain_id].items():  
  
See log for complete Python traceback.  
  

> toolshed show "Modeller Comparative"

No alignments chosen for modeling  

> Instutution of Bioorganic
> ChemistrysMDPLCTASSGPRKKRPRQVGASMASPPHDIKFQNLVLFILEKKMGTTRRNFLMELARRKGFRVENELSDSVTHIVAENNSGSEVLEWLQVQNIRASSQLELLDVSWLIESMGAGKPVEITGKHQLVVRTDYSATPNPGFQKTPPLAVKKISQYACQRKTTLNNYNHIFTDAFEILAENSEFKENEVSYVTFMRAASVLKSLPFTIISMKDTEGIPCLGDKVKCIIEEIIEDGESSEVKAVLNDERYQSFKLFTSVFGVGLKTSEKWFRMGFRSLSKIMSDKTLKFTKMQKAGFLYYEDLVSCVTRAEAEAVGVLVKEAVWAFLPDAFVTMTGGFRRGKKIGHDVDFLITSPGSAEDEEQLLPKVINLWEKKGLLLYYDLVESTFEKFKLPSRQVDTLDHFQKCFLILKLHHQRVDSSKSNQQEGKTWKAIRVDLVMCPYENRAFALLGWTGSRQFERDIRRYATHERKMMLDNHALYDKTKRVFLKAESEEEIFAHLGLDYIEPWERNAMASRGVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKATGEMKEQTEWHRVVLFGKLAEVASEYLRKGSQVYIEGQLRTRKWTDQSGQDRYTTEVVVNVGGTMQMLGGRQGGGAPAGGNIGGGQPQGGWGQPQQPQGGNQFSGGAQSRPQQSAPAAPSNEPPMDFDDDIPFMDPLCTASSGPRKKRPRQVGASMASPPHDIKFQNLVLFILEKKMGTTRRNFLMELARRKGFRVENELSDSVTHIVAENNSGSEVLEWLQVQNIRASSQLELLDVSWLIESMGAGKPVEITGKHQLVVRTDYSATPNPGFQKTPPLAVKKISQYACQRKTTLNNYNHIFTDAFEILAENSEFKENEVSYVTFMRAASVLKSLPFTIISMKDTEGIPCLGDKVKCIIEEIIEDGESSEVKAVLNDERYQSFKLFTSVFGVGLKTSEKWFRMGFRSLSKIMSDKTLKFTKMQKAGFLYYEDLVSCVTRAEAEAVGVLVKEAVWAFLPDAFVTMTGGFRRGKKIGHDVDFLITSPGSAEDEEQLLPKVINLWEKKGLLLYYDLVESTFEKFKLPSRQVDTLDHFQKCFLILKLHHQRVDSSKSNQQEGKTWKAIRVDLVMCPYENRAFALLGWTGSRQFERDIRRYATHERKMMLDNHALYDKTKRVFLKAESEEEIFAHLGLDYIEPWERNAMASRGVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKATGEMKEQTEWHRVVLFGKLAEVASEYLRKGSQVYIEGQLRTRKWTDQSGQDRYTTEVVVNVGGTMQMLGGRQGGGAPAGGNIGGGQPQGGWGQPQQPQGGNQFSGGAQSRPQQSAPAAPSNEPPMDFDDDIPFMDPLCTASSGPRKKRPRQVGASMASPPHDIKFQNLVLFILEKKMGTTRRNFLMELARRKGFRVENELSDSVTHIVAENNSGSEVLEWLQVQNIRASSQLELLDVSWLIESMGAGKPVEITGKHQLVVRTDYSATPNPGFQKTPPLAVKKISQYACQRKTTLNNYNHIFTDAFEILAENSEFKENEVSYVTFMRAASVLKSLPFTIISMKDTEGIPCLGDKVKCIIEEIIEDGESSEVKAVLNDERYQSFKLFTSVFGVGLKTSEKWFRMGFRSLSKIMSDKTLKFTKMQKAGFLYYEDLVSCVTRAEAEAVGVLVKEAVWAFLPDAFVTMTGGFRRGKKIGHDVDFLITSPGSAEDEEQLLPKVINLWEKKGLLLYYDLVESTFEKFKLPSRQVDTLDHFQKCFLILKLHHQRVDSSKSNQQEGKTWKAIRVDLVMCPYENRAFALLGWTGSRQFERDIRRYATHERKMMLDNHALYDKTKRVFLKAESEEEIFAHLGLDYIEPWERNAMASRGVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKATGEMKEQTEWHRVVLFGKLAEVASEYLRKGSQVYIEGQLRTRKWTDQSGQDRYTTEVVVNVGGTMQMLGGRQGGGAPAGGNIGGGQPQGGWGQPQQPQGGNQFSGGAQSRPQQSAPAAPSNEPPMDFDDDIPF

