id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4255 Blast results problem antosuk@… Eric Pettersen "{{{ 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. How to cite UCSF ChimeraX Thank you for registering your copy of ChimeraX. By providing the information requested you will be helping us document the impact this software is having in the scientific community. The information you supplied will only be used for reporting summary usage statistics; no individual data will be released. antosuk@yandex.ru is subscribed to the ChimeraX announcements list > 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"" }}} " defect closed normal Sequence duplicate all ChimeraX