Opened 4 years ago

Closed 4 years ago

#5207 closed defect (fixed)

Matchmaker: 'NoneType' object has no attribute 'setChecked'

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

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19042
ChimeraX Version: 1.3.dev202109080319 (2021-09-08 03:19:35 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3.dev202109080319 (2021-09-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show

> ui tool show AlphaFold

> alphafold predict
> MVKARMTTADVAAEVKCLRRLIGMRLSNVYDITPKTYLFKLMNSSGITESGESEKVLLLMESGVRLHTTQYVRDKSTTPSGFTLKLRKHIRSKRLEDVRMLGYDRIILFQFGLGSNAHFVILELYAQGNILLTDSEYTVLTLLRSHRDDNKGLAIMSRHRYPVEACRVFERTDFTKLKDTLMMNAVDDKESSQVTPGSIDAQEPSVTPSDGVPVTDKSEEPSTTTGKKSASKNKQSSSNAKASNNAQSNKSTLKTLLGEALAYGPALAEHIILDAGLLPSTKVGKDPESSIDDHTIQSLVESISKFEDWLVDVMSGQRIPEGYILMQNKAAAKKNLTPLEGSSASQKIYDEYCPILLNQFKSREFNEFETFDAALDEFYSKIESQRVNQQQKSKEDSAAQRLNKIKLDQENRVHTLRKEVDHSIKMAELIEYNLEDVDAAIVAVRVSLANGMSWDALARMIKEEKKAGNPVAGLIDKLSFERNCITLLLSNNLDDMDEEEKTAPVEKVEVDLSLSAHANARRWYELKKKQESKQEKTVTAHEKAFKAAEKKIRLQLAQEKTVAAITHMRKVHWFEKFNWFISSENYLIISGRDAQQNELIVKRYMSKGDLYVHAELHGASSTIIKNHKPDNPIPPLTLNQAGSFTVCHSKAWDSKIVTSAWWVYPYQVSKTAPTGEYLTVGSFMIRGKKNFLPPHPLVMGFGILFRLDESSLASHLNERRVRGEDEEALPDVESQKLESNAELDGELDSDSETGKEKHDDESSLDNINVKKIDNPIPSNAPYVKDNADSSEQLSEIRTVVNSTTSTSKGQTSDRTVSSQLEDLLDKNLGLGPTKVLGRSSLLSSNSASVADDIDDLDTKKTSVRDKPYISKADRRKLKKGQNVGDSTSDSPNGEAAKKPVNSQQEKGKTNEKPANPKVSRGQKGKLKKIKEKYGEQDEEEREIRMALLASSGRASQKDKPSEDVDGATAAQSKPSTGEDDRSKICYKCKKSGHLSRDCPESTSEVDPADVNVGRAKDGMDRSSAPAGSSVTMDEDDIHELGDEEKEKLIDLDYLTGNPLPSDILLYAVPVCAPYNALQAYKYRVKITPGTAKKGKAAKTAMSLFLHTADATNREKELMKACTDPELVAAIVGNAKITAPGLTQLKQKQKQKGKKSAKEN-

Missing or invalid "sequence" argument: Sequences argument
"MVKARMTTADVAAEVKCLRRLIGMRLSNVYDITPKTYLFKLMNSSGITESGESEKVLLLMESGVRLHTTQYVRDKSTTPSGFTLKLRKHIRSKRLEDVRMLGYDRIILFQFGLGSNAHFVILELYAQGNILLTDSEYTVLTLLRSHRDDNKGLAIMSRHRYPVEACRVFERTDFTKLKDTLMMNAVDDKESSQVTPGSIDAQEPSVTPSDGVPVTDKSEEPSTTTGKKSASKNKQSSSNAKASNNAQSNKSTLKTLLGEALAYGPALAEHIILDAGLLPSTKVGKDPESSIDDHTIQSLVESISKFEDWLVDVMSGQRIPEGYILMQNKAAAKKNLTPLEGSSASQKIYDEYCPILLNQFKSREFNEFETFDAALDEFYSKIESQRVNQQQKSKEDSAAQRLNKIKLDQENRVHTLRKEVDHSIKMAELIEYNLEDVDAAIVAVRVSLANGMSWDALARMIKEEKKAGNPVAGLIDKLSFERNCITLLLSNNLDDMDEEEKTAPVEKVEVDLSLSAHANARRWYELKKKQESKQEKTVTAHEKAFKAAEKKIRLQLAQEKTVAAITHMRKVHWFEKFNWFISSENYLIISGRDAQQNELIVKRYMSKGDLYVHAELHGASSTIIKNHKPDNPIPPLTLNQAGSFTVCHSKAWDSKIVTSAWWVYPYQVSKTAPTGEYLTVGSFMIRGKKNFLPPHPLVMGFGILFRLDESSLASHLNERRVRGEDEEALPDVESQKLESNAELDGELDSDSETGKEKHDDESSLDNINVKKIDNPIPSNAPYVKDNADSSEQLSEIRTVVNSTTSTSKGQTSDRTVSSQLEDLLDKNLGLGPTKVLGRSSLLSSNSASVADDIDDLDTKKTSVRDKPYISKADRRKLKKGQNVGDSTSDSPNGEAAKKPVNSQQEKGKTNEKPANPKVSRGQKGKLKKIKEKYGEQDEEEREIRMALLASSGRASQKDKPSEDVDGATAAQSKPSTGEDDRSKICYKCKKSGHLSRDCPESTSEVDPADVNVGRAKDGMDRSSAPAGSSVTMDEDDIHELGDEEKEKLIDLDYLTGNPLPSDILLYAVPVCAPYNALQAYKYRVKITPGTAKKGKAAKTAMSLFLHTADATNREKELMKACTDPELVAAIVGNAKITAPGLTQLKQKQKQKGKKSAKEN-"
is not a chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold predict
> >M_zhu_sot4_proteinMVKARMTTADVAAEVKCLRRLIGMRLSNVYDITPKTYLFKLMNSSGITESGESEKVLLLMESGVRLHTTQYVRDKSTTPSGFTLKLRKHIRSKRLEDVRMLGYDRIILFQFGLGSNAHFVILELYAQGNILLTDSEYTVLTLLRSHRDDNKGLAIMSRHRYPVEACRVFERTDFTKLKDTLMMNAVDDKESSQVTPGSIDAQEPSVTPSDGVPVTDKSEEPSTTTGKKSASKNKQSSSNAKASNNAQSNKSTLKTLLGEALAYGPALAEHIILDAGLLPSTKVGKDPESSIDDHTIQSLVESISKFEDWLVDVMSGQRIPEGYILMQNKAAAKKNLTPLEGSSASQKIYDEYCPILLNQFKSREFNEFETFDAALDEFYSKIESQRVNQQQKSKEDSAAQRLNKIKLDQENRVHTLRKEVDHSIKMAELIEYNLEDVDAAIVAVRVSLANGMSWDALARMIKEEKKAGNPVAGLIDKLSFERNCITLLLSNNLDDMDEEEKTAPVEKVEVDLSLSAHANARRWYELKKKQESKQEKTVTAHEKAFKAAEKKIRLQLAQEKTVAAITHMRKVHWFEKFNWFISSENYLIISGRDAQQNELIVKRYMSKGDLYVHAELHGASSTIIKNHKPDNPIPPLTLNQAGSFTVCHSKAWDSKIVTSAWWVYPYQVSKTAPTGEYLTVGSFMIRGKKNFLPPHPLVMGFGILFRLDESSLASHLNERRVRGEDEEALPDVESQKLESNAELDGELDSDSETGKEKHDDESSLDNINVKKIDNPIPSNAPYVKDNADSSEQLSEIRTVVNSTTSTSKGQTSDRTVSSQLEDLLDKNLGLGPTKVLGRSSLLSSNSASVADDIDDLDTKKTSVRDKPYISKADRRKLKKGQNVGDSTSDSPNGEAAKKPVNSQQEKGKTNEKPANPKVSRGQKGKLKKIKEKYGEQDEEEREIRMALLASSGRASQKDKPSEDVDGATAAQSKPSTGEDDRSKICYKCKKSGHLSRDCPESTSEVDPADVNVGRAKDGMDRSSAPAGSSVTMDEDDIHELGDEEKEKLIDLDYLTGNPLPSDILLYAVPVCAPYNALQAYKYRVKITPGTAKKGKAAKTAMSLFLHTADATNREKELMKACTDPELVAAIVGNAKITAPGLTQLKQKQKQKGKKSAKEN-

