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Opened 18 months ago
Closed 18 months ago
#14980 closed defect (fixed)
False "BLAST job failed" error on session restore
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sequence | Version: | |
| Keywords: | Cc: | Elaine Meng | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
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
Attachments (1)
Change History (10)
by , 18 months ago
| Attachment: | braf_23.cxs added |
|---|
comment:1 by , 18 months ago
| Component: | Unassigned → Sequence |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → False "BLAST job failed" error on session restore |
comment:2 by , 18 months ago
We have a data structure to save background jobs in sessions and it doesn't forget jobs automatically when they finish so any ModellerLocalJob, ModellerWebJob, Task, BlastProteinJob, etc, is saved and restored. One possibility is that when the job is restored it attempts to contact Plato and get its results, and reports failure when it doesn't find them, I'll download your session and double check whether that's the case.
It might be better behavior if a finished job isn't saved, and if the user has closed the results GUI in the time between the job finishing and the session being saved forget them, otherwise save the results tool as normal. I think this was my intended behavior, and I removed the "check if finished before saving" code for debugging and forgot to ever restored it. Or the job itself could keep the results around indefinitely and restore from its copy when sessions are restored.
comment:3 by , 18 months ago
I would think that a completed job should not be remembering the server job id and checking on it. Any results from the job that are still open in ChimeraX can be saved, for instance the BLAST results GUI. But if the BLAST results GUI is closed, I always assumed that means the results are gone, and that is what "close" means, I no longer want this data, so in that case nothing about the results would go into the session except Log output since we save the Log text.
comment:4 by , 18 months ago
| Cc: | added |
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comment:5 by , 18 months ago
| Cc: | removed |
|---|---|
| Resolution: | → fixed |
| Status: | assigned → closed |
This should be fixed tomorrow.
Previously the session would save all tasks regardless of what state
they were in as long as Task.SESSION_SAVE was set. This resulted in
failed, finished, canceled, etc. tasks polluting sessions. The session
restore code in Tasks would then attempt to restart the task, only for
the task to report a suprious failure. Now, new sessions don't save
tasks in those states and they aren't restored from old sessions.
comment:6 by , 18 months ago
| Cc: | added |
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comment:7 by , 18 months ago
| Resolution: | fixed |
|---|---|
| Status: | closed → reopened |
I discovered to my dismay while looking at something else to do with sessions that this is not fixed.
comment:8 by , 18 months ago
I started the task manager and was confused as to why I would see two copies of restored tasks. It seems like not only does the session restore machinery try to restore the tasks through the Tasks state manager, it also tries to restore the tasks individually.
comment:9 by , 18 months ago
| Resolution: | → fixed |
|---|---|
| Status: | reopened → closed |
OK, this should actually be fixed now but if you see the error again please share that session with me and reopen this ticket so I can continue accounting for possibly corrupt data. To be honest, the Tasks module needs a rewrite at some point.
Previously restored jobs may not have gotten a next_check, so
the module now assigns "1" if any code attempts to access next_check
and it is none. Badly saved jobs may also have their states set to
RUNNING but also have a start and end time. We now prefer the state
of the job over the implicit check of start and end, but still do
the check as a fallback. Finally, if the client attempts to check the
status of a job that is no longer running we set the state of the job
to FINISHED and warn the user to save their results this time, as the
next time the job is restored Plato may have deleted the results.
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