Problems with PDBDEV 12: cannot save IHMModel in session; shader does not have uniform variable "projection_matrix"

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-11-26)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 0.91 (2019-11-26)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/petrawendler/Downloads/PDBDEV_00000010.cif format IHM

Summary of feedback from opening
/Users/petrawendler/Downloads/PDBDEV_00000010.cif  
---  
notes | Fetching zip 10.5281/zenodo.1194547 npc2018-master.zip from
https://zenodo.org/record/1194547/files/npc2018-master.zip  
Fetching zip 10.5281/zenodo.1194547 data_nic96.zip from
https://zenodo.org/record/1194547/files/data_nic96.zip  
Fetching zip 10.5281/zenodo.1194547 validation.zip from
https://zenodo.org/record/1194547/files/validation.zip  
Fetching zip 10.5281/zenodo.1194547 em_gmm_model.zip from
https://zenodo.org/record/1194547/files/em_gmm_model.zip  
Fetching compressed map 7321 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-7321/map/emd_7321.map.gz  
result 1 Missing residues for 10 of 1073 DSS crosslinks:
/BI:392,/BI:407,/BJ:134,/BJ:144,/BJ:248...  
aligned Nic96.1.pdb A, 564 residues, rms 0.0004982  
aligned Nic96.2.pdb A, 564 residues, rms 0.000507  
aligned Nic96.1.pdb A, 564 residues, rms 0.0004985  
aligned Nic96.2.pdb A, 564 residues, rms 0.0005068  
aligned Nup145N_3kep_AB_459_605r_ca.pdb A, 147 residues, rms 0.0005012  
aligned Nup145N_3kep_AB_459_605r_ca.pdb B, 147 residues, rms 0.000498  
aligned Cluster2_noBEA.pdb A, 654 residues, rms 26.32  
aligned Cluster2_noBEA.pdb B, 164 residues, rms 0.0007257  
aligned Cluster2_noBEA.pdb C, 169 residues, rms 0.0007137  
aligned Cluster2_noBEA.pdb D, 217 residues, rms 0.0007187  
aligned Cluster2_noBEA.pdb A, 654 residues, rms 24.64  
aligned Cluster2_noBEA.pdb B, 164 residues, rms 0.0006805  
aligned Cluster2_noBEA.pdb C, 169 residues, rms 0.0007036  
aligned Cluster2_noBEA.pdb D, 217 residues, rms 0.000702  
aligned Cluster2_noBEA.pdb A, 654 residues, rms 26.32  
aligned Cluster2_noBEA.pdb B, 164 residues, rms 0.0007238  
aligned Cluster2_noBEA.pdb C, 169 residues, rms 0.0007164  
aligned Cluster2_noBEA.pdb D, 217 residues, rms 0.0007187  
aligned Cluster2_noBEA.pdb A, 654 residues, rms 24.64  
aligned Cluster2_noBEA.pdb B, 164 residues, rms 0.0006801  
aligned Cluster2_noBEA.pdb C, 169 residues, rms 0.0007043  
aligned Cluster2_noBEA.pdb D, 217 residues, rms 0.0007007  
aligned Nup157_0_noBEA.pdb A, 1113 residues, rms 27.6  
aligned Nup170_0_noBEA.pdb A, 1117 residues, rms 20.66  
aligned Nup188_2_noBEA.pdb A, 1360 residues, rms 0.0007076  
aligned Nup192_4_noBEA.pdb A, 1490 residues, rms 0.0007111  
aligned Nup157_0_noBEA.pdb A, 1113 residues, rms 27.6  
aligned Nup170_0_noBEA.pdb A, 1117 residues, rms 20.66  
aligned Nup188_2_noBEA.pdb A, 1360 residues, rms 0.0007084  
aligned Nup192_4_noBEA.pdb A, 1490 residues, rms 0.0007105  
aligned Nup53_9_noBEA.pdb A, 94 residues, rms 0.0006814  
aligned Nup59_0_noBEA.pdb A, 94 residues, rms 0.00069  
aligned Nup53_9_noBEA.pdb A, 94 residues, rms 0.0006814  
aligned Nup59_0_noBEA.pdb A, 94 residues, rms 0.0006906  
aligned Nup100_3nf5_AB_816_958ca.pdb A, 143 residues, rms 0.0005012  
aligned Nup100_3nf5_AB_816_958ca.pdb B, 143 residues, rms 0.0005038  
aligned Nup116ca.pdb I, 146 residues, rms 0.0005029  
aligned Nup116ca.pdb J, 146 residues, rms 0.000506  
Fetching zip 10.5281/zenodo.1194547 MRC-1spoke.zip from
https://zenodo.org/record/1194547/files/MRC-1spoke.zip  
  
Opened IHM file /Users/petrawendler/Downloads/PDBDEV_00000010.cif  
6 xray and nmr models  
32 comparative models  
17 sequence alignments  
25 templates  
1073 DSS crosslinks  
3 electron microscopy images  
1 sphere models  
68 localization maps  
Entities and chains for PDBDEV_00000010  
---  
Entity | Chains  
Dyn2 | O, P  
Gle1 | BJ  
Mlp1 | BP  
Mlp2 | BQ  
Ndc1 | AW, BB  
Nic96 | W, AA, AE, AI  
Nsp1 | U, V, X, AB, AF, AJ  
Nup1 | BM  
Nup100 | BE, BF  
Nup116 | BG, BH  
Nup120 | C, J  
Nup133 | D, K  
Nup145 | BK, BL  
Nup145c | E, L  
Nup157 | AM, AQ  
Nup159 | S, T  
Nup170 | AN, AR  
Nup188 | AO, AS  
Nup192 | AP, AT  
Nup42 | BI  
Nup49 | Y, AC, AG, AK  
Nup53 | AU, AZ  
Nup57 | Z, AD, AH, AL  
Nup59 | AV, BA  
Nup60 | BN, BO  
Nup82 | Q, R  
Nup84 | A, H  
Nup85 | B, I  
Pom152 | AY, BD  
Pom34 | AX, BC  
Sec13 | G, N  
Seh1 | F, M  
  
Nic96.2.pdb A title:  
NIC96 CTD domain taken from PDB entry 2QX5, rotated and translated to better
align with other starting models [more info...]  
  
Nic96.1.pdb A title:  
NIC96 CTD domain taken from PDB entry 2QX5, rotated and translated to better
align with other starting models [more info...]  
  
Nic96.2.pdb A title:  
NIC96 CTD domain taken from PDB entry 2QX5, rotated and translated to better
align with other starting models [more info...]  
  
Nup145N_3kep_AB_459_605r_ca.pdb A title:  
NUP145 structure from PDB entry 3KEP, Ca atoms ONLY [more info...]  
  
Nup145N_3kep_AB_459_605r_ca.pdb B title:  
NUP145 structure from PDB entry 3KEP, Ca atoms ONLY [more info...]  
  
Nic96.1.pdb A title:  
NIC96 CTD domain taken from PDB entry 2QX5, rotated and translated to better
align with other starting models [more info...]  
  

> volume #1.2.2 level 58.99,0 level 219,0.8 level 255,1

> volume #1.2.3 level 55.01,0 level 227,0.8 level 255,1

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> ui mousemode rightMode pivot

> show #!1.1 models

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> show #!1 models

> close session

> open /Users/petrawendler/Downloads/PDBDEV_00000011.cif format IHM

Summary of feedback from opening
/Users/petrawendler/Downloads/PDBDEV_00000011.cif  
---  
notes | result 1 Missing residues for 10 of 1082 DSS crosslinks:
/FQ:392,/FQ:407,/FR:134,/FR:144,/FR:248...  
aligned Nic96.1.pdb A, 564 residues, rms 0.0004982  
aligned Nic96.2.pdb A, 564 residues, rms 0.000507  
aligned Nic96.1.pdb A, 564 residues, rms 0.000502  
aligned Nic96.2.pdb A, 564 residues, rms 0.0004898  
aligned Nic96.1.pdb A, 564 residues, rms 0.000502  
aligned Nic96.2.pdb A, 564 residues, rms 0.0004898  
aligned Nic96.1.pdb A, 564 residues, rms 0.0004985  
aligned Nic96.2.pdb A, 564 residues, rms 0.0005068  
aligned Nic96.1.pdb A, 564 residues, rms 0.000502  
aligned Nic96.2.pdb A, 564 residues, rms 0.0004898  
aligned Nic96.1.pdb A, 564 residues, rms 0.000502  
aligned Nic96.2.pdb A, 564 residues, rms 0.0004898  
aligned Nup145N_3kep_AB_459_605r_ca.pdb A, 147 residues, rms 0.0005012  
aligned Nup145N_3kep_AB_459_605r_ca.pdb B, 147 residues, rms 0.000498  
aligned Nup145N_3kep_AB_459_605r_ca.pdb A, 147 residues, rms 0.0004974  
aligned Nup145N_3kep_AB_459_605r_ca.pdb B, 147 residues, rms 0.0004892  
aligned Nup145N_3kep_AB_459_605r_ca.pdb A, 147 residues, rms 0.0004974  
aligned Nup145N_3kep_AB_459_605r_ca.pdb B, 147 residues, rms 0.0004892  
aligned Cluster2_noBEA.pdb A, 654 residues, rms 26.32  
aligned Cluster2_noBEA.pdb B, 164 residues, rms 0.0007257  
aligned Cluster2_noBEA.pdb C, 169 residues, rms 0.0007137  
aligned Cluster2_noBEA.pdb D, 217 residues, rms 0.0007187  
aligned Cluster2_noBEA.pdb A, 654 residues, rms 24.64  
aligned Cluster2_noBEA.pdb B, 164 residues, rms 0.0006805  
aligned Cluster2_noBEA.pdb C, 169 residues, rms 0.0007036  
aligned Cluster2_noBEA.pdb D, 217 residues, rms 0.000702  
aligned Cluster2_noBEA.pdb A, 654 residues, rms 26.32  
aligned Cluster2_noBEA.pdb B, 164 residues, rms 0.0007196  
aligned Cluster2_noBEA.pdb C, 169 residues, rms 0.0007074  
aligned Cluster2_noBEA.pdb D, 217 residues, rms 0.000704  
aligned Cluster2_noBEA.pdb A, 654 residues, rms 24.64  
aligned Cluster2_noBEA.pdb B, 164 residues, rms 0.0006759  
aligned Cluster2_noBEA.pdb C, 169 residues, rms 0.0007043  
aligned Cluster2_noBEA.pdb D, 217 residues, rms 0.0006902  
aligned Cluster2_noBEA.pdb A, 654 residues, rms 26.32  
aligned Cluster2_noBEA.pdb B, 164 residues, rms 0.0007196  
aligned Cluster2_noBEA.pdb C, 169 residues, rms 0.0007074  
aligned Cluster2_noBEA.pdb D, 217 residues, rms 0.000704  
aligned Cluster2_noBEA.pdb A, 654 residues, rms 24.64  
aligned Cluster2_noBEA.pdb B, 164 residues, rms 0.0006759  
aligned Cluster2_noBEA.pdb C, 169 residues, rms 0.0007043  
aligned Cluster2_noBEA.pdb D, 217 residues, rms 0.0006902  
aligned Cluster2_noBEA.pdb A, 654 residues, rms 26.32  
aligned Cluster2_noBEA.pdb B, 164 residues, rms 0.0007238  
aligned Cluster2_noBEA.pdb C, 169 residues, rms 0.0007164  
aligned Cluster2_noBEA.pdb D, 217 residues, rms 0.0007187  
aligned Cluster2_noBEA.pdb A, 654 residues, rms 24.64  
aligned Cluster2_noBEA.pdb B, 164 residues, rms 0.0006801  
aligned Cluster2_noBEA.pdb C, 169 residues, rms 0.0007043  
aligned Cluster2_noBEA.pdb D, 217 residues, rms 0.0007007  
aligned Cluster2_noBEA.pdb A, 654 residues, rms 26.32  
aligned Cluster2_noBEA.pdb B, 164 residues, rms 0.0007196  
aligned Cluster2_noBEA.pdb C, 169 residues, rms 0.0007074  
aligned Cluster2_noBEA.pdb D, 217 residues, rms 0.000704  
aligned Cluster2_noBEA.pdb A, 654 residues, rms 24.64  
aligned Cluster2_noBEA.pdb B, 164 residues, rms 0.0006759  
aligned Cluster2_noBEA.pdb C, 169 residues, rms 0.0007043  
aligned Cluster2_noBEA.pdb D, 217 residues, rms 0.0006902  
aligned Cluster2_noBEA.pdb A, 654 residues, rms 26.32  
aligned Cluster2_noBEA.pdb B, 164 residues, rms 0.0007196  
aligned Cluster2_noBEA.pdb C, 169 residues, rms 0.0007074  
aligned Cluster2_noBEA.pdb D, 217 residues, rms 0.000704  
aligned Cluster2_noBEA.pdb A, 654 residues, rms 24.64  
aligned Cluster2_noBEA.pdb B, 164 residues, rms 0.0006759  
aligned Cluster2_noBEA.pdb C, 169 residues, rms 0.0007043  
aligned Cluster2_noBEA.pdb D, 217 residues, rms 0.0006902  
aligned Nup157_0_noBEA.pdb A, 1113 residues, rms 27.6  
aligned Nup170_0_noBEA.pdb A, 1117 residues, rms 20.66  
aligned Nup188_2_noBEA.pdb A, 1360 residues, rms 0.0007076  
aligned Nup192_4_noBEA.pdb A, 1490 residues, rms 0.0007111  
aligned Nup157_0_noBEA.pdb A, 1113 residues, rms 27.6  
aligned Nup170_0_noBEA.pdb A, 1117 residues, rms 20.66  
aligned Nup188_2_noBEA.pdb A, 1360 residues, rms 0.0007022  
aligned Nup192_4_noBEA.pdb A, 1490 residues, rms 0.000703  
aligned Nup157_0_noBEA.pdb A, 1113 residues, rms 27.6  
aligned Nup170_0_noBEA.pdb A, 1117 residues, rms 20.66  
aligned Nup188_2_noBEA.pdb A, 1360 residues, rms 0.0007022  
aligned Nup192_4_noBEA.pdb A, 1490 residues, rms 0.000703  
aligned Nup157_0_noBEA.pdb A, 1113 residues, rms 27.6  
aligned Nup170_0_noBEA.pdb A, 1117 residues, rms 20.66  
aligned Nup188_2_noBEA.pdb A, 1360 residues, rms 0.0007084  
aligned Nup192_4_noBEA.pdb A, 1490 residues, rms 0.0007105  
aligned Nup157_0_noBEA.pdb A, 1113 residues, rms 27.6  
aligned Nup170_0_noBEA.pdb A, 1117 residues, rms 20.66  
aligned Nup188_2_noBEA.pdb A, 1360 residues, rms 0.0007022  
aligned Nup192_4_noBEA.pdb A, 1490 residues, rms 0.000703  
aligned Nup157_0_noBEA.pdb A, 1113 residues, rms 27.6  
aligned Nup170_0_noBEA.pdb A, 1117 residues, rms 20.66  
aligned Nup188_2_noBEA.pdb A, 1360 residues, rms 0.0007022  
aligned Nup192_4_noBEA.pdb A, 1490 residues, rms 0.000703  
aligned Nup53_9_noBEA.pdb A, 94 residues, rms 0.0006814  
aligned Nup59_0_noBEA.pdb A, 94 residues, rms 0.00069  
aligned Nup53_9_noBEA.pdb A, 94 residues, rms 0.0007165  
aligned Nup59_0_noBEA.pdb A, 94 residues, rms 0.0007164  
aligned Nup53_9_noBEA.pdb A, 94 residues, rms 0.0007165  
aligned Nup59_0_noBEA.pdb A, 94 residues, rms 0.0007164  
aligned Nup53_9_noBEA.pdb A, 94 residues, rms 0.0006814  
aligned Nup59_0_noBEA.pdb A, 94 residues, rms 0.0006906  
aligned Nup53_9_noBEA.pdb A, 94 residues, rms 0.0007165  
aligned Nup59_0_noBEA.pdb A, 94 residues, rms 0.0007164  
aligned Nup53_9_noBEA.pdb A, 94 residues, rms 0.0007165  
aligned Nup59_0_noBEA.pdb A, 94 residues, rms 0.0007164  
aligned Nup100_3nf5_AB_816_958ca.pdb A, 143 residues, rms 0.0005012  
aligned Nup100_3nf5_AB_816_958ca.pdb B, 143 residues, rms 0.0005038  
aligned Nup116ca.pdb I, 146 residues, rms 0.0005029  
aligned Nup116ca.pdb J, 146 residues, rms 0.000506  
aligned Nup100_3nf5_AB_816_958ca.pdb A, 143 residues, rms 0.0005004  
aligned Nup100_3nf5_AB_816_958ca.pdb B, 143 residues, rms 0.0004824  
aligned Nup116ca.pdb I, 146 residues, rms 0.0005086  
aligned Nup116ca.pdb J, 146 residues, rms 0.0005131  
aligned Nup100_3nf5_AB_816_958ca.pdb A, 143 residues, rms 0.0005004  
aligned Nup100_3nf5_AB_816_958ca.pdb B, 143 residues, rms 0.0004824  
aligned Nup116ca.pdb I, 146 residues, rms 0.0005086  
aligned Nup116ca.pdb J, 146 residues, rms 0.0005131  
Fetching zip 10.5281/zenodo.1194547 MRC-3spoke.zip from
https://zenodo.org/record/1194547/files/MRC-3spoke.zip  
  
Opened IHM file /Users/petrawendler/Downloads/PDBDEV_00000011.cif  
18 xray and nmr models  
96 comparative models  
51 sequence alignments  
75 templates  
1082 DSS crosslinks  
3 electron microscopy images  
1 sphere models  
204 localization maps  
Entities and chains for PDBDEV_00000011  
---  
Entity | Chains  
Dyn2 | AQ, AR, AY, AZ, BG, BH  
Gle1 | FR, FX, GD  
Mlp1 | GT, GV, GX  
Mlp2 | GU, GW, GY  
Ndc1 | EK, EP, EU, EZ, FE, FJ  
Nic96 | BO, BS, BW, CA, CE, CI, CM, CQ, CU, CY, DC, DG  
Nsp1 | AW, AX, BE, BF, BM, BN, BP, BT, BX, CB, CF, CJ, CN, CR, CV, CZ, DD, DH  
Nup1 | GG, GL, GQ  
Nup100 | FM, FN, FS, FT, FY, FZ  
Nup116 | FO, FP, FU, FV, GA, GB  
Nup120 | C, J, Q, X, AE, AL  
Nup133 | D, K, R, Y, AF, AM  
Nup145 | GE, GF, GJ, GK, GO, GP  
Nup145c | E, L, S, Z, AG, AN  
Nup157 | DK, DO, DS, DW, EA, EE  
Nup159 | AU, AV, BC, BD, BK, BL  
Nup170 | DL, DP, DT, DX, EB, EF  
Nup188 | DM, DQ, DU, DY, EC, EG  
Nup192 | DN, DR, DV, DZ, ED, EH  
Nup42 | FQ, FW, GC  
Nup49 | BQ, BU, BY, CC, CG, CK, CO, CS, CW, DA, DE, DI  
Nup53 | EI, EN, ES, EX, FC, FH  
Nup57 | BR, BV, BZ, CD, CH, CL, CP, CT, CX, DB, DF, DJ  
Nup59 | EJ, EO, ET, EY, FD, FI  
Nup60 | GH, GI, GM, GN, GR, GS  
Nup82 | AS, AT, BA, BB, BI, BJ  
Nup84 | A, H, O, V, AC, AJ  
Nup85 | B, I, P, W, AD, AK  
Pom152 | EM, ER, EW, FB, FG, FL  
Pom34 | EL, EQ, EV, FA, FF, FK  
Sec13 | G, N, U, AB, AI, AP  
Seh1 | F, M, T, AA, AH, AO  
  
Nic96.1.pdb A title:  
NIC96 CTD domain taken from PDB entry 2QX5, rotated and translated to better
align with other starting models [more info...]  
  
Nic96.2.pdb A title:  
NIC96 CTD domain taken from PDB entry 2QX5, rotated and translated to better
align with other starting models [more info...]  
  
Nic96.1.pdb A title:  
NIC96 CTD domain taken from PDB entry 2QX5, rotated and translated to better
align with other starting models [more info...]  
  
Nic96.2.pdb A title:  
NIC96 CTD domain taken from PDB entry 2QX5, rotated and translated to better
align with other starting models [more info...]  
  
Nic96.1.pdb A title:  
NIC96 CTD domain taken from PDB entry 2QX5, rotated and translated to better
align with other starting models [more info...]  
  
Nic96.2.pdb A title:  
NIC96 CTD domain taken from PDB entry 2QX5, rotated and translated to better
align with other starting models [more info...]  
  
Nic96.1.pdb A title:  
NIC96 CTD domain taken from PDB entry 2QX5, rotated and translated to better
align with other starting models [more info...]  
  
Nic96.2.pdb A title:  
NIC96 CTD domain taken from PDB entry 2QX5, rotated and translated to better
align with other starting models [more info...]  
  
Nic96.1.pdb A title:  
NIC96 CTD domain taken from PDB entry 2QX5, rotated and translated to better
align with other starting models [more info...]  
  
Nic96.2.pdb A title:  
NIC96 CTD domain taken from PDB entry 2QX5, rotated and translated to better
align with other starting models [more info...]  
  
Nic96.1.pdb A title:  
NIC96 CTD domain taken from PDB entry 2QX5, rotated and translated to better
align with other starting models [more info...]  
  
Nic96.2.pdb A title:  
NIC96 CTD domain taken from PDB entry 2QX5, rotated and translated to better
align with other starting models [more info...]  
  
Nup145N_3kep_AB_459_605r_ca.pdb A title:  
NUP145 structure from PDB entry 3KEP, Ca atoms ONLY [more info...]  
  
Nup145N_3kep_AB_459_605r_ca.pdb B title:  
NUP145 structure from PDB entry 3KEP, Ca atoms ONLY [more info...]  
  
Nup145N_3kep_AB_459_605r_ca.pdb A title:  
NUP145 structure from PDB entry 3KEP, Ca atoms ONLY [more info...]  
  
Nup145N_3kep_AB_459_605r_ca.pdb B title:  
NUP145 structure from PDB entry 3KEP, Ca atoms ONLY [more info...]  
  
Nup145N_3kep_AB_459_605r_ca.pdb A title:  
NUP145 structure from PDB entry 3KEP, Ca atoms ONLY [more info...]  
  
Nup145N_3kep_AB_459_605r_ca.pdb B title:  
NUP145 structure from PDB entry 3KEP, Ca atoms ONLY [more info...]  
  

> close session

> open /Users/petrawendler/Downloads/PDBDEV_00000012.cif format IHM

Summary of feedback from opening
/Users/petrawendler/Downloads/PDBDEV_00000012.cif  
---  
notes | result 1 Missing residues for 10 of 1073 DSS crosslinks:
/BI:392,/BI:407,/BJ:134,/BJ:144,/BJ:248...  
result 2 Missing residues for 1073 of 1073 DSS crosslinks:
/A:20,/A:23,/A:154,/A:172,/A:459...  
aligned Nic96.1.pdb A, 564 residues, rms 0.0004982  
aligned Nic96.2.pdb A, 564 residues, rms 0.000507  
aligned Nic96.1.pdb A, 564 residues, rms 0.0004985  
aligned Nic96.2.pdb A, 564 residues, rms 0.0005068  
aligned Nup145N_3kep_AB_459_605r_ca.pdb A, 147 residues, rms 0.0005012  
aligned Nup145N_3kep_AB_459_605r_ca.pdb B, 147 residues, rms 0.000498  
aligned Cluster2_noBEA.pdb A, 654 residues, rms 26.32  
aligned Cluster2_noBEA.pdb B, 164 residues, rms 0.0007257  
aligned Cluster2_noBEA.pdb C, 169 residues, rms 0.0007137  
aligned Cluster2_noBEA.pdb D, 217 residues, rms 0.0007187  
aligned Cluster2_noBEA.pdb A, 654 residues, rms 24.64  
aligned Cluster2_noBEA.pdb B, 164 residues, rms 0.0006805  
aligned Cluster2_noBEA.pdb C, 169 residues, rms 0.0007036  
aligned Cluster2_noBEA.pdb D, 217 residues, rms 0.000702  
aligned Cluster2_noBEA.pdb A, 654 residues, rms 26.32  
aligned Cluster2_noBEA.pdb B, 164 residues, rms 0.0007238  
aligned Cluster2_noBEA.pdb C, 169 residues, rms 0.0007164  
aligned Cluster2_noBEA.pdb D, 217 residues, rms 0.0007187  
aligned Cluster2_noBEA.pdb A, 654 residues, rms 24.64  
aligned Cluster2_noBEA.pdb B, 164 residues, rms 0.0006801  
aligned Cluster2_noBEA.pdb C, 169 residues, rms 0.0007043  
aligned Cluster2_noBEA.pdb D, 217 residues, rms 0.0007007  
aligned Nup157_0_noBEA.pdb A, 1113 residues, rms 27.6  
aligned Nup170_0_noBEA.pdb A, 1117 residues, rms 20.66  
aligned Nup188_2_noBEA.pdb A, 1360 residues, rms 0.0007076  
aligned Nup192_4_noBEA.pdb A, 1490 residues, rms 0.0007111  
aligned Nup157_0_noBEA.pdb A, 1113 residues, rms 27.6  
aligned Nup170_0_noBEA.pdb A, 1117 residues, rms 20.66  
aligned Nup188_2_noBEA.pdb A, 1360 residues, rms 0.0007084  
aligned Nup192_4_noBEA.pdb A, 1490 residues, rms 0.0007105  
aligned Nup53_9_noBEA.pdb A, 94 residues, rms 0.0006814  
aligned Nup59_0_noBEA.pdb A, 94 residues, rms 0.00069  
aligned Nup53_9_noBEA.pdb A, 94 residues, rms 0.0006814  
aligned Nup59_0_noBEA.pdb A, 94 residues, rms 0.0006906  
aligned Nup100_3nf5_AB_816_958ca.pdb A, 143 residues, rms 0.0005012  
aligned Nup100_3nf5_AB_816_958ca.pdb B, 143 residues, rms 0.0005038  
aligned Nup116ca.pdb I, 146 residues, rms 0.0005029  
aligned Nup116ca.pdb J, 146 residues, rms 0.000506  
Fetching zip 10.5281/zenodo.1194547 MRC-8spoke.zip from
https://zenodo.org/record/1194547/files/MRC-8spoke.zip  
Fetching zip 10.5281/zenodo.1194533 npc_fg_2018-master.zip from
https://zenodo.org/record/1194533/files/npc_fg_2018-master.zip  
  
Opened IHM file /Users/petrawendler/Downloads/PDBDEV_00000012.cif  
6 xray and nmr models  
32 comparative models  
17 sequence alignments  
25 templates  
1073 DSS crosslinks  
3 electron microscopy images  
2 sphere models  
744 localization maps  
Entities and chains for PDBDEV_00000012  
---  
Entity | Chains  
Dyn2 | O, P, FL, FM, FT, FU, GB, GC, GJ, GK, GR, GS, GZ, HA, HH, HI  
Gle1 | BJ, QY, RE, RK, RQ, RW, SC, SI  
Mlp1 | BP, TS, TU, TW, TY, UA, UC, UE  
Mlp2 | BQ, TT, TV, TX, TZ, UB, UD, UF  
Ndc1 | AW, BB, OD, OI, ON, OS, OX, PC, PH, PM, PR, PW, QB, QG, QL, QQ  
Nic96 | W, AA, AE, AI, HP, HQ, HX, HY, IF, IG, IN, IO, IV, IW, JD, JE, JL, JM,
JT, JU, KB, KC, KJ, KK, KR, KS, KZ, LA, LH, LI, LP, LQ  
Nsp1 | U, V, X, AB, AF, AJ, FR, FS, FZ, GA, GH, GI, GP, GQ, GX, GY, HF, HG,
HN, HO, HR, HS, HZ, IA, IH, II, IP, IQ, IX, IY, JF, JG, JN, JO, JV, JW, KD,
KE, KL, KM, KT, KU, LB, LC, LJ, LK, LR, LS  
Nup1 | BM, SN, SS, SX, TC, TH, TM, TR  
Nup100 | BE, BF, QT, QU, QZ, RA, RF, RG, RL, RM, RR, RS, RX, RY, SD, SE  
Nup116 | BG, BH, QV, QW, RB, RC, RH, RI, RN, RO, RT, RU, RZ, SA, SF, SG  
Nup120 | C, J, BT, CA, CH, CO, CV, DC, DJ, DQ, DX, EE, EL, ES, EZ, FG  
Nup133 | D, K, BU, CB, CI, CP, CW, DD, DK, DR, DY, EF, EM, ET, FA, FH  
Nup145 | BK, BL, SJ, SK, SO, SP, ST, SU, SY, SZ, TD, TE, TI, TJ, TN, TO  
Nup145c | E, L, BV, CC, CJ, CQ, CX, DE, DL, DS, DZ, EG, EN, EU, FB, FI  
Nup157 | AM, AQ, LX, MB, MF, MJ, MN, MR, MV, MZ, ND, NH, NL, NP, NT, NX  
Nup159 | S, T, FP, FQ, FX, FY, GF, GG, GN, GO, GV, GW, HD, HE, HL, HM  
Nup170 | AN, AR, LY, MC, MG, MK, MO, MS, MW, NA, NE, NI, NM, NQ, NU, NY  
Nup188 | AO, AS, LZ, MD, MH, ML, MP, MT, MX, NB, NF, NJ, NN, NR, NV, NZ  
Nup192 | AP, AT, MA, ME, MI, MM, MQ, MU, MY, NC, NG, NK, NO, NS, NW, OA  
Nup42 | BI, QX, RD, RJ, RP, RV, SB, SH  
Nup49 | Y, AC, AG, AK, HT, HU, IB, IC, IJ, IK, IR, IS, IZ, JA, JH, JI, JP, JQ,
JX, JY, KF, KG, KN, KO, KV, KW, LD, LE, LL, LM, LT, LU  
Nup53 | AU, AZ, OB, OG, OL, OQ, OV, PA, PF, PK, PP, PU, PZ, QE, QJ, QO  
Nup57 | Z, AD, AH, AL, HV, HW, ID, IE, IL, IM, IT, IU, JB, JC, JJ, JK, JR, JS,
JZ, KA, KH, KI, KP, KQ, KX, KY, LF, LG, LN, LO, LV, LW  
Nup59 | AV, BA, OC, OH, OM, OR, OW, PB, PG, PL, PQ, PV, QA, QF, QK, QP  
Nup60 | BN, BO, SL, SM, SQ, SR, SV, SW, TA, TB, TF, TG, TK, TL, TP, TQ  
Nup82 | Q, R, FN, FO, FV, FW, GD, GE, GL, GM, GT, GU, HB, HC, HJ, HK  
Nup84 | A, H, BR, BY, CF, CM, CT, DA, DH, DO, DV, EC, EJ, EQ, EX, FE  
Nup85 | B, I, BS, BZ, CG, CN, CU, DB, DI, DP, DW, ED, EK, ER, EY, FF  
Pom152 | AY, BD, OF, OK, OP, OU, OZ, PE, PJ, PO, PT, PY, QD, QI, QN, QS  
Pom34 | AX, BC, OE, OJ, OO, OT, OY, PD, PI, PN, PS, PX, QC, QH, QM, QR  
Sec13 | G, N, BX, CE, CL, CS, CZ, DG, DN, DU, EB, EI, EP, EW, FD, FK  
Seh1 | F, M, BW, CD, CK, CR, CY, DF, DM, DT, EA, EH, EO, EV, FC, FJ  
  
Nic96.2.pdb A title:  
NIC96 CTD domain taken from PDB entry 2QX5, rotated and translated to better
align with other starting models [more info...]  
  
Nic96.1.pdb A title:  
NIC96 CTD domain taken from PDB entry 2QX5, rotated and translated to better
align with other starting models [more info...]  
  
Nic96.2.pdb A title:  
NIC96 CTD domain taken from PDB entry 2QX5, rotated and translated to better
align with other starting models [more info...]  
  
Nup145N_3kep_AB_459_605r_ca.pdb A title:  
NUP145 structure from PDB entry 3KEP, Ca atoms ONLY [more info...]  
  
Nup145N_3kep_AB_459_605r_ca.pdb B title:  
NUP145 structure from PDB entry 3KEP, Ca atoms ONLY [more info...]  
  
Nic96.1.pdb A title:  
NIC96 CTD domain taken from PDB entry 2QX5, rotated and translated to better
align with other starting models [more info...]  
  

> hide #!1 models

> show #!1 models

> hide #!1.1 models

> show #!1.1 models

> hide #!1.2 models

> show #!1.2 models

> hide #!1.3 models

> show #!1.3 models

> hide #!1.3 models

> show #!1.3 models

> hide #1.2.1 models

> show #1.2.1 models

> hide #!1.2.2 models

> show #!1.2.2 models

> hide #!1.2.3 models

> show #!1.2.3 models

> hide #!1.2.4 models

> show #!1.2.4 models

> hide #1.2.4.1 models

> show #1.2.4.1 models

> hide #!1.2.4 models

> show #!1.2.4 models

> select #1.2.4

2 models selected  

> ui mousemode rightMode translate

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode translate

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode translate

> ui mousemode rightMode "translate selected models"

> ~select #1.2.4

Nothing selected  

> hide #!1.1 models

> show #!1.1 models

> hide #!1.2.4 models

> show #!1.3.2 models

> show #!1.2.4 models

> hide #!1.2.4 models

> show #!1.2.4 models

> select #1.2.4

2 models selected  

> ui mousemode rightMode "translate selected models"

> ~select #1.2.4

Nothing selected  

> hide #!1.2 models

> hide #!1.3 models

> hide #!1.3.1 models

> show #!1.3.1 models

> hide #!1.3.1 models

> hide #!1.3.2 models

> show #!1.3.2 models

> hide #!1.3.2 models

> hide #!1.3 models

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

18480 atoms, 18442 pseudobonds, 76 models selected  

> view

> show #!1.2 models

> hide #!1.2 models

> show #!1.2 models

> show #!1.3 models

> show #!1.3.1 models

> show #!1.3.2 models

> view

> hide #!1 models

> open /Users/petrawendler/Downloads/Chimera/EMDB/emd_7321.map

Opened emd_7321.map, grid size 300,300,300, pixel 5.3, shown at level 0.0684,
step 2, values float32  

> close #2

> open /Users/petrawendler/Downloads/Chimera/EMDB/emd_3103.map

Opened emd_3103.map, grid size 208,208,208, pixel 6.84, shown at level 6.55,
step 1, values float32  

> volume #2 level 3.758

> view #2

> ui mousemode rightMode clip

> select clear

> ui mousemode rightMode clip

> save image /Users/petrawendler/Desktop/TUBerlin/NPC_EM.png width 602 height
> 612

> set bgColor #fbfbfb00

> set bgColor #fcfcfc00

> set bgColor #fefefe00

> set bgColor #ffffff00

> set bgColor #ffffff01

> set bgColor #ffffff06

> set bgColor #ffffff12

> set bgColor #ffffff26

> set bgColor #ffffff36

> set bgColor #ffffff44

> set bgColor #ffffff53

> set bgColor #ffffff5f

> set bgColor #ffffff69

> set bgColor #ffffff74

> set bgColor #ffffff80

> set bgColor #ffffff8b

> set bgColor #ffffff96

> set bgColor #ffffffa3

> set bgColor #ffffffb3

> set bgColor #ffffffb9

> set bgColor #ffffffbf

> set bgColor #ffffffc2

> set bgColor #ffffffc5

> set bgColor #ffffffcc

> set bgColor #ffffffd4

> set bgColor #ffffffdd

> set bgColor #ffffffe7

> set bgColor #fffffff0

> set bgColor #fffffff9

> set bgColor white

> set bgColor #fffffff5

> set bgColor #ffffffcb

> set bgColor #ffffff85

> set bgColor #ffffff4d

> set bgColor #ffffff29

> set bgColor #ffffff00

> save image /Users/petrawendler/Desktop/TUBerlin/NPC_EM.png width 602 height
> 612

> set bgColor #ffffff00

> set bgColor white

> set bgColor #fffffffd

> set bgColor #ffffffec

> set bgColor #ffffffdb

> set bgColor #ffffffb2

> set bgColor #ffffff8b

> set bgColor #ffffff5b

> set bgColor #ffffff35

> set bgColor #ffffff14

> set bgColor #ffffff00

> save /Users/petrawendler/Desktop/TUBerlin/NPC_EM.png transparentBackground
> true

> hide #!2 models

> view #1.1.3

No displayed objects specified.  

> show #1.1.7.3 models

Fetching compressed mmCIF 5cws from http://files.rcsb.org/download/5cws.cif  
Fetching CCD OS from http://ligand-expo.rcsb.org/reports/O/OS/OS.cif  
Template 5cws D title:  
Crystal structure of the intact Chaetomium thermophilum Nsp1-Nup49-Nup57
channel nucleoporin heterotrimer bound to its Nic96 nuclear pore complex
attachment site [more info...]  
  
Sequence '5cwsC_1' differs in length from preceding sequences, and it is
therefore impossible to open these sequences as an alignment. If you want to
open the sequences individually, specify 'false' as the value of the
'alignment' keyword in the 'open' command.  

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

> view #1.1.7.3

> open /Users/petrawendler/Downloads/pdb5hb5.ent.txt

Unrecognized file suffix '.txt'  

> open /Users/petrawendler/Downloads/pdb4q9t.ent

Summary of feedback from opening /Users/petrawendler/Downloads/pdb4q9t.ent  
---  
error | Non-ASCII character on line 3 of PDB file  
warnings | Ignored bad PDB record found on line 1  
???  
Ignored bad PDB record found on line 2  
?>W~?Dx?|?6???????????D?e?;Bu??
?????6?C*?M?+??H????Y??r??%dQzl?t??1K????????X??Z?]??#???#?"?6?^?b????AM???n
?.<b,f??;??????bO??&-?@???B#???'????g???-{?c+?]?S???:????????:?????IHv???,?{?t??E`?oP???????v??f]????o`j
??? ? ?????  
  
PDB file contains non-ASCII character or control character  

> open /Users/petrawendler/Downloads/pdb3i5p.pdb

pdb3i5p.pdb title:  
NUP170(AA979-1502), S.cerevisiae [more info...]  
  
Chain information for pdb3i5p.pdb #3  
---  
Chain | Description  
A | nuclear PORE protein NUP170  
  

> view #3

> save /Users/petrawendler/Desktop/TUBerlin/NPC_xray.png transparentBackground
> true

> open /Users/petrawendler/Downloads/pdb2ebq.pdb

pdb2ebq.pdb title:  
Solution structure of the second ZF-ranbp domain from human nuclear pore
complex protein NUP153 [more info...]  
  
Chain information for pdb2ebq.pdb  
---  
Chain | Description  
4.1/A 4.2/A 4.3/A 4.4/A 4.5/A 4.6/A 4.7/A 4.8/A 4.9/A 4.10/A 4.11/A 4.12/A
4.13/A 4.14/A 4.15/A 4.16/A 4.17/A 4.18/A 4.19/A 4.20/A | nuclear pore complex
protein NUP153  
  

> view #4

> hide #!3 models

> select #4.11/A:45

14 atoms, 13 bonds, 1 model selected  

> select up

47 atoms, 46 bonds, 1 model selected  

> select up

667 atoms, 670 bonds, 1 model selected  

> select up

13340 atoms, 13400 bonds, 20 models selected  

> select down

667 atoms, 670 bonds, 1 model selected  

> color sel bychain

> color sel bychain

> select up

13340 atoms, 13400 bonds, 20 models selected  

> select up

13340 atoms, 13400 bonds, 21 models selected  

> color sel bychain

> select #4.11/A:45

14 atoms, 13 bonds, 1 model selected  

> undo

> undo

> undo

> select clear

> select #4.18/A:47

14 atoms, 13 bonds, 1 model selected  

> select up

47 atoms, 46 bonds, 1 model selected  

> select up

667 atoms, 670 bonds, 1 model selected  

> color sel bychain

> rainbow sel

> mlp sel

Map values for surface "pdb2ebq.pdb_A SES surface": minimum -26.41, mean
-4.25, maximum 21.1  

> mlp sel

Map values for surface "pdb2ebq.pdb_A SES surface": minimum -26.41, mean
-4.25, maximum 21.1  

> undo

> color sel bychain

> show sel cartoons

> hide sel surfaces

> color #4.18 green

> color #4.11 darkgreen

> color #4.8 olive

> color #4.14 dark olive green

> color #4.15 lime

> color #4.7 chartreuse

> color #4.9 seagreen

> color #4.2 medium seagreen

> color #4.5 dark khaki

> select clear

> color #4.12 dark green

> color #4.17 green yellow

> color #4.19 lime green

> color #4.1 dark sea green

> color #4.1 turquoise

> color #4.1 medium aquamarine

> color #4.20 olive drab

> select clear

> save /Users/petrawendler/Desktop/TUBerlin/NPC_NMR.png transparentBackground
> true

> save session /Users/petrawendler/Desktop/TUBerlin/NPC_session.cxs

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 796, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 556, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 288, in process  
return copy_state(data, convert=convert)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 208, in copy_state  
return _copy(data)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 195, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 195, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 195, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 195, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 206, in _copy  
return convert(data)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 287, in convert  
return add_obj(obj, parents)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 142, in from_obj  
(obj_cls.__name__, bundle_info.name))  
RuntimeError: Unable to restore objects of IHMModel class in ChimeraX-IHM
bundle because the class name is not listed in the name to class table for
session restore  
  
RuntimeError: Unable to restore objects of IHMModel class in ChimeraX-IHM
bundle because the class name is not listed in the name to class table for
session restore  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 142, in from_obj  
(obj_cls.__name__, bundle_info.name))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 911, in <lambda>  
save_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_save_cb(sess))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 641, in file_save_cb  
self.save_dialog.display(self, session)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/save_dialog.py", line 139, in display  
fmt.save(session, filename)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 1100, in save  
run(session, cmd)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2837, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 992, in save_session  
save(session, filename, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/save.py", line 61, in save  
fmt.export(session, filename, fmt.nicknames[0], **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/io.py", line 220, in export  
result = self.export_func(session, path, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 796, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 556, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 288, in process  
return copy_state(data, convert=convert)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 208, in copy_state  
return _copy(data)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 195, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 195, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 195, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 195, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/state.py", line 206, in _copy  
return convert(data)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 287, in convert  
return add_obj(obj, parents)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 261, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 142, in from_obj  
(obj_cls.__name__, bundle_info.name))  
RuntimeError: Unable to restore objects of IHMModel class in ChimeraX-IHM
bundle because the class name is not listed in the name to class table for
session restore  
  
RuntimeError: Unable to restore objects of IHMModel class in ChimeraX-IHM
bundle because the class name is not listed in the name to class table for
session restore  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 142, in from_obj  
(obj_cls.__name__, bundle_info.name))  
  
See log for complete Python traceback.  
  

> hide #!4 models

> show #!1 models

> view #1

> hide #!1.1 models

> hide #!1.1.1 models

> hide #!1.1.2 models

> hide #!1.1.3 models

> hide #!1.1.4 models

> hide #!1.1.5 models

> hide #!1.1.6 models

> hide #!1.1.7 models

> hide #!1.1.8 models

> hide #!1.1.9 models

> hide #!1.1.10 models

> hide #!1.1.11 models

> hide #!1.1.12 models

> hide #!1.1.13 models

> hide #!1.1.14 models

> hide #!1.1.15 models

> hide #!1.1.16 models

> hide #!1.1.17 models

> hide #!1.1.18 models

> hide #!1.1.19 models

> hide #!1.1.20 models

> hide #!1.1.21 models

> hide #!1.1.22 models

> hide #!1.1.23 models

> hide #!1.1.24 models

> hide #!1.1.25 models

> hide #!1.1.26 models

> hide #!1.1.27 models

> hide #!1.1.28 models

> hide #!1.1.29 models

> hide #!1.1.30 models

> hide #!1.1.31 models

> hide #!1.1.32 models

> hide #!1.1.33 models

> hide #!1.1.34 models

> hide #!1.2 models

> hide #!1.3.1 models

> show #!1.3.1 models

> hide #!1.3.2 models

> save /Users/petrawendler/Desktop/TUBerlin/NPC_1.png transparentBackground
> true

> show #!1.3.2 models

> hide #!1.3.1 models

> show #!1.3.1 models

> hide #!1.3.2.1 models

> show #!1.3.2.1 models

> hide #!1.3.2.2 models

> hide #!1.3.1.1 models

> hide #!1.3.1.2 models

> show #!1.3.1.1 models

> toolshed show "Side View"

> view orient

> save /Users/petrawendler/Desktop/TUBerlin/NPC_2.png transparentBackground
> true

> show #!1.3.1.2 models

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> lighting shadows true

> lighting shadows false

> lighting flat

> lighting flat

> lighting full

> lighting simple

> lighting simple

> lighting shadows true

> lighting shadows false

> volume #!1.3.1.2.1-544 style solid

An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 73, in draw_new_frame  
view.draw(check_for_changes = False)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 166, in draw  
self._draw_scene(camera, drawings)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 240, in _draw_scene  
draw_transparent(r, transparent_drawings)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1426, in draw_transparent  
lambda: _draw_multiple(drawings, r, Drawing.TRANSPARENT_DRAW_PASS))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 1159, in draw_transparent  
draw()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1426, in <lambda>  
lambda: _draw_multiple(drawings, r, Drawing.TRANSPARENT_DRAW_PASS))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1431, in _draw_multiple  
d.draw(renderer, draw_pass)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/image3d.py", line 705, in draw  
bi.draw(renderer, draw_pass)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/image3d.py", line 1156, in draw  
Image3d.draw(self, renderer, draw_pass)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/image3d.py", line 715, in draw  
pd = self._update_planes(renderer)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/image3d.py", line 485, in _update_planes  
pd = self._update_view_aligned_planes(view_dir)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/image3d.py", line 537, in _update_view_aligned_planes  
pd = self._view_planes()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/image3d.py", line 547, in _view_planes  
pd = ViewAlignedPlanes(self)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/image3d.py", line 986, in __init__  
self._fill_textures()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/image3d.py", line 1035, in _fill_textures  
self._fill_texture_blend(t)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/image3d.py", line 1085, in _fill_texture_blend  
b.blend3d(vap.texture, modulation_color, self.texture)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 1852, in blend3d  
tw.draw()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 3053, in draw  
eb.draw_elements(eb.triangles, offset = offset, count = count)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2578, in draw_elements  
GL.glDrawElements(element_type, ne, GL.GL_UNSIGNED_INT, eo)  
File "src/latebind.pyx", line 32, in
OpenGL_accelerate.latebind.LateBind.__call__  
File "src/wrapper.pyx", line 318, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "src/wrapper.pyx", line 311, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "src/errorchecker.pyx", line 53, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1285,  
description = b'out of memory',  
baseOperation = glDrawElements,  
pyArgs = (  
GL_TRIANGLES,  
6,  
GL_UNSIGNED_INT,  
c_void_p(None),  
),  
cArgs = (  
GL_TRIANGLES,  
6,  
GL_UNSIGNED_INT,  
c_void_p(None),  
),  
cArguments = (  
GL_TRIANGLES,  
6,  
GL_UNSIGNED_INT,  
c_void_p(None),  
)  
)  
  
Exception ignored in: <function Drawing.__del__ at 0x119780290>  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1113, in __del__  
self.delete()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1127, in delete  
raise RuntimeError("Don't have opengl context needed to delete texture from
drawing '%s' because drawing was never drawn" % self.name)  
RuntimeError: Don't have opengl context needed to delete texture from drawing
'Image3D view aligned planes' because drawing was never drawn  
Exception ignored in: <function Texture.__del__ at 0x119e9c830>  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2856, in __del__  
raise OpenGLError('OpenGL texture was not deleted before core.graphics.Texture
destroyed')  
chimerax.core.graphics.opengl.OpenGLError: OpenGL texture was not deleted
before core.graphics.Texture destroyed  

> volume #!1.3.1.2.1-544 style solid

> hide #!1.3.2.1 models

> hide #!1.3.2 models

> hide #!1.3.1.2 models

> hide #!1.3.1.1 models

> hide #!1.3.1 models

> hide #!1.3 models

> hide #!1 models

> show #!1 models

> show #!1.3.1 models

> show #!1.3.1.1 models

> show #!1.3.1.2 models

> show #!1.3.2 models

> hide #!1.3.2 models

> hide #!1.3.1.2 models

> hide #!1.3.1 target m

> hide #!1 models

> show #!2 models

> select up

3955 atoms, 19 pseudobonds, 2 models selected  

> select up

234184 atoms, 233640 pseudobonds, 2 models selected  

> view #2

> view #2

> view #2

> hide #!1.3.1 models

> hide #!1.3.1.1 models

> select #1

259571 atoms, 2815 bonds, 256906 pseudobonds, 2205 models selected  

> ~select #1

Nothing selected  

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #!2 models

> show #!2 models

> show #!3 models

> show #!4 models

> view #3

> view #4

> view #2

> view #!1.3.1 clip false

No displayed objects specified.  

> view #!2 clip false

No displayed objects specified.  

> view #!2.1 clip false

> toolshed show "Side View"

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/sideview/tool.py", line 116, in exposeEvent  
self.render()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/sideview/tool.py", line 276, in render  
self.view.draw()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 166, in draw  
self._draw_scene(camera, drawings)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 214, in _draw_scene  
self._update_projection(camera, vnum)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 834, in _update_projection  
r.set_projection_matrix(pm)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 698, in set_projection_matrix  
p.set_matrix('projection_matrix', pm)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2625, in set_matrix  
GL.glUniformMatrix4fv(self.uniform_id(name), 1, False, matrix)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2636, in uniform_id  
% (name, ', '.join(shader_capability_names(self.capabilities))))  
chimerax.core.graphics.opengl.OpenGLError: Shader does not have uniform
variable "projection_matrix"  
shader capabilities SHADER_BLEND_TEXTURE_3D  
  
chimerax.core.graphics.opengl.OpenGLError: Shader does not have uniform
variable "projection_matrix"  
shader capabilities SHADER_BLEND_TEXTURE_3D  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2636, in uniform_id  
% (name, ', '.join(shader_capability_names(self.capabilities))))  
  
See log for complete Python traceback.  
  

> open /Users/petrawendler/Desktop/TUBerlin/NuclearPore.py

ChimeraX cannot open a regular Chimera session.  
An exporter from Chimera to ChimeraX is being worked on but is not ready at
this time.  

> close session

> open /Users/petrawendler/Desktop/TUBerlin/NuclearPore.py

ChimeraX cannot open a regular Chimera session.  
An exporter from Chimera to ChimeraX is being worked on but is not ready at
this time.  

> open /Users/petrawendler/Downloads/PDBDEV_00000012.cif format IHM

Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  

[_many_ of these deleted]

Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Error processing trigger "model display changed":  
TypeError: 'NoneType' object is not subscriptable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
return self._colors[0]  
  
See log for complete Python traceback.  
  
Summary of feedback from opening
/Users/petrawendler/Downloads/PDBDEV_00000012.cif  
---  
notes | result 1 Missing residues for 10 of 1073 DSS crosslinks:
/BI:392,/BI:407,/BJ:134,/BJ:144,/BJ:248...  
result 2 Missing residues for 1073 of 1073 DSS crosslinks:
/A:20,/A:23,/A:154,/A:172,/A:459...  
aligned Nic96.1.pdb A, 564 residues, rms 0.0004982  
aligned Nic96.2.pdb A, 564 residues, rms 0.000507  
aligned Nic96.1.pdb A, 564 residues, rms 0.0004985  
aligned Nic96.2.pdb A, 564 residues, rms 0.0005068  
aligned Nup145N_3kep_AB_459_605r_ca.pdb A, 147 residues, rms 0.0005012  
aligned Nup145N_3kep_AB_459_605r_ca.pdb B, 147 residues, rms 0.000498  
aligned Cluster2_noBEA.pdb A, 654 residues, rms 26.32  
aligned Cluster2_noBEA.pdb B, 164 residues, rms 0.0007257  
aligned Cluster2_noBEA.pdb C, 169 residues, rms 0.0007137  
aligned Cluster2_noBEA.pdb D, 217 residues, rms 0.0007187  
aligned Cluster2_noBEA.pdb A, 654 residues, rms 24.64  
aligned Cluster2_noBEA.pdb B, 164 residues, rms 0.0006805  
aligned Cluster2_noBEA.pdb C, 169 residues, rms 0.0007036  
aligned Cluster2_noBEA.pdb D, 217 residues, rms 0.000702  
aligned Cluster2_noBEA.pdb A, 654 residues, rms 26.32  
aligned Cluster2_noBEA.pdb B, 164 residues, rms 0.0007238  
aligned Cluster2_noBEA.pdb C, 169 residues, rms 0.0007164  
aligned Cluster2_noBEA.pdb D, 217 residues, rms 0.0007187  
aligned Cluster2_noBEA.pdb A, 654 residues, rms 24.64  
aligned Cluster2_noBEA.pdb B, 164 residues, rms 0.0006801  
aligned Cluster2_noBEA.pdb C, 169 residues, rms 0.0007043  
aligned Cluster2_noBEA.pdb D, 217 residues, rms 0.0007007  
aligned Nup157_0_noBEA.pdb A, 1113 residues, rms 27.6  
aligned Nup170_0_noBEA.pdb A, 1117 residues, rms 20.66  
aligned Nup188_2_noBEA.pdb A, 1360 residues, rms 0.0007076  
aligned Nup192_4_noBEA.pdb A, 1490 residues, rms 0.0007111  
aligned Nup157_0_noBEA.pdb A, 1113 residues, rms 27.6  
aligned Nup170_0_noBEA.pdb A, 1117 residues, rms 20.66  
aligned Nup188_2_noBEA.pdb A, 1360 residues, rms 0.0007084  
aligned Nup192_4_noBEA.pdb A, 1490 residues, rms 0.0007105  
aligned Nup53_9_noBEA.pdb A, 94 residues, rms 0.0006814  
aligned Nup59_0_noBEA.pdb A, 94 residues, rms 0.00069  
aligned Nup53_9_noBEA.pdb A, 94 residues, rms 0.0006814  
aligned Nup59_0_noBEA.pdb A, 94 residues, rms 0.0006906  
aligned Nup100_3nf5_AB_816_958ca.pdb A, 143 residues, rms 0.0005012  
aligned Nup100_3nf5_AB_816_958ca.pdb B, 143 residues, rms 0.0005038  
aligned Nup116ca.pdb I, 146 residues, rms 0.0005029  
aligned Nup116ca.pdb J, 146 residues, rms 0.000506  
Traceback (most recent call last):  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
  
return self._func(self._name, data)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 80, in <lambda>  
  
lambda *args: self._initiate_fill_tree(*args, simple_change=True,
countdown=(0,3)))  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 151, in _initiate_fill_tree  
  
self._fill_tree(always_rebuild=always_rebuild)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 190, in _fill_tree  
  
self._get_info(model, all_selected_models, part_selected_models)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 263, in _get_info  
  
bg_color = self._model_color(obj)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 286, in _model_color  
  
return model.single_color  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 228, in _get_single_color  
  
return self.color if self.vertex_colors is None else None  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
  
return self._colors[0]  
  
TypeError: 'NoneType' object is not subscriptable  
  
  
Traceback (most recent call last):  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
  
return self._func(self._name, data)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 80, in <lambda>  
  
lambda *args: self._initiate_fill_tree(*args, simple_change=True,
countdown=(0,3)))  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 151, in _initiate_fill_tree  
  
self._fill_tree(always_rebuild=always_rebuild)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 190, in _fill_tree  
  
self._get_info(model, all_selected_models, part_selected_models)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 263, in _get_info  
  
bg_color = self._model_color(obj)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 286, in _model_color  
  
return model.single_color  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 228, in _get_single_color  
  
return self.color if self.vertex_colors is None else None  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
  
return self._colors[0]  
  
TypeError: 'NoneType' object is not subscriptable  
  
  
Traceback (most recent call last):  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
  
return self._func(self._name, data)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 80, in <lambda>  
  
lambda *args: self._initiate_fill_tree(*args, simple_change=True,
countdown=(0,3)))  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 151, in _initiate_fill_tree  
  
self._fill_tree(always_rebuild=always_rebuild)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 190, in _fill_tree  
  
self._get_info(model, all_selected_models, part_selected_models)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 263, in _get_info  
  
bg_color = self._model_color(obj)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 286, in _model_color  
  
return model.single_color  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 228, in _get_single_color  
  
return self.color if self.vertex_colors is None else None  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
  
return self._colors[0]  
  
TypeError: 'NoneType' object is not subscriptable  
  
  
Traceback (most recent call last):  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
  
return self._func(self._name, data)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 80, in <lambda>  
  
lambda *args: self._initiate_fill_tree(*args, simple_change=True,
countdown=(0,3)))  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 151, in _initiate_fill_tree  
  
self._fill_tree(always_rebuild=always_rebuild)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 190, in _fill_tree  
  
self._get_info(model, all_selected_models, part_selected_models)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 263, in _get_info  
  
bg_color = self._model_color(obj)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 286, in _model_color  
  
return model.single_color  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 228, in _get_single_color  
  
return self.color if self.vertex_colors is None else None  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
  
return self._colors[0]  
  
TypeError: 'NoneType' object is not subscriptable  
  
  
Traceback (most recent call last):  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
  
return self._func(self._name, data)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 80, in <lambda>  
  
lambda *args: self._initiate_fill_tree(*args, simple_change=True,
countdown=(0,3)))  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 151, in _initiate_fill_tree  
  
self._fill_tree(always_rebuild=always_rebuild)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 190, in _fill_tree  
  
self._get_info(model, all_selected_models, part_selected_models)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 263, in _get_info  
  
bg_color = self._model_color(obj)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 286, in _model_color  
  
return model.single_color  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 228, in _get_single_color  
  
return self.color if self.vertex_colors is None else None  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 530, in get_color  
  
return self._colors[0]  
  
TypeError: 'NoneType' object is not subscriptable  
  
  
2228 messages similar to the above omitted  
  
Opened IHM file /Users/petrawendler/Downloads/PDBDEV_00000012.cif  
6 xray and nmr models  
32 comparative models  
17 sequence alignments  
25 templates  
1073 DSS crosslinks  
3 electron microscopy images  
2 sphere models  
744 localization maps  
Entities and chains for PDBDEV_00000012  
---  
Entity | Chains  
Dyn2 | O, P, FL, FM, FT, FU, GB, GC, GJ, GK, GR, GS, GZ, HA, HH, HI  
Gle1 | BJ, QY, RE, RK, RQ, RW, SC, SI  
Mlp1 | BP, TS, TU, TW, TY, UA, UC, UE  
Mlp2 | BQ, TT, TV, TX, TZ, UB, UD, UF  
Ndc1 | AW, BB, OD, OI, ON, OS, OX, PC, PH, PM, PR, PW, QB, QG, QL, QQ  
Nic96 | W, AA, AE, AI, HP, HQ, HX, HY, IF, IG, IN, IO, IV, IW, JD, JE, JL, JM,
JT, JU, KB, KC, KJ, KK, KR, KS, KZ, LA, LH, LI, LP, LQ  
Nsp1 | U, V, X, AB, AF, AJ, FR, FS, FZ, GA, GH, GI, GP, GQ, GX, GY, HF, HG,
HN, HO, HR, HS, HZ, IA, IH, II, IP, IQ, IX, IY, JF, JG, JN, JO, JV, JW, KD,
KE, KL, KM, KT, KU, LB, LC, LJ, LK, LR, LS  
Nup1 | BM, SN, SS, SX, TC, TH, TM, TR  
Nup100 | BE, BF, QT, QU, QZ, RA, RF, RG, RL, RM, RR, RS, RX, RY, SD, SE  
Nup116 | BG, BH, QV, QW, RB, RC, RH, RI, RN, RO, RT, RU, RZ, SA, SF, SG  
Nup120 | C, J, BT, CA, CH, CO, CV, DC, DJ, DQ, DX, EE, EL, ES, EZ, FG  
Nup133 | D, K, BU, CB, CI, CP, CW, DD, DK, DR, DY, EF, EM, ET, FA, FH  
Nup145 | BK, BL, SJ, SK, SO, SP, ST, SU, SY, SZ, TD, TE, TI, TJ, TN, TO  
Nup145c | E, L, BV, CC, CJ, CQ, CX, DE, DL, DS, DZ, EG, EN, EU, FB, FI  
Nup157 | AM, AQ, LX, MB, MF, MJ, MN, MR, MV, MZ, ND, NH, NL, NP, NT, NX  
Nup159 | S, T, FP, FQ, FX, FY, GF, GG, GN, GO, GV, GW, HD, HE, HL, HM  
Nup170 | AN, AR, LY, MC, MG, MK, MO, MS, MW, NA, NE, NI, NM, NQ, NU, NY  
Nup188 | AO, AS, LZ, MD, MH, ML, MP, MT, MX, NB, NF, NJ, NN, NR, NV, NZ  
Nup192 | AP, AT, MA, ME, MI, MM, MQ, MU, MY, NC, NG, NK, NO, NS, NW, OA  
Nup42 | BI, QX, RD, RJ, RP, RV, SB, SH  
Nup49 | Y, AC, AG, AK, HT, HU, IB, IC, IJ, IK, IR, IS, IZ, JA, JH, JI, JP, JQ,
JX, JY, KF, KG, KN, KO, KV, KW, LD, LE, LL, LM, LT, LU  
Nup53 | AU, AZ, OB, OG, OL, OQ, OV, PA, PF, PK, PP, PU, PZ, QE, QJ, QO  
Nup57 | Z, AD, AH, AL, HV, HW, ID, IE, IL, IM, IT, IU, JB, JC, JJ, JK, JR, JS,
JZ, KA, KH, KI, KP, KQ, KX, KY, LF, LG, LN, LO, LV, LW  
Nup59 | AV, BA, OC, OH, OM, OR, OW, PB, PG, PL, PQ, PV, QA, QF, QK, QP  
Nup60 | BN, BO, SL, SM, SQ, SR, SV, SW, TA, TB, TF, TG, TK, TL, TP, TQ  
Nup82 | Q, R, FN, FO, FV, FW, GD, GE, GL, GM, GT, GU, HB, HC, HJ, HK  
Nup84 | A, H, BR, BY, CF, CM, CT, DA, DH, DO, DV, EC, EJ, EQ, EX, FE  
Nup85 | B, I, BS, BZ, CG, CN, CU, DB, DI, DP, DW, ED, EK, ER, EY, FF  
Pom152 | AY, BD, OF, OK, OP, OU, OZ, PE, PJ, PO, PT, PY, QD, QI, QN, QS  
Pom34 | AX, BC, OE, OJ, OO, OT, OY, PD, PI, PN, PS, PX, QC, QH, QM, QR  
Sec13 | G, N, BX, CE, CL, CS, CZ, DG, DN, DU, EB, EI, EP, EW, FD, FK  
Seh1 | F, M, BW, CD, CK, CR, CY, DF, DM, DT, EA, EH, EO, EV, FC, FJ  
  
Nic96.2.pdb A title:  
NIC96 CTD domain taken from PDB entry 2QX5, rotated and translated to better
align with other starting models [more info...]  
  
Nic96.1.pdb A title:  
NIC96 CTD domain taken from PDB entry 2QX5, rotated and translated to better
align with other starting models [more info...]  
  
Nic96.2.pdb A title:  
NIC96 CTD domain taken from PDB entry 2QX5, rotated and translated to better
align with other starting models [more info...]  
  
Nup145N_3kep_AB_459_605r_ca.pdb A title:  
NUP145 structure from PDB entry 3KEP, Ca atoms ONLY [more info...]  
  
Nup145N_3kep_AB_459_605r_ca.pdb B title:  
NUP145 structure from PDB entry 3KEP, Ca atoms ONLY [more info...]  
  
Nic96.1.pdb A title:  
NIC96 CTD domain taken from PDB entry 2QX5, rotated and translated to better
align with other starting models [more info...]  
  




OpenGL version: 4.1 INTEL-12.10.12
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.

[Tom Goddard]

That is quite a collection of errors. Here is a summary.

1) User tried to save an IHM model in a session file. IHM session saving is not supported and gives a traceback.

2) They opened the massive 8-spoke nuclear pore model pdbdev 12, tried to show some volumes in solid style, and got an "out of memory" error in OpenGL glDrawElements.

3) They then tried to show side view and got a shader error caused by a missing variable SHADER_BLEND_TEXTURE_3D.

4) They then closed the session and tried to open a Chimera 1 session file and got an error message saying that is not supported in ChimeraX.

5) They then reopened nuclear pore pdbdev 12 and errors were spewed on every frame draw from trying to render a closed drawing (self._colors = None).

[Tom Goddard]

Response.

1) IHM does not support session saving. It would be a good bit of work to add and we have no funding for it. I've made another ticket #2662 to note we would like IHM session saving.

2) Out of graphics memory. We could try to catch that error and do something, but I'm not sure what can be done at that point.

3) This is a real bug in our OpenGL code where it was trying to set the projection_matrix variable in a shader that doesn't have that variable. The bug could only occur because of bug 2 which left this weird shader (used for blending volume data) as the current shader. I will fix this problem.

4) Not a bug -- error message explains it, although the user tried repeatedly to open the Chimera 1 session, probably didn't see the error message.

5) Earlier opening pdbdev 12 worked correctly. Now it is spewing errors due to a closed model being drawn. I suspect this is somehow related to the prior errors leaving a dead model in the list of models.

[Tom Goddard]

Fixed opengl bug 3.