Missing or invalid "sequence" argument: too many values to unpack (expected 2)  

> alphafold predict
> >MVKARMTTADVAAEVKCLRRLIGMRLSNVYDITPKTYLFKLMNSSGITESGESEKVLLLMESGVRLHTTQYVRDKSTTPSGFTLKLRKHIRSKRLEDVRMLGYDRIILFQFGLGSNAHFVILELYAQGNILLTDSEYTVLTLLRSHRDDNKGLAIMSRHRYPVEACRVFERTDFTKLKDTLMMNAVDDKESSQVTPGSIDAQEPSVTPSDGVPVTDKSEEPSTTTGKKSASKNKQSSSNAKASNNAQSNKSTLKTLLGEALAYGPALAEHIILDAGLLPSTKVGKDPESSIDDHTIQSLVESISKFEDWLVDVMSGQRIPEGYILMQNKAAAKKNLTPLEGSSASQKIYDEYCPILLNQFKSREFNEFETFDAALDEFYSKIESQRVNQQQKSKEDSAAQRLNKIKLDQENRVHTLRKEVDHSIKMAELIEYNLEDVDAAIVAVRVSLANGMSWDALARMIKEEKKAGNPVAGLIDKLSFERNCITLLLSNNLDDMDEEEKTAPVEKVEVDLSLSAHANARRWYELKKKQESKQEKTVTAHEKAFKAAEKKIRLQLAQEKTVAAITHMRKVHWFEKFNWFISSENYLIISGRDAQQNELIVKRYMSKGDLYVHAELHGASSTIIKNHKPDNPIPPLTLNQAGSFTVCHSKAWDSKIVTSAWWVYPYQVSKTAPTGEYLTVGSFMIRGKKNFLPPHPLVMGFGILFRLDESSLASHLNERRVRGEDEEALPDVESQKLESNAELDGELDSDSETGKEKHDDESSLDNINVKKIDNPIPSNAPYVKDNADSSEQLSEIRTVVNSTTSTSKGQTSDRTVSSQLEDLLDKNLGLGPTKVLGRSSLLSSNSASVADDIDDLDTKKTSVRDKPYISKADRRKLKKGQNVGDSTSDSPNGEAAKKPVNSQQEKGKTNEKPANPKVSRGQKGKLKKIKEKYGEQDEEEREIRMALLASSGRASQKDKPSEDVDGATAAQSKPSTGEDDRSKICYKCKKSGHLSRDCPESTSEVDPADVNVGRAKDGMDRSSAPAGSSVTMDEDDIHELGDEEKEKLIDLDYLTGNPLPSDILLYAVPVCAPYNALQAYKYRVKITPGTAKKGKAAKTAMSLFLHTADATNREKELMKACTDPELVAAIVGNAKITAPGLTQLKQKQKQKGKKSAKEN-

Missing or invalid "sequence" argument: Sequences argument
">MVKARMTTADVAAEVKCLRRLIGMRLSNVYDITPKTYLFKLMNSSGITESGESEKVLLLMESGVRLHTTQYVRDKSTTPSGFTLKLRKHIRSKRLEDVRMLGYDRIILFQFGLGSNAHFVILELYAQGNILLTDSEYTVLTLLRSHRDDNKGLAIMSRHRYPVEACRVFERTDFTKLKDTLMMNAVDDKESSQVTPGSIDAQEPSVTPSDGVPVTDKSEEPSTTTGKKSASKNKQSSSNAKASNNAQSNKSTLKTLLGEALAYGPALAEHIILDAGLLPSTKVGKDPESSIDDHTIQSLVESISKFEDWLVDVMSGQRIPEGYILMQNKAAAKKNLTPLEGSSASQKIYDEYCPILLNQFKSREFNEFETFDAALDEFYSKIESQRVNQQQKSKEDSAAQRLNKIKLDQENRVHTLRKEVDHSIKMAELIEYNLEDVDAAIVAVRVSLANGMSWDALARMIKEEKKAGNPVAGLIDKLSFERNCITLLLSNNLDDMDEEEKTAPVEKVEVDLSLSAHANARRWYELKKKQESKQEKTVTAHEKAFKAAEKKIRLQLAQEKTVAAITHMRKVHWFEKFNWFISSENYLIISGRDAQQNELIVKRYMSKGDLYVHAELHGASSTIIKNHKPDNPIPPLTLNQAGSFTVCHSKAWDSKIVTSAWWVYPYQVSKTAPTGEYLTVGSFMIRGKKNFLPPHPLVMGFGILFRLDESSLASHLNERRVRGEDEEALPDVESQKLESNAELDGELDSDSETGKEKHDDESSLDNINVKKIDNPIPSNAPYVKDNADSSEQLSEIRTVVNSTTSTSKGQTSDRTVSSQLEDLLDKNLGLGPTKVLGRSSLLSSNSASVADDIDDLDTKKTSVRDKPYISKADRRKLKKGQNVGDSTSDSPNGEAAKKPVNSQQEKGKTNEKPANPKVSRGQKGKLKKIKEKYGEQDEEEREIRMALLASSGRASQKDKPSEDVDGATAAQSKPSTGEDDRSKICYKCKKSGHLSRDCPESTSEVDPADVNVGRAKDGMDRSSAPAGSSVTMDEDDIHELGDEEKEKLIDLDYLTGNPLPSDILLYAVPVCAPYNALQAYKYRVKITPGTAKKGKAAKTAMSLFLHTADATNREKELMKACTDPELVAAIVGNAKITAPGLTQLKQKQKQKGKKSAKEN-"
is not a chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold predict
> >MVKARMTTADVAAEVKCLRRLIGMRLSNVYDITPKTYLFKLMNSSGITESGESEKVLLLMESGVRLHTTQYVRDKSTTPSGFTLKLRKHIRSKRLEDVRMLGYDRIILFQFGLGSNAHFVILELYAQGNILLTDSEYTVLTLLRSHRDDNKGLAIMSRHRYPVEACRVFERTDFTKLKDTLMMNAVDDKESSQVTPGSIDAQEPSVTPSDGVPVTDKSEEPSTTTGKKSASKNKQSSSNAKASNNAQSNKSTLKTLLGEALAYGPALAEHIILDAGLLPSTKVGKDPESSIDDHTIQSLVESISKFEDWLVDVMSGQRIPEGYILMQNKAAAKKNLTPLEGSSASQKIYDEYCPILLNQFKSREFNEFETFDAALDEFYSKIESQRVNQQQKSKEDSAAQRLNKIKLDQENRVHTLRKEVDHSIKMAELIEYNLEDVDAAIVAVRVSLANGMSWDALARMIKEEKKAGNPVAGLIDKLSFERNCITLLLSNNLDDMDEEEKTAPVEKVEVDLSLSAHANARRWYELKKKQESKQEKTVTAHEKAFKAAEKKIRLQLAQEKTVAAITHMRKVHWFEKFNWFISSENYLIISGRDAQQNELIVKRYMSKGDLYVHAELHGASSTIIKNHKPDNPIPPLTLNQAGSFTVCHSKAWDSKIVTSAWWVYPYQVSKTAPTGEYLTVGSFMIRGKKNFLPPHPLVMGFGILFRLDESSLASHLNERRVRGEDEEALPDVESQKLESNAELDGELDSDSETGKEKHDDESSLDNINVKKIDNPIPSNAPYVKDNADSSEQLSEIRTVVNSTTSTSKGQTSDRTVSSQLEDLLDKNLGLGPTKVLGRSSLLSSNSASVADDIDDLDTKKTSVRDKPYISKADRRKLKKGQNVGDSTSDSPNGEAAKKPVNSQQEKGKTNEKPANPKVSRGQKGKLKKIKEKYGEQDEEEREIRMALLASSGRASQKDKPSEDVDGATAAQSKPSTGEDDRSKICYKCKKSGHLSRDCPESTSEVDPADVNVGRAKDGMDRSSAPAGSSVTMDEDDIHELGDEEKEKLIDLDYLTGNPLPSDILLYAVPVCAPYNALQAYKYRVKITPGTAKKGKAAKTAMSLFLHTADATNREKELMKACTDPELVAAIVGNAKITAPGLTQLKQKQKQKGKKSAKEN

Missing or invalid "sequence" argument: Sequences argument
">MVKARMTTADVAAEVKCLRRLIGMRLSNVYDITPKTYLFKLMNSSGITESGESEKVLLLMESGVRLHTTQYVRDKSTTPSGFTLKLRKHIRSKRLEDVRMLGYDRIILFQFGLGSNAHFVILELYAQGNILLTDSEYTVLTLLRSHRDDNKGLAIMSRHRYPVEACRVFERTDFTKLKDTLMMNAVDDKESSQVTPGSIDAQEPSVTPSDGVPVTDKSEEPSTTTGKKSASKNKQSSSNAKASNNAQSNKSTLKTLLGEALAYGPALAEHIILDAGLLPSTKVGKDPESSIDDHTIQSLVESISKFEDWLVDVMSGQRIPEGYILMQNKAAAKKNLTPLEGSSASQKIYDEYCPILLNQFKSREFNEFETFDAALDEFYSKIESQRVNQQQKSKEDSAAQRLNKIKLDQENRVHTLRKEVDHSIKMAELIEYNLEDVDAAIVAVRVSLANGMSWDALARMIKEEKKAGNPVAGLIDKLSFERNCITLLLSNNLDDMDEEEKTAPVEKVEVDLSLSAHANARRWYELKKKQESKQEKTVTAHEKAFKAAEKKIRLQLAQEKTVAAITHMRKVHWFEKFNWFISSENYLIISGRDAQQNELIVKRYMSKGDLYVHAELHGASSTIIKNHKPDNPIPPLTLNQAGSFTVCHSKAWDSKIVTSAWWVYPYQVSKTAPTGEYLTVGSFMIRGKKNFLPPHPLVMGFGILFRLDESSLASHLNERRVRGEDEEALPDVESQKLESNAELDGELDSDSETGKEKHDDESSLDNINVKKIDNPIPSNAPYVKDNADSSEQLSEIRTVVNSTTSTSKGQTSDRTVSSQLEDLLDKNLGLGPTKVLGRSSLLSSNSASVADDIDDLDTKKTSVRDKPYISKADRRKLKKGQNVGDSTSDSPNGEAAKKPVNSQQEKGKTNEKPANPKVSRGQKGKLKKIKEKYGEQDEEEREIRMALLASSGRASQKDKPSEDVDGATAAQSKPSTGEDDRSKICYKCKKSGHLSRDCPESTSEVDPADVNVGRAKDGMDRSSAPAGSSVTMDEDDIHELGDEEKEKLIDLDYLTGNPLPSDILLYAVPVCAPYNALQAYKYRVKITPGTAKKGKAAKTAMSLFLHTADATNREKELMKACTDPELVAAIVGNAKITAPGLTQLKQKQKQKGKKSAKEN"
is not a chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold predict
> >128MMVKARMTTADVAAEVKCLRRLIGMRLSNVYDITPKTYLFKLMNSSGITESGESEKVLLLMESGVRLHTTQYVRDKSTTPSGFTLKLRKHIRSKRLEDVRMLGYDRIILFQFGLGSNAHFVILELYAQGNILLTDSEYTVLTLLRSHRDDNKGLAIMSRHRYPVEACRVFERTDFTKLKDTLMMNAVDDKESSQVTPGSIDAQEPSVTPSDGVPVTDKSEEPSTTTGKKSASKNKQSSSNAKASNNAQSNKSTLKTLLGEALAYGPALAEHIILDAGLLPSTKVGKDPESSIDDHTIQSLVESISKFEDWLVDVMSGQRIPEGYILMQNKAAAKKNLTPLEGSSASQKIYDEYCPILLNQFKSREFNEFETFDAALDEFYSKIESQRVNQQQKSKEDSAAQRLNKIKLDQENRVHTLRKEVDHSIKMAELIEYNLEDVDAAIVAVRVSLANGMSWDALARMIKEEKKAGNPVAGLIDKLSFERNCITLLLSNNLDDMDEEEKTAPVEKVEVDLSLSAHANARRWYELKKKQESKQEKTVTAHEKAFKAAEKKIRLQLAQEKTVAAITHMRKVHWFEKFNWFISSENYLIISGRDAQQNELIVKRYMSKGDLYVHAELHGASSTIIKNHKPDNPIPPLTLNQAGSFTVCHSKAWDSKIVTSAWWVYPYQVSKTAPTGEYLTVGSFMIRGKKNFLPPHPLVMGFGILFRLDESSLASHLNERRVRGEDEEALPDVESQKLESNAELDGELDSDSETGKEKHDDESSLDNINVKKIDNPIPSNAPYVKDNADSSEQLSEIRTVVNSTTSTSKGQTSDRTVSSQLEDLLDKNLGLGPTKVLGRSSLLSSNSASVADDIDDLDTKKTSVRDKPYISKADRRKLKKGQNVGDSTSDSPNGEAAKKPVNSQQEKGKTNEKPANPKVSRGQKGKLKKIKEKYGEQDEEEREIRMALLASSGRASQKDKPSEDVDGATAAQSKPSTGEDDRSKICYKCKKSGHLSRDCPESTSEVDPADVNVGRAKDGMDRSSAPAGSSVTMDEDDIHELGDEEKEKLIDLDYLTGNPLPSDILLYAVPVCAPYNALQAYKYRVKITPGTAKKGKAAKTAMSLFLHTADATNREKELMKACTDPELVAAIVGNAKITAPGLTQLKQKQKQKGKKSAKEN

Missing or invalid "sequence" argument: Sequences argument
">128MMVKARMTTADVAAEVKCLRRLIGMRLSNVYDITPKTYLFKLMNSSGITESGESEKVLLLMESGVRLHTTQYVRDKSTTPSGFTLKLRKHIRSKRLEDVRMLGYDRIILFQFGLGSNAHFVILELYAQGNILLTDSEYTVLTLLRSHRDDNKGLAIMSRHRYPVEACRVFERTDFTKLKDTLMMNAVDDKESSQVTPGSIDAQEPSVTPSDGVPVTDKSEEPSTTTGKKSASKNKQSSSNAKASNNAQSNKSTLKTLLGEALAYGPALAEHIILDAGLLPSTKVGKDPESSIDDHTIQSLVESISKFEDWLVDVMSGQRIPEGYILMQNKAAAKKNLTPLEGSSASQKIYDEYCPILLNQFKSREFNEFETFDAALDEFYSKIESQRVNQQQKSKEDSAAQRLNKIKLDQENRVHTLRKEVDHSIKMAELIEYNLEDVDAAIVAVRVSLANGMSWDALARMIKEEKKAGNPVAGLIDKLSFERNCITLLLSNNLDDMDEEEKTAPVEKVEVDLSLSAHANARRWYELKKKQESKQEKTVTAHEKAFKAAEKKIRLQLAQEKTVAAITHMRKVHWFEKFNWFISSENYLIISGRDAQQNELIVKRYMSKGDLYVHAELHGASSTIIKNHKPDNPIPPLTLNQAGSFTVCHSKAWDSKIVTSAWWVYPYQVSKTAPTGEYLTVGSFMIRGKKNFLPPHPLVMGFGILFRLDESSLASHLNERRVRGEDEEALPDVESQKLESNAELDGELDSDSETGKEKHDDESSLDNINVKKIDNPIPSNAPYVKDNADSSEQLSEIRTVVNSTTSTSKGQTSDRTVSSQLEDLLDKNLGLGPTKVLGRSSLLSSNSASVADDIDDLDTKKTSVRDKPYISKADRRKLKKGQNVGDSTSDSPNGEAAKKPVNSQQEKGKTNEKPANPKVSRGQKGKLKKIKEKYGEQDEEEREIRMALLASSGRASQKDKPSEDVDGATAAQSKPSTGEDDRSKICYKCKKSGHLSRDCPESTSEVDPADVNVGRAKDGMDRSSAPAGSSVTMDEDDIHELGDEEKEKLIDLDYLTGNPLPSDILLYAVPVCAPYNALQAYKYRVKITPGTAKKGKAAKTAMSLFLHTADATNREKELMKACTDPELVAAIVGNAKITAPGLTQLKQKQKQKGKKSAKEN"
is not a chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold predict
> MVKARMTTADVAAEVKCLRRLIGMRLSNVYDITPKTYLFKLMNSSGITESGESEKVLLLMESGVRLHTTQYVRDKSTTPSGFTLKLRKHIRSKRLEDVRMLGYDRIILFQFGLGSNAHFVILELYAQGNILLTDSEYTVLTLLRSHRDDNKGLAIMSRHRYPVEACRVFERTDFTKLKDTLMMNAVDDKESSQVTPGSIDAQEPSVTPSDGVPVTDKSEEPSTTTGKKSASKNKQSSSNAKASNNAQSNKSTLKTLLGEALAYGPALAEHIILDAGLLPSTKVGKDPESSIDDHTIQSLVESISKFEDWLVDVMSGQRIPEGYILMQNKAAAKKNLTPLEGSSASQKIYDEYCPILLNQFKSREFNEFETFDAALDEFYSKIESQRVNQQQKSKEDSAAQRLNKIKLDQENRVHTLRKEVDHSIKMAELIEYNLEDVDAAIVAVRVSLANGMSWDALARMIKEEKKAGNPVAGLIDKLSFERNCITLLLSNNLDDMDEEEKTAPVEKVEVDLSLSAHANARRWYELKKKQESKQEKTVTAHEKAFKAAEKKIRLQLAQEKTVAAITHMRKVHWFEKFNWFISSENYLIISGRDAQQNELIVKRYMSKGDLYVHAELHGASSTIIKNHKPDNPIPPLTLNQAGSFTVCHSKAWDSKIVTSAWWVYPYQVSKTAPTGEYLTVGSFMIRGKKNFLPPHPLVMGFGILFRLDESSLASHLNERRVRGEDEEALPDVESQKLESNAELDGELDSDSETGKEKHDDESSLDNINVKKIDNPIPSNAPYVKDNADSSEQLSEIRTVVNSTTSTSKGQTSDRTVSSQLEDLLDKNLGLGPTKVLGRSSLLSSNSASVADDIDDLDTKKTSVRDKPYISKADRRKLKKGQNVGDSTSDSPNGEAAKKPVNSQQEKGKTNEKPANPKVSRGQKGKLKKIKEKYGEQDEEEREIRMALLASSGRASQKDKPSEDVDGATAAQSKPSTGEDDRSKICYKCKKSGHLSRDCPESTSEVDPADVNVGRAKDGMDRSSAPAGSSVTMDEDDIHELGDEEKEKLIDLDYLTGNPLPSDILLYAVPVCAPYNALQAYKYRVKITPGTAKKGKAAKTAMSLFLHTADATNREKELMKACTDPELVAAIVGNAKITAPGLTQLKQKQKQKGKKSAKEN

> alphafold search
> MVKARMTTADVAAEVKCLRRLIGMRLSNVYDITPKTYLFKLMNSSGITESGESEKVLLLMESGVRLHTTQYVRDKSTTPSGFTLKLRKHIRSKRLEDVRMLGYDRIILFQFGLGSNAHFVILELYAQGNILLTDSEYTVLTLLRSHRDDNKGLAIMSRHRYPVEACRVFERTDFTKLKDTLMMNAVDDKESSQVTPGSIDAQEPSVTPSDGVPVTDKSEEPSTTTGKKSASKNKQSSSNAKASNNAQSNKSTLKTLLGEALAYGPALAEHIILDAGLLPSTKVGKDPESSIDDHTIQSLVESISKFEDWLVDVMSGQRIPEGYILMQNKAAAKKNLTPLEGSSASQKIYDEYCPILLNQFKSREFNEFETFDAALDEFYSKIESQRVNQQQKSKEDSAAQRLNKIKLDQENRVHTLRKEVDHSIKMAELIEYNLEDVDAAIVAVRVSLANGMSWDALARMIKEEKKAGNPVAGLIDKLSFERNCITLLLSNNLDDMDEEEKTAPVEKVEVDLSLSAHANARRWYELKKKQESKQEKTVTAHEKAFKAAEKKIRLQLAQEKTVAAITHMRKVHWFEKFNWFISSENYLIISGRDAQQNELIVKRYMSKGDLYVHAELHGASSTIIKNHKPDNPIPPLTLNQAGSFTVCHSKAWDSKIVTSAWWVYPYQVSKTAPTGEYLTVGSFMIRGKKNFLPPHPLVMGFGILFRLDESSLASHLNERRVRGEDEEALPDVESQKLESNAELDGELDSDSETGKEKHDDESSLDNINVKKIDNPIPSNAPYVKDNADSSEQLSEIRTVVNSTTSTSKGQTSDRTVSSQLEDLLDKNLGLGPTKVLGRSSLLSSNSASVADDIDDLDTKKTSVRDKPYISKADRRKLKKGQNVGDSTSDSPNGEAAKKPVNSQQEKGKTNEKPANPKVSRGQKGKLKKIKEKYGEQDEEEREIRMALLASSGRASQKDKPSEDVDGATAAQSKPSTGEDDRSKICYKCKKSGHLSRDCPESTSEVDPADVNVGRAKDGMDRSSAPAGSSVTMDEDDIHELGDEEKEKLIDLDYLTGNPLPSDILLYAVPVCAPYNALQAYKYRVKITPGTAKKGKAAKTAMSLFLHTADATNREKELMKACTDPELVAAIVGNAKITAPGLTQLKQKQKQKGKKSAKEN

ChimeraX REST job id: job_hxs08pup  

> alphafold search
> MVKARMTTADVAAEVKCLRRLIGMRLSNVYDITPKTYLFKLMNSSGITESGESEKVLLLMESGVRLHTTQYVRDKSTTPSGFTLKLRKHIRSKRLEDVRMLGYDRIILFQFGLGSNAHFVILELYAQGNILLTDSEYTVLTLLRSHRDDNKGLAIMSRHRYPVEACRVFERTDFTKLKDTLMMNAVDDKESSQVTPGSIDAQEPSVTPSDGVPVTDKSEEPSTTTGKKSASKNKQSSSNAKASNNAQSNKSTLKTLLGEALAYGPALAEHIILDAGLLPSTKVGKDPESSIDDHTIQSLVESISKFEDWLVDVMSGQRIPEGYILMQNKAAAKKNLTPLEGSSASQKIYDEYCPILLNQFKSREFNEFETFDAALDEFYSKIESQRVNQQQKSKEDSAAQRLNKIKLDQENRVHTLRKEVDHSIKMAELIEYNLEDVDAAIVAVRVSLANGMSWDALARMIKEEKKAGNPVAGLIDKLSFERNCITLLLSNNLDDMDEEEKTAPVEKVEVDLSLSAHANARRWYELKKKQESKQEKTVTAHEKAFKAAEKKIRLQLAQEKTVAAITHMRKVHWFEKFNWFISSENYLIISGRDAQQNELIVKRYMSKGDLYVHAELHGASSTIIKNHKPDNPIPPLTLNQAGSFTVCHSKAWDSKIVTSAWWVYPYQVSKTAPTGEYLTVGSFMIRGKKNFLPPHPLVMGFGILFRLDESSLASHLNERRVRGEDEEALPDVESQKLESNAELDGELDSDSETGKEKHDDESSLDNINVKKIDNPIPSNAPYVKDNADSSEQLSEIRTVVNSTTSTSKGQTSDRTVSSQLEDLLDKNLGLGPTKVLGRSSLLSSNSASVADDIDDLDTKKTSVRDKPYISKADRRKLKKGQNVGDSTSDSPNGEAAKKPVNSQQEKGKTNEKPANPKVSRGQKGKLKKIKEKYGEQDEEEREIRMALLASSGRASQKDKPSEDVDGATAAQSKPSTGEDDRSKICYKCKKSGHLSRDCPESTSEVDPADVNVGRAKDGMDRSSAPAGSSVTMDEDDIHELGDEEKEKLIDLDYLTGNPLPSDILLYAVPVCAPYNALQAYKYRVKITPGTAKKGKAAKTAMSLFLHTADATNREKELMKACTDPELVAAIVGNAKITAPGLTQLKQKQKQKGKKSAKEN

ChimeraX REST job id: job_l4xzohow  

> alphafold search
> MVKARMTTADVAAEVKCLRRLIGMRLSNVYDITPKTYLFKLMNSSGITESGESEKVLLLMESGVRLHTTQYVRDKSTTPSGFTLKLRKHIRSKRLEDVRMLGYDRIILFQFGLGSNAHFVILELYAQGNILLTDSEYTVLTLLRSHRDDNKGLAIMSRHRYPVEACRVFERTDFTKLKDTLMMNAVDDKESSQVTPGSIDAQEPSVTPSDGVPVTDKSEEPSTTTGKKSASKNKQSSSNAKASNNAQSNKSTLKTLLGEALAYGPALAEHIILDAGLLPSTKVGKDPESSIDDHTIQSLVESISKFEDWLVDVMSGQRIPEGYILMQNKAAAKKNLTPLEGSSASQKIYDEYCPILLNQFKSREFNEFETFDAALDEFYSKIESQRVNQQQKSKEDSAAQRLNKIKLDQENRVHTLRKEVDHSIKMAELIEYNLEDVDAAIVAVRVSLANGMSWDALARMIKEEKKAGNPVAGLIDKLSFERNCITLLLSNNLDDMDEEEKTAPVEKVEVDLSLSAHANARRWYELKKKQESKQEKTVTAHEKAFKAAEKKIRLQLAQEKTVAAITHMRKVHWFEKFNWFISSENYLIISGRDAQQNELIVKRYMSKGDLYVHAELHGASSTIIKNHKPDNPIPPLTLNQAGSFTVCHSKAWDSKIVTSAWWVYPYQVSKTAPTGEYLTVGSFMIRGKKNFLPPHPLVMGFGILFRLDESSLASHLNERRVRGEDEEALPDVESQKLESNAELDGELDSDSETGKEKHDDESSLDNINVKKIDNPIPSNAPYVKDNADSSEQLSEIRTVVNSTTSTSKGQTSDRTVSSQLEDLLDKNLGLGPTKVLGRSSLLSSNSASVADDIDDLDTKKTSVRDKPYISKADRRKLKKGQNVGDSTSDSPNGEAAKKPVNSQQEKGKTNEKPANPKVSRGQKGKLKKIKEKYGEQDEEEREIRMALLASSGRASQKDKPSEDVDGATAAQSKPSTGEDDRSKICYKCKKSGHLSRDCPESTSEVDPADVNVGRAKDGMDRSSAPAGSSVTMDEDDIHELGDEEKEKLIDLDYLTGNPLPSDILLYAVPVCAPYNALQAYKYRVKITPGTAKKGKAAKTAMSLFLHTADATNREKELMKACTDPELVAAIVGNAKITAPGLTQLKQKQKQKGKKSAKEN

[Repeated 1 time(s)]ChimeraX REST job id: job_go972u2g  
ChimeraX REST job id: job_ivfq_c1s  
BlastProtein finished.  
Parsing BLAST results.  
BlastProtein finished.  
Parsing BLAST results.  
BlastProtein finished.  
Parsing BLAST results.  
BlastProtein finished.  
Parsing BLAST results.  

> alphafold fetch Q2QNI2_ORYSJ

Fetching compressed AlphaFold Q2QNI2 from
https://alphafold.ebi.ac.uk/files/AF-Q2QNI2-F1-model_v1.cif  
Chain information for AlphaFold Q2QNI2_ORYSJ #1  
---  
Chain | Description | UniProt  
A | Os12g0564600 protein | Q2QNI2_ORYSJ  
  
Sequence Similarity  
---  
AlphaFold Model| Query Sequence| Identity %| Coverage %  
Q2QNI2_ORYSJ | MVKAR...SAKEN | 99.6 | 100.0  

> select clear

> show atoms

[Repeated 1 time(s)]

> hide atoms

Drag select of 35 residues  
Drag select of 16 residues  

> select /A:552

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

> show sel atoms

> style sel stick

Changed 7 atom styles  

> style sel ball

Changed 7 atom styles  

> style sel sphere

Changed 7 atom styles  

> style sel stick

Changed 7 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel tube/slab shape box

> nucleotides sel tube/slab shape ellipsoid

> nucleotides sel stubs

> ui mousemode right "link markers"

> close

> open C:\Users\DELL\Desktop\128W-full_model_110011_3.pdb format pdb

| Summary of feedback from opening
C:\Users\DELL\Desktop\128W-full_model_110011_3.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
PFRMAT TS  
  
Ignored bad PDB record found on line 2  
TARGET zc-128W  
  
Ignored bad PDB record found on line 4  
METHOD ROSETTA provides both ab initio and  
  
Ignored bad PDB record found on line 5  
METHOD comparative models of protein domains.  
  
Ignored bad PDB record found on line 6  
METHOD Comparative models are built from structures  
  
9 messages similar to the above omitted  
  
Chain information for 128W-full_model_110011_3.pdb #1  
---  
Chain | Description  
A | No description available  
  

> focus

Unknown command: focus  

> focus

Unknown command: focus  

> ui windowfill toggle

[Repeated 1 time(s)]

> open C:\Users\DELL\Desktop\128W-full_model_110011_3.pdb format pdb

Summary of feedback from opening
C:\Users\DELL\Desktop\128W-full_model_110011_3.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
PFRMAT TS  
  
Ignored bad PDB record found on line 2  
TARGET zc-128W  
  
Ignored bad PDB record found on line 4  
METHOD ROSETTA provides both ab initio and  
  
Ignored bad PDB record found on line 5  
METHOD comparative models of protein domains.  
  
Ignored bad PDB record found on line 6  
METHOD Comparative models are built from structures  
  
9 messages similar to the above omitted  
  
Chain information for 128W-full_model_110011_3.pdb #2  
---  
Chain | Description  
A | No description available  
  

> close

> open C:\Users\DELL\Desktop\128M-full_model_110012_1.pdb format pdb

Summary of feedback from opening
C:\Users\DELL\Desktop\128M-full_model_110012_1.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
PFRMAT TS  
  
Ignored bad PDB record found on line 2  
TARGET zc-128M  
  
Ignored bad PDB record found on line 4  
METHOD ROSETTA provides both ab initio and  
  
Ignored bad PDB record found on line 5  
METHOD comparative models of protein domains.  
  
Ignored bad PDB record found on line 6  
METHOD Comparative models are built from structures  
  
9 messages similar to the above omitted  
  
Chain information for 128M-full_model_110012_1.pdb #1  
---  
Chain | Description  
A | No description available  
  

> focus

Unknown command: focus  

> preset apply int 1

No preset name matches 'apply int 1'  

> preset apply

No preset name matches 'apply'  

> color gold #0

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color gold #1

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> ui tool show "Side View"

> color gold #1

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> ui tool show "Side View"

> view orient

[Repeated 2 time(s)]

> ui tool show "Side View"

> set bgColor white

> set bgColor gray

> set bgColor black

> set bgColor white

[Repeated 1 time(s)]

> set bgColor black

> select ::name="THR"

784 atoms, 734 bonds, 56 residues, 1 model selected  

> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"

15665 atoms, 15786 bonds, 999 residues, 1 model selected  

> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"

15665 atoms, 15786 bonds, 999 residues, 1 model selected  

> ~select #1

Nothing selected  

> close

> open C:\Users\DELL\Desktop\128W-full_model_110011_3.pdb format pdb

Summary of feedback from opening
C:\Users\DELL\Desktop\128W-full_model_110011_3.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
PFRMAT TS  
  
Ignored bad PDB record found on line 2  
TARGET zc-128W  
  
Ignored bad PDB record found on line 4  
METHOD ROSETTA provides both ab initio and  
  
Ignored bad PDB record found on line 5  
METHOD comparative models of protein domains.  
  
Ignored bad PDB record found on line 6  
METHOD Comparative models are built from structures  
  
9 messages similar to the above omitted  
  
Chain information for 128W-full_model_110011_3.pdb #1  
---  
Chain | Description  
A | No description available  
  

> view orient

[Repeated 3 time(s)]

> close

> open C:\Users\DELL\Desktop\128M-full_model_110012_1.pdb format pdb

Summary of feedback from opening
C:\Users\DELL\Desktop\128M-full_model_110012_1.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
PFRMAT TS  
  
Ignored bad PDB record found on line 2  
TARGET zc-128M  
  
Ignored bad PDB record found on line 4  
METHOD ROSETTA provides both ab initio and  
  
Ignored bad PDB record found on line 5  
METHOD comparative models of protein domains.  
  
Ignored bad PDB record found on line 6  
METHOD Comparative models are built from structures  
  
9 messages similar to the above omitted  
  
Chain information for 128M-full_model_110012_1.pdb #1  
---  
Chain | Description  
A | No description available  
  

> view orient

> close

> open C:\Users\DELL\Desktop\128W-full_model_110011_3.pdb format pdb

Summary of feedback from opening
C:\Users\DELL\Desktop\128W-full_model_110011_3.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
PFRMAT TS  
  
Ignored bad PDB record found on line 2  
TARGET zc-128W  
  
Ignored bad PDB record found on line 4  
METHOD ROSETTA provides both ab initio and  
  
Ignored bad PDB record found on line 5  
METHOD comparative models of protein domains.  
  
Ignored bad PDB record found on line 6  
METHOD Comparative models are built from structures  
  
9 messages similar to the above omitted  
  
Chain information for 128W-full_model_110011_3.pdb #1  
---  
Chain | Description  
A | No description available  
  

> view orient

[Repeated 1 time(s)]

> select ::name="THR"

798 atoms, 747 bonds, 57 residues, 1 model selected  

> close

> open C:\Users\DELL\Desktop\128W-full_model_110011_3.pdb format pdb

Summary of feedback from opening
C:\Users\DELL\Desktop\128W-full_model_110011_3.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
PFRMAT TS  
  
Ignored bad PDB record found on line 2  
TARGET zc-128W  
  
Ignored bad PDB record found on line 4  
METHOD ROSETTA provides both ab initio and  
  
Ignored bad PDB record found on line 5  
METHOD comparative models of protein domains.  
  
Ignored bad PDB record found on line 6  
METHOD Comparative models are built from structures  
  
9 messages similar to the above omitted  
  
Chain information for 128W-full_model_110011_3.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open C:/Users/DELL/Desktop/128M-full_model_110012_1.pdb

Summary of feedback from opening
C:/Users/DELL/Desktop/128M-full_model_110012_1.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
PFRMAT TS  
  
Ignored bad PDB record found on line 2  
TARGET zc-128M  
  
Ignored bad PDB record found on line 4  
METHOD ROSETTA provides both ab initio and  
  
Ignored bad PDB record found on line 5  
METHOD comparative models of protein domains.  
  
Ignored bad PDB record found on line 6  
METHOD Comparative models are built from structures  
  
9 messages similar to the above omitted  
  
Chain information for 128M-full_model_110012_1.pdb #2  
---  
Chain | Description  
A | No description available  
  

> view orient

[Repeated 1 time(s)]

> hide #1 models

> hide #2 models

> show #1 models

> show #2 models

> hide #2 models

> show #2 models

> select #1

15658 atoms, 15779 bonds, 999 residues, 1 model selected  

> ~select #1

Nothing selected  

> ui mousemode right "tape measure"

> ui mousemode right "pick blobs"

> ui mousemode right "map eraser"

[Repeated 2 time(s)]

> ui mousemode right "pick blobs"

> ui mousemode right "tape measure"

[Repeated 2 time(s)]

> ui mousemode right "map eraser"

[Repeated 3 time(s)]

> hide #3 models

> show #3 models

> hide #3 models

> ui mousemode right "translate selected models"

> 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 128W-full_model_110011_3.pdb, chain A (#1) with
128M-full_model_110012_1.pdb, chain A (#2), sequence alignment score = 4747.1  
RMSD between 464 pruned atom pairs is 0.824 angstroms; (across all 999 pairs:
28.153)  
  

> 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 128W-full_model_110011_3.pdb, chain A (#1) with
128M-full_model_110012_1.pdb, chain A (#2), sequence alignment score = 4747.1  
RMSD between 464 pruned atom pairs is 0.824 angstroms; (across all 999 pairs:
28.153)  
  

> color #2 lime

> undo

> color #1 blue

> color #1 red

> color #1 #55ff7f

> color #1 lime

> color #2 #ffff7f

> color #2 yellow

> color #2 white

> color #1 yellow

> color #1 white

> color #2 yellow

> color #1 yellow

> color #2 #55ffff

> show #3 models

> hide #3 models

> show atoms

[Repeated 1 time(s)]

> hide atoms

> undo

> hide atoms

Drag select of 29 residues  

> set bgColor white

> set bgColor black

> select down

449 atoms, 29 residues, 2 models selected  

> select down

449 atoms, 29 residues, 2 models selected  

> select down

449 atoms, 29 residues, 2 models selected  

> select down

449 atoms, 29 residues, 2 models selected  

> select down

449 atoms, 29 residues, 2 models selected  

> select down

449 atoms, 29 residues, 2 models selected  

> view orient

> select clear

[Repeated 1 time(s)]

> open C:/Users/DELL/Desktop/AF-Q2QNI2-F1-model_v1.pdb

AF-Q2QNI2-F1-model_v1.pdb title:  
Alphafold V2.0 prediction for OS12G0564600 protein (Q2QNI2) [more info...]  
  
Chain information for AF-Q2QNI2-F1-model_v1.pdb #4  
---  
Chain | Description | UniProt  
A | OS12G0564600 protein | Q2QNI2_ORYSJ  
  

> ui tool show Matchmaker

> matchmaker #1-2 to #4

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 AF-Q2QNI2-F1-model_v1.pdb, chain A (#4) with
128W-full_model_110011_3.pdb, chain A (#1), sequence alignment score = 4203.6  
RMSD between 148 pruned atom pairs is 1.388 angstroms; (across all 999 pairs:
68.723)  
  
Matchmaker AF-Q2QNI2-F1-model_v1.pdb, chain A (#4) with
128M-full_model_110012_1.pdb, chain A (#2), sequence alignment score = 4229.4  
RMSD between 164 pruned atom pairs is 0.791 angstroms; (across all 999 pairs:
69.877)  
  

> matchmaker #1-2 to #4

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 AF-Q2QNI2-F1-model_v1.pdb, chain A (#4) with
128W-full_model_110011_3.pdb, chain A (#1), sequence alignment score = 4203.6  
RMSD between 148 pruned atom pairs is 1.388 angstroms; (across all 999 pairs:
68.723)  
  
Matchmaker AF-Q2QNI2-F1-model_v1.pdb, chain A (#4) with
128M-full_model_110012_1.pdb, chain A (#2), sequence alignment score = 4229.4  
RMSD between 164 pruned atom pairs is 0.791 angstroms; (across all 999 pairs:
69.877)  
  

> hide #2 models

> show #2 models

> hide #1 models

> hide #5 models

> show #5 models

> hide #5 models

> ~select #5

Nothing selected  

> show #1 models

> hide #4 models

> ui tool show Matchmaker

Traceback (most recent call last):  
File "D:\Program Files (x86)\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "D:\Program Files (x86)\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\ui\options\options.py", line 50, in <lambda>  
data[0] == pself.attr_name and setattr(pself, "value", pself.get_attribute()))  
File "D:\Program Files (x86)\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\ui\options\options.py", line 339, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "D:\Program Files (x86)\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\ui\options\options.py", line 339, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\Program Files (x86)\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "D:\Program Files (x86)\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\ui\options\options.py", line 50, in <lambda>  
data[0] == pself.attr_name and setattr(pself, "value", pself.get_attribute()))  
File "D:\Program Files (x86)\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\ui\options\options.py", line 339, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "D:\Program Files (x86)\ChimeraX 1.3.dev202109080319\bin\lib\site-
packages\chimerax\ui\options\options.py", line 339, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 27.20.100.8935
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel
Manufacturer: Dell Inc.
Model: OptiPlex 7080
OS: Microsoft Windows 10 专业版 (Build 19042)
Memory: 8,291,131,392
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i7-10700 CPU @ 2.90GHz
OSLanguage: zh-CN
Locale: ('zh_CN', 'cp936')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.0
    chardet: 4.0.0
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.29.1
    ChimeraX-AtomicLibrary: 4.1.4
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.3
    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: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.4.1
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202109080319
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.4
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.1
    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-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    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: 2.0.1
    ChimeraX-MDcrds: 2.5
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.1.1
    ChimeraX-ModelPanel: 1.1
    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-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.3
    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: 1.6
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.12
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    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: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.10.0
    Cython: 0.29.23
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.4.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.20
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 2.11.3
    jupyter-client: 6.1.12
    jupyter-core: 4.7.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 1.1.1
    matplotlib: 3.4.2
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.6
    networkx: 2.6.2
    numexpr: 2.7.3
    numpy: 1.21.0
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.2
    pickleshare: 0.7.5
    Pillow: 8.2.0
    pip: 21.1.1
    pkginfo: 1.7.0
    prompt-toolkit: 3.0.20
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.9.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pywin32: 228
    pyzmq: 22.2.1
    qtconsole: 5.1.0
    QtPy: 1.11.0
    RandomWords: 0.3.0
    requests: 2.25.1
    scipy: 1.6.3
    setuptools: 57.0.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.4.0
    Sphinx: 4.0.1
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.0
    urllib3: 1.26.6
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.2
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Structure Comparison
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Matchmaker: 'NoneType' object has no attribute 'setChecked'

comment:2 by Eric Pettersen, 4 years ago

Resolution: → fixed
Status: accepted → closed

The settings/options callback loop doesn't get broken quickly enough by garbage collection. Force a garbage-collection cycle when a tool is closed.

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