id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14980 "False ""BLAST job failed"" error on session restore" goddard@… Zach Pearson "{{{ The following bug report has been submitted: Platform: macOS-14.4.1-arm64-arm-64bit ChimeraX Version: 1.8.dev202404120015 (2024-04-12 00:15:06 UTC) Description Opening this session brings up an error dialog saying ""BLAST job failed"". Not sure why. The blast job succeeded before the session was saved. The session was saved in a development build of ChimeraX made about a week ago. I've attached the offending session -- sorry it is big (212 structures). Log: UCSF ChimeraX version: 1.8.dev202404120015 (2024-04-12) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/goddard/ucsf/umap/braf/braf_23.cxs format session Log from Thu Apr 18 19:23:37 2024 > diffplot residues ca23 cluster 5 Comparing residues [463 471 481 482 483 501 505 508 513 514 527 529 530 531 532 567 572 574 583 592 593 594 595] of 4XV9_A #2/A in alignment columns [40, 48, 58, 59, 60, 78, 82, 85, 90, 91, 104, 106, 107, 108, 109, 144, 149, 151, 160, 169, 170, 171, 172] Chain 8GFT_D #204/D has no residue in 8GFT_D alignment columns [40, 48, 58, 59, 60, 78, 82, 85] Chain 7ZR6_K #156/K has no residue in 7ZR6_K alignment columns [40, 48, 58, 59, 60, 78, 82, 85, 90, 91] Chain 7Z38_C #211/C has no residue in 7Z38_C alignment columns [40, 48, 58, 59, 60, 78, 82, 85, 90] Chain 7ZR5_K #155/K has no residue in 7ZR5_K alignment columns [40, 48, 58, 59, 60, 78, 82, 85, 90, 91] Chain 7ZR0_K #154/K has no residue in 7ZR0_K alignment columns [40, 48, 58, 59, 60, 78, 82, 85, 90, 91] Chain 8GAE_D #212/D has no residue in 8GAE_D alignment columns [40, 48, 58, 59, 60, 78, 82, 85] Chain 5FD2_B #132/B has no residue in 5FD2_B alignment columns [40] Chain 8U1L_C #209/C has no residue in 8U1L_C alignment columns [40, 48, 58, 59, 60, 78, 82, 85, 90, 91] Chain 7Z37_CP1 #210/CP1 has no residue in 7Z37_CP1 alignment columns [40, 48, 58, 59, 60, 78, 82, 85, 90] Excluded 9 structures because they did not have alignment matches for all the residues being compared: 8GFT_D #204/D, 7ZR6_K #156/K, 7Z38_C #211/C, 7ZR5_K #155/K, 7ZR0_K #154/K, 8GAE_D #212/D, 5FD2_B #132/B, 8U1L_C #209/C, 7Z37_CP1 #210/CP1 Comparing positions of 23 atoms in 202 chains /Users/goddard/Library/Application Support/ChimeraX/1.8/lib/python/site- packages/umap/umap_.py:1945: UserWarning: n_jobs value 1 overridden to 1 by setting random_state. Use no seed for parallelism. warn(f""n_jobs value {self.n_jobs} overridden to 1 by setting random_state. Use no seed for parallelism."") Cluster 1: 5HIE_A, 4MBJ_B, 4XV1_A, 7P3V_A, 3TV6_A, 6V2U_A, 4EHE_B, 6V2U_B, 5HIE_C, 4EHG_B, 3TV6_B, 5CSW_A, 3SKC_A, 5FD2_A, 5HIE_D, 4E4X_A, 4CQE_B, 5ITA_B, 4EHG_A, 6UUO_A, 4EHE_A, 3SKC_B, 4FK3_A, 6UUO_B, 3TV4_A, 4PP7_A, 7P3V_B, 5HIE_B, 4PP7_B, 4E4X_B, 4XV3_A, 8DGS_A, 3C4C_A, 4XV2_B, 3OG7_A, 3TV4_B, 4CQE_A, 5ITA_A, 5CSW_B, 4MBJ_A, 4XV2_A Cluster 2: 3Q4C_A, 7SHV_A, 4MNE_B, 4MNE_G, 4MNE_F, 6Q0T_B, 3OMV_A, 6Q0K_B, 6UAN_C, 8CPD_B, 3PRI_A, 3PRI_B, 3Q4C_B, 4MNF_A, 2FB8_B, 7MFF_B, 3PPK_A, 3PRF_A, 3PSD_A, 4FK3_B, 4H58_A, 3D4Q_B, 6Q0K_A, 4E26_B, 6UAN_B, 6Q0J_A, 7SHV_B, 4XV3_B, 6Q0T_A, 3D4Q_A, 6U2H_C, 3PPK_B, 4MNE_C, 4XV1_B, 3PPJ_B, 3PSD_B, 2FB8_A, 3OMV_B, 7MFF_A, 3PSB_A, 4YHT_A, 6XAG_D, 8CPD_A, 3OG7_B, 3PRF_B, 3PSB_B, 4E26_A, 8CHF_B, 3PPJ_A, 6Q0J_B, 4MNF_B, 6XAG_C, 6U2H_D, 4H58_B, 8CHF_A, 4YHT_B Cluster 3: 5JSM_B, 5JSM_C, 5JRQ_A, 5JSM_D, 5JT2_A, 5JRQ_B, 4WO5_B, 5JT2_D, 4RZV_A, 4WO5_A, 5JT2_B, 5JSM_A, 5JT2_C, 4RZV_B Cluster 4: 7M0V_A, 7M0Z_A, 7M0X_A, 7MFE_A, 8DGT_A, 7M0U_A, 6NYB_A, 6PP9_A, 6V2W_A, 7M0T_A, 7M0W_A, 7M0Y_A, 6U2G_B, 7MFD_A Cluster 5: 8F7P_A, 5VAM_B, 3C4C_B, 6CAD_A, 1UWH_B, 4KSQ_A, 7K0V_A, 8C7Y_A, 4JVG_D, 6V34_A, 6B8U_A, 6XFP_A, 4G9R_A, 4KSP_B, 3Q96_A, 4DBN_B, 8C7X_B, 5HID_A, 7K0V_B, 4G9C_A, 6B8U_B, 4FC0_B, 1UWJ_B, 4DBN_A, 6N0P_A, 3II5_A, 3II5_B, 3Q96_B, 6NSQ_B, 4KSP_A, 6N0P_B, 1UWH_A, 5HID_B, 5CT7_B, 8F7O_B, 8F7P_B, 4RZW_A, 4G9C_B, 3IDP_B, 5C9C_B, 6N0Q_A, 4JVG_C, 8C7X_A, 5VAM_A, 4XV9_A, 6P7G_A, 6P7G_B, 6P3D_A, 4G9R_B, 3IDP_A, 8F7O_A, 6P7G_C, 5HI2_A, 6V34_B, 6P7G_D, 4R5Y_B, 6XLO_A, 6XLO_B, 5CSX_A, 4KSQ_B, 7K0V_D, 4JVG_A, 6N0Q_B, 4H58_C, 7K0V_C, 5C9C_A, 8C7Y_B, 5CT7_A, 4FC0_A, 5VAL_A, 4RZW_B, 4JVG_B, 6NSQ_A, 6CAD_B, 1UWJ_A, 5VAL_B, 4R5Y_A Already setting window visible! > diffplot residues ca23 cluster 5 Comparing residues [463 471 481 482 483 501 505 508 513 514 527 529 530 531 532 567 572 574 583 592 593 594 595] of 4XV9_A #2/A in alignment columns [40, 48, 58, 59, 60, 78, 82, 85, 90, 91, 104, 106, 107, 108, 109, 144, 149, 151, 160, 169, 170, 171, 172] Chain 8GFT_D #204/D has no residue in 8GFT_D alignment columns [40, 48, 58, 59, 60, 78, 82, 85] Chain 7ZR6_K #156/K has no residue in 7ZR6_K alignment columns [40, 48, 58, 59, 60, 78, 82, 85, 90, 91] Chain 7Z38_C #211/C has no residue in 7Z38_C alignment columns [40, 48, 58, 59, 60, 78, 82, 85, 90] Chain 7ZR5_K #155/K has no residue in 7ZR5_K alignment columns [40, 48, 58, 59, 60, 78, 82, 85, 90, 91] Chain 7ZR0_K #154/K has no residue in 7ZR0_K alignment columns [40, 48, 58, 59, 60, 78, 82, 85, 90, 91] Chain 8GAE_D #212/D has no residue in 8GAE_D alignment columns [40, 48, 58, 59, 60, 78, 82, 85] Chain 5FD2_B #132/B has no residue in 5FD2_B alignment columns [40] Chain 8U1L_C #209/C has no residue in 8U1L_C alignment columns [40, 48, 58, 59, 60, 78, 82, 85, 90, 91] Chain 7Z37_CP1 #210/CP1 has no residue in 7Z37_CP1 alignment columns [40, 48, 58, 59, 60, 78, 82, 85, 90] Excluded 9 structures because they did not have alignment matches for all the residues being compared: 8GFT_D #204/D, 7ZR6_K #156/K, 7Z38_C #211/C, 7ZR5_K #155/K, 7ZR0_K #154/K, 8GAE_D #212/D, 5FD2_B #132/B, 8U1L_C #209/C, 7Z37_CP1 #210/CP1 Comparing positions of 23 atoms in 202 chains /Users/goddard/Library/Application Support/ChimeraX/1.8/lib/python/site- packages/umap/umap_.py:1945: UserWarning: n_jobs value 1 overridden to 1 by setting random_state. Use no seed for parallelism. warn(f""n_jobs value {self.n_jobs} overridden to 1 by setting random_state. Use no seed for parallelism."") Cluster 1: 5HIE_A, 4MBJ_B, 4XV1_A, 7P3V_A, 3TV6_A, 6V2U_A, 4EHE_B, 6V2U_B, 5HIE_C, 4EHG_B, 3TV6_B, 5CSW_A, 3SKC_A, 5FD2_A, 5HIE_D, 4E4X_A, 4CQE_B, 5ITA_B, 4EHG_A, 6UUO_A, 4EHE_A, 3SKC_B, 4FK3_A, 6UUO_B, 3TV4_A, 4PP7_A, 7P3V_B, 5HIE_B, 4PP7_B, 4E4X_B, 4XV3_A, 8DGS_A, 3C4C_A, 4XV2_B, 3OG7_A, 3TV4_B, 4CQE_A, 5ITA_A, 5CSW_B, 4MBJ_A, 4XV2_A Cluster 2: 3Q4C_A, 7SHV_A, 4MNE_B, 4MNE_G, 4MNE_F, 6Q0T_B, 3OMV_A, 6Q0K_B, 6UAN_C, 8CPD_B, 3PRI_A, 3PRI_B, 3Q4C_B, 4MNF_A, 2FB8_B, 7MFF_B, 3PPK_A, 3PRF_A, 3PSD_A, 4FK3_B, 4H58_A, 3D4Q_B, 6Q0K_A, 4E26_B, 6UAN_B, 6Q0J_A, 7SHV_B, 4XV3_B, 6Q0T_A, 3D4Q_A, 6U2H_C, 3PPK_B, 4MNE_C, 4XV1_B, 3PPJ_B, 3PSD_B, 2FB8_A, 3OMV_B, 7MFF_A, 3PSB_A, 4YHT_A, 6XAG_D, 8CPD_A, 3OG7_B, 3PRF_B, 3PSB_B, 4E26_A, 8CHF_B, 3PPJ_A, 6Q0J_B, 4MNF_B, 6XAG_C, 6U2H_D, 4H58_B, 8CHF_A, 4YHT_B Cluster 3: 7M0V_A, 7M0Z_A, 7M0X_A, 7MFE_A, 8DGT_A, 7M0U_A, 6NYB_A, 6PP9_A, 6V2W_A, 7M0T_A, 7M0W_A, 7M0Y_A, 6U2G_B, 7MFD_A Cluster 4: 8F7P_A, 5VAM_B, 3C4C_B, 6CAD_A, 1UWH_B, 4KSQ_A, 7K0V_A, 8C7Y_A, 4JVG_D, 6V34_A, 6B8U_A, 6XFP_A, 4G9R_A, 4KSP_B, 3Q96_A, 4DBN_B, 8C7X_B, 5HID_A, 7K0V_B, 4G9C_A, 6B8U_B, 4FC0_B, 1UWJ_B, 4DBN_A, 6N0P_A, 3II5_A, 3II5_B, 3Q96_B, 6NSQ_B, 4KSP_A, 6N0P_B, 1UWH_A, 5HID_B, 5CT7_B, 8F7O_B, 8F7P_B, 4RZW_A, 4G9C_B, 3IDP_B, 5C9C_B, 6N0Q_A, 4JVG_C, 8C7X_A, 5VAM_A, 4XV9_A, 6P7G_A, 6P7G_B, 6P3D_A, 4G9R_B, 3IDP_A, 8F7O_A, 6P7G_C, 5HI2_A, 6V34_B, 6P7G_D, 4R5Y_B, 6XLO_A, 6XLO_B, 5CSX_A, 4KSQ_B, 7K0V_D, 4JVG_A, 6N0Q_B, 4H58_C, 7K0V_C, 5C9C_A, 8C7Y_B, 5CT7_A, 4FC0_A, 5VAL_A, 4RZW_B, 4JVG_B, 6NSQ_A, 6CAD_B, 1UWJ_A, 5VAL_B, 4R5Y_A Cluster 5: 5JSM_B, 5JSM_C, 5JRQ_A, 5JSM_D, 5JT2_A, 5JRQ_B, 4WO5_B, 5JT2_D, 4RZV_A, 4WO5_A, 5JT2_B, 5JSM_A, 5JT2_C, 4RZV_B > diffplot residues ca23 cluster 5 Comparing residues [463 471 481 482 483 501 505 508 513 514 527 529 530 531 532 567 572 574 583 592 593 594 595] of 4XV9_A #2/A in alignment columns [40, 48, 58, 59, 60, 78, 82, 85, 90, 91, 104, 106, 107, 108, 109, 144, 149, 151, 160, 169, 170, 171, 172] Chain 8GFT_D #204/D has no residue in 8GFT_D alignment columns [40, 48, 58, 59, 60, 78, 82, 85] Chain 7ZR6_K #156/K has no residue in 7ZR6_K alignment columns [40, 48, 58, 59, 60, 78, 82, 85, 90, 91] Chain 7Z38_C #211/C has no residue in 7Z38_C alignment columns [40, 48, 58, 59, 60, 78, 82, 85, 90] Chain 7ZR5_K #155/K has no residue in 7ZR5_K alignment columns [40, 48, 58, 59, 60, 78, 82, 85, 90, 91] Chain 7ZR0_K #154/K has no residue in 7ZR0_K alignment columns [40, 48, 58, 59, 60, 78, 82, 85, 90, 91] Chain 8GAE_D #212/D has no residue in 8GAE_D alignment columns [40, 48, 58, 59, 60, 78, 82, 85] Chain 5FD2_B #132/B has no residue in 5FD2_B alignment columns [40] Chain 8U1L_C #209/C has no residue in 8U1L_C alignment columns [40, 48, 58, 59, 60, 78, 82, 85, 90, 91] Chain 7Z37_CP1 #210/CP1 has no residue in 7Z37_CP1 alignment columns [40, 48, 58, 59, 60, 78, 82, 85, 90] Excluded 9 structures because they did not have alignment matches for all the residues being compared: 8GFT_D #204/D, 7ZR6_K #156/K, 7Z38_C #211/C, 7ZR5_K #155/K, 7ZR0_K #154/K, 8GAE_D #212/D, 5FD2_B #132/B, 8U1L_C #209/C, 7Z37_CP1 #210/CP1 Comparing positions of 23 atoms in 202 chains /Users/goddard/Library/Application Support/ChimeraX/1.8/lib/python/site- packages/umap/umap_.py:1945: UserWarning: n_jobs value 1 overridden to 1 by setting random_state. Use no seed for parallelism. warn(f""n_jobs value {self.n_jobs} overridden to 1 by setting random_state. Use no seed for parallelism."") Cluster 1: 5JSM_B, 5JSM_C, 5JRQ_A, 5JSM_D, 5JT2_A, 5JRQ_B, 4WO5_B, 5JT2_D, 4RZV_A, 4WO5_A, 5JT2_B, 5JSM_A, 5JT2_C, 4RZV_B Cluster 2: 3Q4C_A, 7SHV_A, 4MNE_B, 4MNE_G, 4MNE_F, 6Q0T_B, 3OMV_A, 6Q0K_B, 6UAN_C, 8CPD_B, 3PRI_A, 3PRI_B, 3Q4C_B, 4MNF_A, 2FB8_B, 7MFF_B, 3PPK_A, 3PRF_A, 3PSD_A, 4FK3_B, 4H58_A, 3D4Q_B, 6Q0K_A, 4E26_B, 6UAN_B, 6Q0J_A, 7SHV_B, 4XV3_B, 6Q0T_A, 3D4Q_A, 6U2H_C, 3PPK_B, 4MNE_C, 4XV1_B, 3PPJ_B, 3PSD_B, 2FB8_A, 3OMV_B, 7MFF_A, 3PSB_A, 4YHT_A, 6XAG_D, 8CPD_A, 3OG7_B, 3PRF_B, 3PSB_B, 4E26_A, 8CHF_B, 3PPJ_A, 6Q0J_B, 4MNF_B, 6XAG_C, 6U2H_D, 4H58_B, 8CHF_A, 4YHT_B Cluster 3: 8F7P_A, 5VAM_B, 3C4C_B, 6CAD_A, 1UWH_B, 4KSQ_A, 7K0V_A, 8C7Y_A, 4JVG_D, 6V34_A, 6B8U_A, 6XFP_A, 4G9R_A, 4KSP_B, 3Q96_A, 4DBN_B, 8C7X_B, 5HID_A, 7K0V_B, 4G9C_A, 6B8U_B, 4FC0_B, 1UWJ_B, 4DBN_A, 6N0P_A, 3II5_A, 3II5_B, 3Q96_B, 6NSQ_B, 4KSP_A, 6N0P_B, 1UWH_A, 5HID_B, 5CT7_B, 8F7O_B, 8F7P_B, 4RZW_A, 4G9C_B, 3IDP_B, 5C9C_B, 6N0Q_A, 4JVG_C, 8C7X_A, 5VAM_A, 4XV9_A, 6P7G_A, 6P7G_B, 6P3D_A, 4G9R_B, 3IDP_A, 8F7O_A, 6P7G_C, 5HI2_A, 6V34_B, 6P7G_D, 4R5Y_B, 6XLO_A, 6XLO_B, 5CSX_A, 4KSQ_B, 7K0V_D, 4JVG_A, 6N0Q_B, 4H58_C, 7K0V_C, 5C9C_A, 8C7Y_B, 5CT7_A, 4FC0_A, 5VAL_A, 4RZW_B, 4JVG_B, 6NSQ_A, 6CAD_B, 1UWJ_A, 5VAL_B, 4R5Y_A Cluster 4: 5HIE_A, 4MBJ_B, 4XV1_A, 7P3V_A, 3TV6_A, 6V2U_A, 4EHE_B, 6V2U_B, 5HIE_C, 4EHG_B, 3TV6_B, 5CSW_A, 3SKC_A, 5FD2_A, 5HIE_D, 4E4X_A, 4CQE_B, 5ITA_B, 4EHG_A, 6UUO_A, 4EHE_A, 3SKC_B, 4FK3_A, 6UUO_B, 3TV4_A, 4PP7_A, 7P3V_B, 5HIE_B, 4PP7_B, 4E4X_B, 4XV3_A, 8DGS_A, 3C4C_A, 4XV2_B, 3OG7_A, 3TV4_B, 4CQE_A, 5ITA_A, 5CSW_B, 4MBJ_A, 4XV2_A Cluster 5: 7M0V_A, 7M0Z_A, 7M0X_A, 7MFE_A, 8DGT_A, 7M0U_A, 6NYB_A, 6PP9_A, 6V2W_A, 7M0T_A, 7M0W_A, 7M0Y_A, 6U2G_B, 7MFD_A > diffplot residues ca23 cluster 5 Comparing residues [463 471 481 482 483 501 505 508 513 514 527 529 530 531 532 567 572 574 583 592 593 594 595] of 4XV9_A #2/A in alignment columns [40, 48, 58, 59, 60, 78, 82, 85, 90, 91, 104, 106, 107, 108, 109, 144, 149, 151, 160, 169, 170, 171, 172] Chain 8GFT_D #204/D has no residue in 8GFT_D alignment columns [40, 48, 58, 59, 60, 78, 82, 85] Chain 7ZR6_K #156/K has no residue in 7ZR6_K alignment columns [40, 48, 58, 59, 60, 78, 82, 85, 90, 91] Chain 7Z38_C #211/C has no residue in 7Z38_C alignment columns [40, 48, 58, 59, 60, 78, 82, 85, 90] Chain 7ZR5_K #155/K has no residue in 7ZR5_K alignment columns [40, 48, 58, 59, 60, 78, 82, 85, 90, 91] Chain 7ZR0_K #154/K has no residue in 7ZR0_K alignment columns [40, 48, 58, 59, 60, 78, 82, 85, 90, 91] Chain 8GAE_D #212/D has no residue in 8GAE_D alignment columns [40, 48, 58, 59, 60, 78, 82, 85] Chain 5FD2_B #132/B has no residue in 5FD2_B alignment columns [40] Chain 8U1L_C #209/C has no residue in 8U1L_C alignment columns [40, 48, 58, 59, 60, 78, 82, 85, 90, 91] Chain 7Z37_CP1 #210/CP1 has no residue in 7Z37_CP1 alignment columns [40, 48, 58, 59, 60, 78, 82, 85, 90] Excluded 9 structures because they did not have alignment matches for all the residues being compared: 8GFT_D #204/D, 7ZR6_K #156/K, 7Z38_C #211/C, 7ZR5_K #155/K, 7ZR0_K #154/K, 8GAE_D #212/D, 5FD2_B #132/B, 8U1L_C #209/C, 7Z37_CP1 #210/CP1 Comparing positions of 23 atoms in 202 chains /Users/goddard/Library/Application Support/ChimeraX/1.8/lib/python/site- packages/umap/umap_.py:1945: UserWarning: n_jobs value 1 overridden to 1 by setting random_state. Use no seed for parallelism. warn(f""n_jobs value {self.n_jobs} overridden to 1 by setting random_state. Use no seed for parallelism."") Cluster 1: 5HIE_A, 4MBJ_B, 4XV1_A, 7P3V_A, 3TV6_A, 6V2U_A, 4EHE_B, 6V2U_B, 5HIE_C, 4EHG_B, 3TV6_B, 5CSW_A, 3SKC_A, 5FD2_A, 5HIE_D, 4E4X_A, 4CQE_B, 5ITA_B, 4EHG_A, 6UUO_A, 4EHE_A, 3SKC_B, 4FK3_A, 6UUO_B, 3TV4_A, 4PP7_A, 7P3V_B, 5HIE_B, 4PP7_B, 4E4X_B, 4XV3_A, 8DGS_A, 3C4C_A, 4XV2_B, 3OG7_A, 3TV4_B, 4CQE_A, 5ITA_A, 5CSW_B, 4MBJ_A, 4XV2_A Cluster 2: 8F7P_A, 5VAM_B, 3C4C_B, 6CAD_A, 1UWH_B, 4KSQ_A, 7K0V_A, 8C7Y_A, 4JVG_D, 6V34_A, 6B8U_A, 6XFP_A, 4G9R_A, 4KSP_B, 3Q96_A, 4DBN_B, 8C7X_B, 5HID_A, 7K0V_B, 4G9C_A, 6B8U_B, 4FC0_B, 1UWJ_B, 4DBN_A, 6N0P_A, 3II5_A, 3II5_B, 3Q96_B, 6NSQ_B, 4KSP_A, 6N0P_B, 1UWH_A, 5HID_B, 5CT7_B, 8F7O_B, 8F7P_B, 4RZW_A, 4G9C_B, 3IDP_B, 5C9C_B, 6N0Q_A, 4JVG_C, 8C7X_A, 5VAM_A, 4XV9_A, 6P7G_A, 6P7G_B, 6P3D_A, 4G9R_B, 3IDP_A, 8F7O_A, 6P7G_C, 5HI2_A, 6V34_B, 6P7G_D, 4R5Y_B, 6XLO_A, 6XLO_B, 5CSX_A, 4KSQ_B, 7K0V_D, 4JVG_A, 6N0Q_B, 4H58_C, 7K0V_C, 5C9C_A, 8C7Y_B, 5CT7_A, 4FC0_A, 5VAL_A, 4RZW_B, 4JVG_B, 6NSQ_A, 6CAD_B, 1UWJ_A, 5VAL_B, 4R5Y_A Cluster 3: 7M0V_A, 7M0Z_A, 7M0X_A, 7MFE_A, 8DGT_A, 7M0U_A, 6NYB_A, 6PP9_A, 6V2W_A, 7M0T_A, 7M0W_A, 7M0Y_A, 6U2G_B, 7MFD_A Cluster 4: 3Q4C_A, 7SHV_A, 4MNE_B, 4MNE_G, 4MNE_F, 6Q0T_B, 3OMV_A, 6Q0K_B, 6UAN_C, 8CPD_B, 3PRI_A, 3PRI_B, 3Q4C_B, 4MNF_A, 2FB8_B, 7MFF_B, 3PPK_A, 3PRF_A, 3PSD_A, 4FK3_B, 4H58_A, 3D4Q_B, 6Q0K_A, 4E26_B, 6UAN_B, 6Q0J_A, 7SHV_B, 4XV3_B, 6Q0T_A, 3D4Q_A, 6U2H_C, 3PPK_B, 4MNE_C, 4XV1_B, 3PPJ_B, 3PSD_B, 2FB8_A, 3OMV_B, 7MFF_A, 3PSB_A, 4YHT_A, 6XAG_D, 8CPD_A, 3OG7_B, 3PRF_B, 3PSB_B, 4E26_A, 8CHF_B, 3PPJ_A, 6Q0J_B, 4MNF_B, 6XAG_C, 6U2H_D, 4H58_B, 8CHF_A, 4YHT_B Cluster 5: 5JSM_B, 5JSM_C, 5JRQ_A, 5JSM_D, 5JT2_A, 5JRQ_B, 4WO5_B, 5JT2_D, 4RZV_A, 4WO5_A, 5JT2_B, 5JSM_A, 5JT2_C, 4RZV_B > diffplot residues ca23 cluster 5 Comparing residues [463 471 481 482 483 501 505 508 513 514 527 529 530 531 532 567 572 574 583 592 593 594 595] of 4XV9_A #2/A in alignment columns [40, 48, 58, 59, 60, 78, 82, 85, 90, 91, 104, 106, 107, 108, 109, 144, 149, 151, 160, 169, 170, 171, 172] Chain 8GFT_D #204/D has no residue in 8GFT_D alignment columns [40, 48, 58, 59, 60, 78, 82, 85] Chain 7ZR6_K #156/K has no residue in 7ZR6_K alignment columns [40, 48, 58, 59, 60, 78, 82, 85, 90, 91] Chain 7Z38_C #211/C has no residue in 7Z38_C alignment columns [40, 48, 58, 59, 60, 78, 82, 85, 90] Chain 7ZR5_K #155/K has no residue in 7ZR5_K alignment columns [40, 48, 58, 59, 60, 78, 82, 85, 90, 91] Chain 7ZR0_K #154/K has no residue in 7ZR0_K alignment columns [40, 48, 58, 59, 60, 78, 82, 85, 90, 91] Chain 8GAE_D #212/D has no residue in 8GAE_D alignment columns [40, 48, 58, 59, 60, 78, 82, 85] Chain 5FD2_B #132/B has no residue in 5FD2_B alignment columns [40] Chain 8U1L_C #209/C has no residue in 8U1L_C alignment columns [40, 48, 58, 59, 60, 78, 82, 85, 90, 91] Chain 7Z37_CP1 #210/CP1 has no residue in 7Z37_CP1 alignment columns [40, 48, 58, 59, 60, 78, 82, 85, 90] Excluded 9 structures because they did not have alignment matches for all the residues being compared: 8GFT_D #204/D, 7ZR6_K #156/K, 7Z38_C #211/C, 7ZR5_K #155/K, 7ZR0_K #154/K, 8GAE_D #212/D, 5FD2_B #132/B, 8U1L_C #209/C, 7Z37_CP1 #210/CP1 Comparing positions of 23 atoms in 202 chains /Users/goddard/Library/Application Support/ChimeraX/1.8/lib/python/site- packages/umap/umap_.py:1945: UserWarning: n_jobs value 1 overridden to 1 by setting random_state. Use no seed for parallelism. warn(f""n_jobs value {self.n_jobs} overridden to 1 by setting random_state. Use no seed for parallelism."") Cluster 1: 5JSM_B, 5JSM_C, 5JRQ_A, 5JSM_D, 5JT2_A, 5JRQ_B, 4WO5_B, 5JT2_D, 4RZV_A, 4WO5_A, 5JT2_B, 5JSM_A, 5JT2_C, 4RZV_B Cluster 2: 7M0V_A, 7M0Z_A, 7M0X_A, 7MFE_A, 8DGT_A, 7M0U_A, 6NYB_A, 6PP9_A, 6V2W_A, 7M0T_A, 7M0W_A, 7M0Y_A, 6U2G_B, 7MFD_A Cluster 3: 3Q4C_A, 7SHV_A, 4MNE_B, 4MNE_G, 4MNE_F, 6Q0T_B, 3OMV_A, 6Q0K_B, 6UAN_C, 8CPD_B, 3PRI_A, 3PRI_B, 3Q4C_B, 4MNF_A, 2FB8_B, 7MFF_B, 3PPK_A, 3PRF_A, 3PSD_A, 4FK3_B, 4H58_A, 3D4Q_B, 6Q0K_A, 4E26_B, 6UAN_B, 6Q0J_A, 7SHV_B, 4XV3_B, 6Q0T_A, 3D4Q_A, 6U2H_C, 3PPK_B, 4MNE_C, 4XV1_B, 3PPJ_B, 3PSD_B, 2FB8_A, 3OMV_B, 7MFF_A, 3PSB_A, 4YHT_A, 6XAG_D, 8CPD_A, 3OG7_B, 3PRF_B, 3PSB_B, 4E26_A, 8CHF_B, 3PPJ_A, 6Q0J_B, 4MNF_B, 6XAG_C, 6U2H_D, 4H58_B, 8CHF_A, 4YHT_B Cluster 4: 5HIE_A, 4MBJ_B, 4XV1_A, 7P3V_A, 3TV6_A, 6V2U_A, 4EHE_B, 6V2U_B, 5HIE_C, 4EHG_B, 3TV6_B, 5CSW_A, 3SKC_A, 5FD2_A, 5HIE_D, 4E4X_A, 4CQE_B, 5ITA_B, 4EHG_A, 6UUO_A, 4EHE_A, 3SKC_B, 4FK3_A, 6UUO_B, 3TV4_A, 4PP7_A, 7P3V_B, 5HIE_B, 4PP7_B, 4E4X_B, 4XV3_A, 8DGS_A, 3C4C_A, 4XV2_B, 3OG7_A, 3TV4_B, 4CQE_A, 5ITA_A, 5CSW_B, 4MBJ_A, 4XV2_A Cluster 5: 8F7P_A, 5VAM_B, 3C4C_B, 6CAD_A, 1UWH_B, 4KSQ_A, 7K0V_A, 8C7Y_A, 4JVG_D, 6V34_A, 6B8U_A, 6XFP_A, 4G9R_A, 4KSP_B, 3Q96_A, 4DBN_B, 8C7X_B, 5HID_A, 7K0V_B, 4G9C_A, 6B8U_B, 4FC0_B, 1UWJ_B, 4DBN_A, 6N0P_A, 3II5_A, 3II5_B, 3Q96_B, 6NSQ_B, 4KSP_A, 6N0P_B, 1UWH_A, 5HID_B, 5CT7_B, 8F7O_B, 8F7P_B, 4RZW_A, 4G9C_B, 3IDP_B, 5C9C_B, 6N0Q_A, 4JVG_C, 8C7X_A, 5VAM_A, 4XV9_A, 6P7G_A, 6P7G_B, 6P3D_A, 4G9R_B, 3IDP_A, 8F7O_A, 6P7G_C, 5HI2_A, 6V34_B, 6P7G_D, 4R5Y_B, 6XLO_A, 6XLO_B, 5CSX_A, 4KSQ_B, 7K0V_D, 4JVG_A, 6N0Q_B, 4H58_C, 7K0V_C, 5C9C_A, 8C7Y_B, 5CT7_A, 4FC0_A, 5VAL_A, 4RZW_B, 4JVG_B, 6NSQ_A, 6CAD_B, 1UWJ_A, 5VAL_B, 4R5Y_A > color #2:801 yellow > color ca23 yellow atoms > color ca23 red atoms > size ballScale .5 Changed 212 ball scales > style #2:801 stick Changed 34 atom styles > style #2:801 ball Changed 34 atom styles > size ballScale .3 Changed 212 ball scales > color #2:801 byelement > color ca23 yellow atoms > color #2:801 yellow > color #2:801 byhetero > style ca22 sphere Expected a keyword > style ca23 sphere Changed 188 atom styles > usage size size [objects] [atomRadius atomRadius] [stickRadius a number >= 0 or a +/- delta] [pseudobondRadius a number >= 0 or a +/- delta] [ballScale a number >= 0 or a +/- delta] — change atom and bond sizes objects: an objects specifier or nothing atomRadius: default or a number >= 0 or a +/- delta size byattribute attrName [atoms] [wayPoints] [average average] [noValueRadius noValueRadius] [style style] — size atoms by attribute value attrName: a text string atoms: an atoms specifier or nothing wayPoints: attr-value:radius pair, repeatable average: residues noValueRadius: a number > 0 style: one of ball, sphere, or unchanged > size ca22 atom 1 Expected a keyword > size ca23 atomRadius 1 Changed 188 atom radii > color ca23 red > save /Users/goddard/Desktop/image1.png supersample 3 Already setting window visible! Traceback (most recent call last): File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/interfaces/graph.py"", line 342, in _mouse_press self.tool_window._show_context_menu(event) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/gui.py"", line 2325, in _show_context_menu self.__toolkit.show_context_menu(event) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/gui.py"", line 2571, in show_context_menu self.tool_window.tool_instance.tool_info in self.main_window._tools_cache, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/tools.py"", line 151, in tool_info for ti in self.bundle_info.tools: ^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'tools' AttributeError: 'NoneType' object has no attribute 'tools' File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/tools.py"", line 151, in tool_info for ti in self.bundle_info.tools: ^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. > save braf_23.cxs ——— End of log from Thu Apr 18 19:23:37 2024 ——— opened ChimeraX session BLAST job failed OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M2 Ultra OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: Mac Studio Model Identifier: Mac14,14 Model Number: Z1800003VLL/A Chip: Apple M2 Ultra Total Number of Cores: 24 (16 performance and 8 efficiency) Memory: 64 GB System Firmware Version: 10151.101.3 OS Loader Version: 10151.101.3 Software: System Software Overview: System Version: macOS 14.4.1 (23E224) Kernel Version: Darwin 23.4.0 Time since boot: 9 hours, 30 minutes Graphics/Displays: Apple M2 Ultra: Chipset Model: Apple M2 Ultra Type: GPU Bus: Built-In Total Number of Cores: 60 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: PHL 278B1: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.16 alphashape: 1.3.1 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.14.0 beautifulsoup4: 4.12.3 biopython: 1.83 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.16 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.4.3 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.5 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.56.1 ChimeraX-AtomicLibrary: 14.0.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 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-Clipper: 0.23.0 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8.dev202404120015 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-crai: 0.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 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: 1.1.9 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 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.15 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: 1.1 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.4 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PhenixUI: 1.2.2 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.1 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: 1.0 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: 1.16.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2 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-TetraScapeCommand: 0.1 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: 1.37.2 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4 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: 1.1.3 ChimeraX-Zone: 1.0.1 click: 8.1.7 click-log: 0.4.0 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cripser: 0.0.13 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.3 fonttools: 4.51.0 fsspec: 2024.3.1 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 0.43 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.2 jedi: 0.19.1 Jinja2: 3.1.3 joblib: 1.4.0 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.10 kiwisolver: 1.4.5 line-profiler: 4.1.2 llvmlite: 0.42.0 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.6 mpmath: 1.3.0 mrcfile: 1.5.0 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.0.1 nptyping: 2.5.0 numba: 0.59.1 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 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: 4.2.0 prompt-toolkit: 3.0.43 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.3.0 pygments: 2.17.2 pynmrstar: 3.3.4 pynndescent: 0.5.12 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3302 pyparsing: 3.1.2 pyproject-hooks: 1.0.0 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: 25.1.2 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 Rtree: 1.1.0 scikit-learn: 1.4.2 scipy: 1.13.0 setuptools: 69.2.0 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 shapely: 2.0.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.0 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 sympy: 1.12 tables: 3.8.0 tcia-utils: 1.5.1 threadpoolctl: 3.4.0 tifffile: 2024.1.30 tinyarray: 1.2.4 torch: 2.2.2 tornado: 6.4 tqdm: 4.66.2 traitlets: 5.14.2 trimesh: 4.0.10 typing-extensions: 4.11.0 tzdata: 2024.1 umap-learn: 0.5.6 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.10 File attachment: braf_23.cxs }}} [attachment:""braf_23.cxs""] " defect closed normal Sequence fixed Elaine Meng all ChimeraX