Unknown command: Instutution of Bioorganic
ChemistrysMDPLCTASSGPRKKRPRQVGASMASPPHDIKFQNLVLFILEKKMGTTRRNFLMELARRKGFRVENELSDSVTHIVAENNSGSEVLEWLQVQNIRASSQLELLDVSWLIESMGAGKPVEITGKHQLVVRTDYSATPNPGFQKTPPLAVKKISQYACQRKTTLNNYNHIFTDAFEILAENSEFKENEVSYVTFMRAASVLKSLPFTIISMKDTEGIPCLGDKVKCIIEEIIEDGESSEVKAVLNDERYQSFKLFTSVFGVGLKTSEKWFRMGFRSLSKIMSDKTLKFTKMQKAGFLYYEDLVSCVTRAEAEAVGVLVKEAVWAFLPDAFVTMTGGFRRGKKIGHDVDFLITSPGSAEDEEQLLPKVINLWEKKGLLLYYDLVESTFEKFKLPSRQVDTLDHFQKCFLILKLHHQRVDSSKSNQQEGKTWKAIRVDLVMCPYENRAFALLGWTGSRQFERDIRRYATHERKMMLDNHALYDKTKRVFLKAESEEEIFAHLGLDYIEPWERNAMASRGVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKATGEMKEQTEWHRVVLFGKLAEVASEYLRKGSQVYIEGQLRTRKWTDQSGQDRYTTEVVVNVGGTMQMLGGRQGGGAPAGGNIGGGQPQGGWGQPQQPQGGNQFSGGAQSRPQQSAPAAPSNEPPMDFDDDIPFMDPLCTASSGPRKKRPRQVGASMASPPHDIKFQNLVLFILEKKMGTTRRNFLMELARRKGFRVENELSDSVTHIVAENNSGSEVLEWLQVQNIRASSQLELLDVSWLIESMGAGKPVEITGKHQLVVRTDYSATPNPGFQKTPPLAVKKISQYACQRKTTLNNYNHIFTDAFEILAENSEFKENEVSYVTFMRAASVLKSLPFTIISMKDTEGIPCLGDKVKCIIEEIIEDGESSEVKAVLNDERYQSFKLFTSVFGVGLKTSEKWFRMGFRSLSKIMSDKTLKFTKMQKAGFLYYEDLVSCVTRAEAEAVGVLVKEAVWAFLPDAFVTMTGGFRRGKKIGHDVDFLITSPGSAEDEEQLLPKVINLWEKKGLLLYYDLVESTFEKFKLPSRQVDTLDHFQKCFLILKLHHQRVDSSKSNQQEGKTWKAIRVDLVMCPYENRAFALLGWTGSRQFERDIRRYATHERKMMLDNHALYDKTKRVFLKAESEEEIFAHLGLDYIEPWERNAMASRGVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKATGEMKEQTEWHRVVLFGKLAEVASEYLRKGSQVYIEGQLRTRKWTDQSGQDRYTTEVVVNVGGTMQMLGGRQGGGAPAGGNIGGGQPQGGWGQPQQPQGGNQFSGGAQSRPQQSAPAAPSNEPPMDFDDDIPFMDPLCTASSGPRKKRPRQVGASMASPPHDIKFQNLVLFILEKKMGTTRRNFLMELARRKGFRVENELSDSVTHIVAENNSGSEVLEWLQVQNIRASSQLELLDVSWLIESMGAGKPVEITGKHQLVVRTDYSATPNPGFQKTPPLAVKKISQYACQRKTTLNNYNHIFTDAFEILAENSEFKENEVSYVTFMRAASVLKSLPFTIISMKDTEGIPCLGDKVKCIIEEIIEDGESSEVKAVLNDERYQSFKLFTSVFGVGLKTSEKWFRMGFRSLSKIMSDKTLKFTKMQKAGFLYYEDLVSCVTRAEAEAVGVLVKEAVWAFLPDAFVTMTGGFRRGKKIGHDVDFLITSPGSAEDEEQLLPKVINLWEKKGLLLYYDLVESTFEKFKLPSRQVDTLDHFQKCFLILKLHHQRVDSSKSNQQEGKTWKAIRVDLVMCPYENRAFALLGWTGSRQFERDIRRYATHERKMMLDNHALYDKTKRVFLKAESEEEIFAHLGLDYIEPWERNAMASRGVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKATGEMKEQTEWHRVVLFGKLAEVASEYLRKGSQVYIEGQLRTRKWTDQSGQDRYTTEVVVNVGGTMQMLGGRQGGGAPAGGNIGGGQPQGGWGQPQQPQGGNQFSGGAQSRPQQSAPAAPSNEPPMDFDDDIPF  

> toolshed show "Blast Protein"

QObject::startTimer: Timers can only be used with threads started with QThread  

QObject::startTimer: Timers can only be used with threads started with QThread  

> blastprotein #1 database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 name
> bp2

Web Service: BlastProtein2 is a Python wrapper that calls blastp to search nr
or pdb for sequences similar to the given protein sequence  
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service  
Opal job id: appBlastProtein2Service16135439977691314939631  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appBlastProtein2Service16135439977691314939631  
stdout.txt = standard output  
stderr.txt = standard error  
BlastProtein finished.  

Fetching BLAST PDB info using URL:  
https://www.rcsb.org/pdb/rest/describePDB?structureId=d,f,p,4pgy,7dep,k,5xgt,7d8j,h,b,e,a,g,5yyu,c,i,m  
Failed HTTP Error 404: Not Found  
  

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\ui\gui.py", line 603, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\blastprotein\job.py", line 104, in on_finish  
self.tool.job_finished(self, p, self._params())  
File "C:\Program Files\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\blastprotein\tool.py", line 281, in job_finished  
self._show_results(job.atomspec, blast_results)  
File "C:\Program Files\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\blastprotein\tool.py", line 323, in _show_results  
self._add_pdbinfo(pdb_chains)  
File "C:\Program Files\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\blastprotein\tool.py", line 342, in _add_pdbinfo  
for k, v in data[chain_id].items():  
KeyError: 'A'  
  
KeyError: 'A'  
  
File "C:\Program Files\ChimeraX 1.0rc202005070439\bin\lib\site-
packages\chimerax\blastprotein\tool.py", line 342, in _add_pdbinfo  
for k, v in data[chain_id].items():  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 460.79
OpenGL renderer: GeForce GTX 1660 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: LENOVO
Model: 81SX
OS: Майкрософт Windows 10 Pro (Build 18363)
Memory: 17,096,134,656
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-9300H CPU @ 2.40GHz"

[Eric Pettersen]

Hello,

Thanks for reporting this problem. It is fixed in the daily build, so if you use that you should be okay.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab