![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 weeks ago
Closed 4 weeks ago
#19188 closed defect (not a bug)
boltz predict: cannot execute Boltz
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Prediction | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.3.2-arm64-arm-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/bonellpatinoescobar/Desktop/UCSF/Wiita Lab/AlphaFold
> 3/fold_2025_09_26_gorasp2_golgin45_cd8tm/GORASP2-Golgin45-CD8TM.cxs"
Log from Thu Oct 2 11:18:21 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/bonellpatinoescobar/Downloads/fold_2025_09_26_gorasp2_golgin45_cd8tm-2/fold_2025_09_26_gorasp2_golgin45_cd8tm_model_0.cif
Chain information for fold_2025_09_26_gorasp2_golgin45_cd8tm_model_0.cif #1
---
Chain | Description
A | .
B | .
Computing secondary structure
> select /A:1-452
3316 atoms, 3404 bonds, 452 residues, 1 model selected
> select add #1
4067 atoms, 4177 bonds, 551 residues, 1 model selected
> select subtract #1
Nothing selected
> select /A:1-452
3316 atoms, 3404 bonds, 452 residues, 1 model selected
> ui tool show "Color Key"
> ui mousemode right "color key"
> select add #2
3316 atoms, 3404 bonds, 452 residues, 2 models selected
> select subtract #2
3316 atoms, 3404 bonds, 452 residues, 1 model selected
> select add #1
4067 atoms, 4177 bonds, 551 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #2
1 model selected
> select subtract #2
Nothing selected
> hide #2 models
> select /A:1-452
3316 atoms, 3404 bonds, 452 residues, 1 model selected
> ui tool show "Color Actions"
> color sel orange red
> show sel surfaces
> select add #1
4067 atoms, 4177 bonds, 551 residues, 2 models selected
> select subtract #1
1 model selected
> select /B:1-99
751 atoms, 773 bonds, 99 residues, 1 model selected
> select #1/B:1-30
250 atoms, 256 bonds, 30 residues, 1 model selected
> ui tool show "Color Actions"
> color sel cornflower blue
> select /B:1-99
751 atoms, 773 bonds, 99 residues, 1 model selected
> select #1/B:31-99
501 atoms, 516 bonds, 69 residues, 1 model selected
> ui tool show "Color Actions"
> color sel hot pink
> select add #1
4067 atoms, 4177 bonds, 551 residues, 1 model selected
> select subtract #1
1 model selected
> select #1/B:31-99
501 atoms, 516 bonds, 69 residues, 1 model selected
> ui tool show "Color Actions"
> color sel lime
> select add #1
4067 atoms, 4177 bonds, 551 residues, 1 model selected
> select subtract #1
1 model selected
> ui tool show Contacts
> contacts intraMol false ignoreHiddenModels true color #5d9918 log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
136 contacts
atom1 atom2 overlap distance
/B THR 32 CG2 /A ASN 88 OD1 0.808 2.492
/B THR 31 CA /A GLY 94 CA 0.688 3.072
/B THR 10 CG2 /A ARG 174 CD 0.572 3.188
/A ASN 111 ND2 /B ASN 21 ND2 0.558 2.722
/A GLY 94 CA /B LEU 30 O 0.531 2.769
/A LEU 126 O /B HIS 7 CE1 0.457 2.723
/A CYS 173 CB /B PHE 17 CZ 0.388 3.252
/A GLN 93 CG /B THR 31 CG2 0.344 3.416
/A GLY 94 CA /B THR 32 N 0.282 3.238
/B THR 32 CG2 /A LEU 95 CD2 0.256 3.504
/B THR 32 CG2 /A LEU 95 CG 0.247 3.513
/B LEU 27 CA /A ARG 101 CG 0.209 3.551
/B LEU 30 CD1 /A LEU 96 CD1 0.201 3.559
/A VAL 142 CG1 /B ASN 21 CA 0.199 3.561
/B ILE 15 CD1 /A GLU 175 N 0.172 3.348
/B ASN 18 OD1 /A ARG 101 CD 0.148 3.152
/A LEU 20 CD2 /B PHE 17 O 0.140 3.160
/A HIS 18 ND1 /B CYS 20 CB 0.138 3.382
/B ASN 21 CB /A ASN 144 OD1 0.121 3.179
/A VAL 142 CG1 /B ASN 21 CB 0.111 3.649
/B PHE 17 CE1 /A CYS 173 CB 0.088 3.552
/A ARG 174 CB /B TYR 12 CE1 0.074 3.566
/A LEU 59 CD1 /B LEU 30 CD1 0.069 3.691
/A CYS 103 SG /B HIS 22 CB 0.067 3.583
/A ARG 21 CD /B THR 16 OG1 0.052 3.288
/B LEU 30 CD1 /A VAL 98 CG2 0.037 3.723
/B CYS 23 CB /A ARG 101 NH1 0.028 3.492
/B CYS 19 CB /A ALA 139 O 0.021 3.279
/A ASP 51 OD2 /B GLY 25 CA 0.017 3.283
/B ILE 15 CG2 /A TYR 164 CE1 0.015 3.625
/B CYS 20 SG /A CYS 103 SG 0.012 3.128
/B TYR 12 CE1 /A ARG 174 CD 0.011 3.629
/B THR 31 CG2 /A GLN 93 CD 0.009 3.481
/A CYS 103 SG /B HIS 22 C 0.002 3.378
/A GLU 175 O /B THR 10 CA -0.001 3.301
/A ARG 174 CB /B TYR 12 CD1 -0.003 3.643
/A LEU 126 O /B TYR 9 CD2 -0.011 3.191
/B CYS 23 CB /A ARG 101 CZ -0.012 3.502
/A ASN 111 ND2 /B ASN 21 CG -0.013 3.263
/B LEU 30 CD1 /A ILE 100 CD1 -0.014 3.774
/A LEU 20 CD1 /B LEU 27 CD1 -0.026 3.786
/A ARG 174 CD /B TYR 12 OH -0.028 3.368
/B CYS 23 SG /A CYS 103 CB -0.029 3.679
/B ILE 15 O /A ARG 21 CG -0.032 3.332
/A GLY 94 CA /B THR 31 C -0.043 3.533
/B CYS 20 CB /A HIS 18 CE1 -0.043 3.683
/A SER 99 CA /B ILE 28 O -0.057 3.357
/A GLY 138 CA /B CYS 19 CB -0.070 3.830
/B LEU 27 CD1 /A ARG 101 CG -0.079 3.839
/B PHE 17 CD2 /A PRO 35 CB -0.082 3.722
/A ARG 174 CA /B ARG 11 O -0.084 3.384
/A ARG 174 CD /B TYR 12 CZ -0.084 3.574
/B PHE 17 CD1 /A TYR 164 CD1 -0.092 3.612
/B ARG 11 O /A ARG 174 CB -0.094 3.394
/B CYS 23 CA /A CYS 103 SG -0.097 3.747
/B ARG 11 O /A GLU 175 N -0.097 2.757
/A ARG 174 CA /B ILE 15 CD1 -0.101 3.861
/B THR 10 CG2 /A ARG 174 CG -0.102 3.862
/B ILE 15 CD1 /A GLU 175 CB -0.103 3.863
/B HIS 22 CB /A SER 104 O -0.111 3.411
/A GLN 93 CG /B THR 31 CB -0.112 3.872
/A GLY 94 CA /B LEU 30 C -0.113 3.603
/B THR 10 CG2 /A ARG 174 NE -0.125 3.645
/A ARG 101 NE /B GLY 25 O -0.136 2.796
/A LEU 20 O /B PHE 17 N -0.138 2.798
/A ILE 177 O /B TYR 9 CB -0.138 3.438
/A VAL 176 CA /B TYR 9 O -0.141 3.441
/A GLY 94 N /B THR 31 CA -0.143 3.663
/B THR 32 CG2 /A LEU 95 N -0.146 3.666
/A LEU 20 O /B THR 16 CA -0.166 3.466
/A ILE 100 O /B ILE 28 N -0.175 2.835
/B CYS 19 CB /A TYR 164 CD2 -0.177 3.817
/A TYR 164 CB /B PHE 17 CD1 -0.177 3.817
/A GLU 175 O /B ARG 11 N -0.183 2.843
/A ASN 88 OD1 /B THR 32 CB -0.186 3.486
/B LEU 30 O /A GLY 94 C -0.193 3.223
/A GLY 94 CA /B THR 31 N -0.194 3.714
/A PHE 102 O /B ARG 24 N -0.199 2.859
/B PHE 17 CB /A PHE 36 CB -0.203 3.963
/A ARG 174 CB /B THR 10 CG2 -0.205 3.965
/B LEU 27 CD1 /A SER 99 CB -0.205 3.965
/A ILE 100 CD1 /B LEU 30 CG -0.205 3.965
/A ASN 88 CG /B THR 32 CG2 -0.208 3.698
/A PHE 102 O /B CYS 23 CA -0.215 3.515
/A LEU 20 O /B PHE 17 CD2 -0.220 3.400
/B CYS 23 CA /A CYS 103 CB -0.221 3.981
/A PRO 35 CB /B PHE 17 CE2 -0.230 3.870
/A ASP 106 O /B HIS 22 CE1 -0.233 3.413
/B CYS 23 CB /A ARG 101 NE -0.234 3.754
/A ARG 21 CB /B ILE 15 O -0.234 3.534
/A ARG 101 CG /B GLU 26 O -0.245 3.545
/A GLU 175 CB /B ARG 11 CB -0.247 4.007
/B GLY 25 CA /A PHE 102 CB -0.247 4.007
/B CYS 23 SG /A ARG 101 CB -0.253 3.903
/A ARG 101 CG /B LEU 27 N -0.254 3.774
/B ILE 28 O /A ILE 100 N -0.256 2.916
/A LEU 59 CD1 /B LEU 30 CD2 -0.262 4.022
/B LEU 30 O /A LEU 95 N -0.262 2.922
/B THR 32 CG2 /A GLY 94 C -0.273 3.763
/A TYR 164 CD1 /B PHE 17 CE1 -0.279 3.799
/A ILE 100 O /B LEU 27 CA -0.280 3.580
/A TYR 164 CD1 /B ILE 15 CG2 -0.281 3.921
/B TYR 9 O /A ILE 177 N -0.289 2.949
/B ILE 28 O /A ILE 100 CG1 -0.294 3.594
/B PHE 17 CE2 /A PRO 35 CG -0.295 3.935
/B ASN 18 OD1 /A ARG 101 NH1 -0.295 2.955
/A ARG 101 CG /B LEU 27 CB -0.304 4.064
/B CYS 19 CB /A ALA 139 N -0.305 3.825
/A LEU 20 CD1 /B ASN 18 CA -0.310 4.070
/B THR 32 CG2 /A GLY 94 CA -0.318 4.078
/A LEU 20 CD1 /B ASN 18 OD1 -0.320 3.620
/B CYS 19 SG /A TYR 164 CD2 -0.325 3.855
/B THR 16 CA /A ARG 21 CB -0.326 4.086
/B CYS 23 CB /A ARG 101 CD -0.331 4.091
/B THR 31 CG2 /A GLN 93 NE2 -0.331 3.851
/A ARG 101 CB /B CYS 23 CB -0.341 4.101
/A ARG 101 CG /B GLU 26 C -0.343 3.833
/B LEU 30 CD2 /A ILE 100 CD1 -0.354 4.114
/A PHE 36 CE2 /B CYS 19 SG -0.354 3.884
/B CYS 23 SG /A CYS 103 SG -0.354 3.494
/B GLY 25 O /A ARG 101 CZ -0.354 3.384
/A CYS 103 SG /B HIS 22 CA -0.360 4.010
/B ARG 11 O /A GLU 175 CA -0.362 3.662
/A CYS 103 CA /B HIS 22 O -0.365 3.665
/B HIS 7 CE1 /A ALA 127 C -0.366 3.736
/A VAL 98 O /B LEU 30 N -0.368 3.028
/A ILE 100 CG1 /B ILE 28 CB -0.370 4.130
/B ILE 15 CD1 /A ARG 174 C -0.373 3.863
/A GLU 175 CD /B ARG 11 CD -0.377 4.137
/B THR 31 CB /A GLY 94 CA -0.378 4.138
/B PHE 17 CD1 /A TYR 164 CG -0.380 3.750
/A LEU 20 O /B PHE 17 CB -0.382 3.682
/A HIS 18 CE1 /B CYS 20 SG -0.385 3.915
/B PHE 17 CE2 /A CYS 173 CB -0.385 4.025
/A HIS 18 CB /B CYS 23 SG -0.386 4.036
/B ARG 11 O /A GLU 175 CB -0.399 3.699
136 contacts
> contacts intraMol false ignoreHiddenModels true color #5d9918 log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
136 contacts
atom1 atom2 overlap distance
/B THR 32 CG2 /A ASN 88 OD1 0.808 2.492
/B THR 31 CA /A GLY 94 CA 0.688 3.072
/B THR 10 CG2 /A ARG 174 CD 0.572 3.188
/A ASN 111 ND2 /B ASN 21 ND2 0.558 2.722
/A GLY 94 CA /B LEU 30 O 0.531 2.769
/A LEU 126 O /B HIS 7 CE1 0.457 2.723
/A CYS 173 CB /B PHE 17 CZ 0.388 3.252
/A GLN 93 CG /B THR 31 CG2 0.344 3.416
/A GLY 94 CA /B THR 32 N 0.282 3.238
/B THR 32 CG2 /A LEU 95 CD2 0.256 3.504
/B THR 32 CG2 /A LEU 95 CG 0.247 3.513
/B LEU 27 CA /A ARG 101 CG 0.209 3.551
/B LEU 30 CD1 /A LEU 96 CD1 0.201 3.559
/A VAL 142 CG1 /B ASN 21 CA 0.199 3.561
/B ILE 15 CD1 /A GLU 175 N 0.172 3.348
/B ASN 18 OD1 /A ARG 101 CD 0.148 3.152
/A LEU 20 CD2 /B PHE 17 O 0.140 3.160
/A HIS 18 ND1 /B CYS 20 CB 0.138 3.382
/B ASN 21 CB /A ASN 144 OD1 0.121 3.179
/A VAL 142 CG1 /B ASN 21 CB 0.111 3.649
/B PHE 17 CE1 /A CYS 173 CB 0.088 3.552
/A ARG 174 CB /B TYR 12 CE1 0.074 3.566
/A LEU 59 CD1 /B LEU 30 CD1 0.069 3.691
/A CYS 103 SG /B HIS 22 CB 0.067 3.583
/A ARG 21 CD /B THR 16 OG1 0.052 3.288
/B LEU 30 CD1 /A VAL 98 CG2 0.037 3.723
/B CYS 23 CB /A ARG 101 NH1 0.028 3.492
/B CYS 19 CB /A ALA 139 O 0.021 3.279
/A ASP 51 OD2 /B GLY 25 CA 0.017 3.283
/B ILE 15 CG2 /A TYR 164 CE1 0.015 3.625
/B CYS 20 SG /A CYS 103 SG 0.012 3.128
/B TYR 12 CE1 /A ARG 174 CD 0.011 3.629
/B THR 31 CG2 /A GLN 93 CD 0.009 3.481
/A CYS 103 SG /B HIS 22 C 0.002 3.378
/A GLU 175 O /B THR 10 CA -0.001 3.301
/A ARG 174 CB /B TYR 12 CD1 -0.003 3.643
/A LEU 126 O /B TYR 9 CD2 -0.011 3.191
/B CYS 23 CB /A ARG 101 CZ -0.012 3.502
/A ASN 111 ND2 /B ASN 21 CG -0.013 3.263
/B LEU 30 CD1 /A ILE 100 CD1 -0.014 3.774
/A LEU 20 CD1 /B LEU 27 CD1 -0.026 3.786
/A ARG 174 CD /B TYR 12 OH -0.028 3.368
/B CYS 23 SG /A CYS 103 CB -0.029 3.679
/B ILE 15 O /A ARG 21 CG -0.032 3.332
/A GLY 94 CA /B THR 31 C -0.043 3.533
/B CYS 20 CB /A HIS 18 CE1 -0.043 3.683
/A SER 99 CA /B ILE 28 O -0.057 3.357
/A GLY 138 CA /B CYS 19 CB -0.070 3.830
/B LEU 27 CD1 /A ARG 101 CG -0.079 3.839
/B PHE 17 CD2 /A PRO 35 CB -0.082 3.722
/A ARG 174 CA /B ARG 11 O -0.084 3.384
/A ARG 174 CD /B TYR 12 CZ -0.084 3.574
/B PHE 17 CD1 /A TYR 164 CD1 -0.092 3.612
/B ARG 11 O /A ARG 174 CB -0.094 3.394
/B CYS 23 CA /A CYS 103 SG -0.097 3.747
/B ARG 11 O /A GLU 175 N -0.097 2.757
/A ARG 174 CA /B ILE 15 CD1 -0.101 3.861
/B THR 10 CG2 /A ARG 174 CG -0.102 3.862
/B ILE 15 CD1 /A GLU 175 CB -0.103 3.863
/B HIS 22 CB /A SER 104 O -0.111 3.411
/A GLN 93 CG /B THR 31 CB -0.112 3.872
/A GLY 94 CA /B LEU 30 C -0.113 3.603
/B THR 10 CG2 /A ARG 174 NE -0.125 3.645
/A ARG 101 NE /B GLY 25 O -0.136 2.796
/A LEU 20 O /B PHE 17 N -0.138 2.798
/A ILE 177 O /B TYR 9 CB -0.138 3.438
/A VAL 176 CA /B TYR 9 O -0.141 3.441
/A GLY 94 N /B THR 31 CA -0.143 3.663
/B THR 32 CG2 /A LEU 95 N -0.146 3.666
/A LEU 20 O /B THR 16 CA -0.166 3.466
/A ILE 100 O /B ILE 28 N -0.175 2.835
/B CYS 19 CB /A TYR 164 CD2 -0.177 3.817
/A TYR 164 CB /B PHE 17 CD1 -0.177 3.817
/A GLU 175 O /B ARG 11 N -0.183 2.843
/A ASN 88 OD1 /B THR 32 CB -0.186 3.486
/B LEU 30 O /A GLY 94 C -0.193 3.223
/A GLY 94 CA /B THR 31 N -0.194 3.714
/A PHE 102 O /B ARG 24 N -0.199 2.859
/B PHE 17 CB /A PHE 36 CB -0.203 3.963
/A ARG 174 CB /B THR 10 CG2 -0.205 3.965
/B LEU 27 CD1 /A SER 99 CB -0.205 3.965
/A ILE 100 CD1 /B LEU 30 CG -0.205 3.965
/A ASN 88 CG /B THR 32 CG2 -0.208 3.698
/A PHE 102 O /B CYS 23 CA -0.215 3.515
/A LEU 20 O /B PHE 17 CD2 -0.220 3.400
/B CYS 23 CA /A CYS 103 CB -0.221 3.981
/A PRO 35 CB /B PHE 17 CE2 -0.230 3.870
/A ASP 106 O /B HIS 22 CE1 -0.233 3.413
/B CYS 23 CB /A ARG 101 NE -0.234 3.754
/A ARG 21 CB /B ILE 15 O -0.234 3.534
/A ARG 101 CG /B GLU 26 O -0.245 3.545
/A GLU 175 CB /B ARG 11 CB -0.247 4.007
/B GLY 25 CA /A PHE 102 CB -0.247 4.007
/B CYS 23 SG /A ARG 101 CB -0.253 3.903
/A ARG 101 CG /B LEU 27 N -0.254 3.774
/B ILE 28 O /A ILE 100 N -0.256 2.916
/A LEU 59 CD1 /B LEU 30 CD2 -0.262 4.022
/B LEU 30 O /A LEU 95 N -0.262 2.922
/B THR 32 CG2 /A GLY 94 C -0.273 3.763
/A TYR 164 CD1 /B PHE 17 CE1 -0.279 3.799
/A ILE 100 O /B LEU 27 CA -0.280 3.580
/A TYR 164 CD1 /B ILE 15 CG2 -0.281 3.921
/B TYR 9 O /A ILE 177 N -0.289 2.949
/B ILE 28 O /A ILE 100 CG1 -0.294 3.594
/B PHE 17 CE2 /A PRO 35 CG -0.295 3.935
/B ASN 18 OD1 /A ARG 101 NH1 -0.295 2.955
/A ARG 101 CG /B LEU 27 CB -0.304 4.064
/B CYS 19 CB /A ALA 139 N -0.305 3.825
/A LEU 20 CD1 /B ASN 18 CA -0.310 4.070
/B THR 32 CG2 /A GLY 94 CA -0.318 4.078
/A LEU 20 CD1 /B ASN 18 OD1 -0.320 3.620
/B CYS 19 SG /A TYR 164 CD2 -0.325 3.855
/B THR 16 CA /A ARG 21 CB -0.326 4.086
/B CYS 23 CB /A ARG 101 CD -0.331 4.091
/B THR 31 CG2 /A GLN 93 NE2 -0.331 3.851
/A ARG 101 CB /B CYS 23 CB -0.341 4.101
/A ARG 101 CG /B GLU 26 C -0.343 3.833
/B LEU 30 CD2 /A ILE 100 CD1 -0.354 4.114
/A PHE 36 CE2 /B CYS 19 SG -0.354 3.884
/B CYS 23 SG /A CYS 103 SG -0.354 3.494
/B GLY 25 O /A ARG 101 CZ -0.354 3.384
/A CYS 103 SG /B HIS 22 CA -0.360 4.010
/B ARG 11 O /A GLU 175 CA -0.362 3.662
/A CYS 103 CA /B HIS 22 O -0.365 3.665
/B HIS 7 CE1 /A ALA 127 C -0.366 3.736
/A VAL 98 O /B LEU 30 N -0.368 3.028
/A ILE 100 CG1 /B ILE 28 CB -0.370 4.130
/B ILE 15 CD1 /A ARG 174 C -0.373 3.863
/A GLU 175 CD /B ARG 11 CD -0.377 4.137
/B THR 31 CB /A GLY 94 CA -0.378 4.138
/B PHE 17 CD1 /A TYR 164 CG -0.380 3.750
/A LEU 20 O /B PHE 17 CB -0.382 3.682
/A HIS 18 CE1 /B CYS 20 SG -0.385 3.915
/B PHE 17 CE2 /A CYS 173 CB -0.385 4.025
/A HIS 18 CB /B CYS 23 SG -0.386 4.036
/B ARG 11 O /A GLU 175 CB -0.399 3.699
136 contacts
> key pos 0.513104,0.277605 size 0.125184,0.147722
> key pos 0.505192,0.377668 size 0.105778,0.179901
> ui mousemode right translate
> ui tool show Contacts
> contacts saveFile
> "/Users/bonellpatinoescobar/Downloads/fold_2025_09_26_gorasp2_golgin45_cd8tm-2/GORASP2-Golgin45-CD8TM
> contacts" intraMol false ignoreHiddenModels true color #5d9918 log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
136 contacts
atom1 atom2 overlap distance
/B THR 32 CG2 /A ASN 88 OD1 0.808 2.492
/B THR 31 CA /A GLY 94 CA 0.688 3.072
/B THR 10 CG2 /A ARG 174 CD 0.572 3.188
/A ASN 111 ND2 /B ASN 21 ND2 0.558 2.722
/A GLY 94 CA /B LEU 30 O 0.531 2.769
/A LEU 126 O /B HIS 7 CE1 0.457 2.723
/A CYS 173 CB /B PHE 17 CZ 0.388 3.252
/A GLN 93 CG /B THR 31 CG2 0.344 3.416
/A GLY 94 CA /B THR 32 N 0.282 3.238
/B THR 32 CG2 /A LEU 95 CD2 0.256 3.504
/B THR 32 CG2 /A LEU 95 CG 0.247 3.513
/B LEU 27 CA /A ARG 101 CG 0.209 3.551
/B LEU 30 CD1 /A LEU 96 CD1 0.201 3.559
/A VAL 142 CG1 /B ASN 21 CA 0.199 3.561
/B ILE 15 CD1 /A GLU 175 N 0.172 3.348
/B ASN 18 OD1 /A ARG 101 CD 0.148 3.152
/A LEU 20 CD2 /B PHE 17 O 0.140 3.160
/A HIS 18 ND1 /B CYS 20 CB 0.138 3.382
/B ASN 21 CB /A ASN 144 OD1 0.121 3.179
/A VAL 142 CG1 /B ASN 21 CB 0.111 3.649
/B PHE 17 CE1 /A CYS 173 CB 0.088 3.552
/A ARG 174 CB /B TYR 12 CE1 0.074 3.566
/A LEU 59 CD1 /B LEU 30 CD1 0.069 3.691
/A CYS 103 SG /B HIS 22 CB 0.067 3.583
/A ARG 21 CD /B THR 16 OG1 0.052 3.288
/B LEU 30 CD1 /A VAL 98 CG2 0.037 3.723
/B CYS 23 CB /A ARG 101 NH1 0.028 3.492
/B CYS 19 CB /A ALA 139 O 0.021 3.279
/A ASP 51 OD2 /B GLY 25 CA 0.017 3.283
/B ILE 15 CG2 /A TYR 164 CE1 0.015 3.625
/B CYS 20 SG /A CYS 103 SG 0.012 3.128
/B TYR 12 CE1 /A ARG 174 CD 0.011 3.629
/B THR 31 CG2 /A GLN 93 CD 0.009 3.481
/A CYS 103 SG /B HIS 22 C 0.002 3.378
/A GLU 175 O /B THR 10 CA -0.001 3.301
/A ARG 174 CB /B TYR 12 CD1 -0.003 3.643
/A LEU 126 O /B TYR 9 CD2 -0.011 3.191
/B CYS 23 CB /A ARG 101 CZ -0.012 3.502
/A ASN 111 ND2 /B ASN 21 CG -0.013 3.263
/B LEU 30 CD1 /A ILE 100 CD1 -0.014 3.774
/A LEU 20 CD1 /B LEU 27 CD1 -0.026 3.786
/A ARG 174 CD /B TYR 12 OH -0.028 3.368
/B CYS 23 SG /A CYS 103 CB -0.029 3.679
/B ILE 15 O /A ARG 21 CG -0.032 3.332
/A GLY 94 CA /B THR 31 C -0.043 3.533
/B CYS 20 CB /A HIS 18 CE1 -0.043 3.683
/A SER 99 CA /B ILE 28 O -0.057 3.357
/A GLY 138 CA /B CYS 19 CB -0.070 3.830
/B LEU 27 CD1 /A ARG 101 CG -0.079 3.839
/B PHE 17 CD2 /A PRO 35 CB -0.082 3.722
/A ARG 174 CA /B ARG 11 O -0.084 3.384
/A ARG 174 CD /B TYR 12 CZ -0.084 3.574
/B PHE 17 CD1 /A TYR 164 CD1 -0.092 3.612
/B ARG 11 O /A ARG 174 CB -0.094 3.394
/B CYS 23 CA /A CYS 103 SG -0.097 3.747
/B ARG 11 O /A GLU 175 N -0.097 2.757
/A ARG 174 CA /B ILE 15 CD1 -0.101 3.861
/B THR 10 CG2 /A ARG 174 CG -0.102 3.862
/B ILE 15 CD1 /A GLU 175 CB -0.103 3.863
/B HIS 22 CB /A SER 104 O -0.111 3.411
/A GLN 93 CG /B THR 31 CB -0.112 3.872
/A GLY 94 CA /B LEU 30 C -0.113 3.603
/B THR 10 CG2 /A ARG 174 NE -0.125 3.645
/A ARG 101 NE /B GLY 25 O -0.136 2.796
/A LEU 20 O /B PHE 17 N -0.138 2.798
/A ILE 177 O /B TYR 9 CB -0.138 3.438
/A VAL 176 CA /B TYR 9 O -0.141 3.441
/A GLY 94 N /B THR 31 CA -0.143 3.663
/B THR 32 CG2 /A LEU 95 N -0.146 3.666
/A LEU 20 O /B THR 16 CA -0.166 3.466
/A ILE 100 O /B ILE 28 N -0.175 2.835
/B CYS 19 CB /A TYR 164 CD2 -0.177 3.817
/A TYR 164 CB /B PHE 17 CD1 -0.177 3.817
/A GLU 175 O /B ARG 11 N -0.183 2.843
/A ASN 88 OD1 /B THR 32 CB -0.186 3.486
/B LEU 30 O /A GLY 94 C -0.193 3.223
/A GLY 94 CA /B THR 31 N -0.194 3.714
/A PHE 102 O /B ARG 24 N -0.199 2.859
/B PHE 17 CB /A PHE 36 CB -0.203 3.963
/A ARG 174 CB /B THR 10 CG2 -0.205 3.965
/B LEU 27 CD1 /A SER 99 CB -0.205 3.965
/A ILE 100 CD1 /B LEU 30 CG -0.205 3.965
/A ASN 88 CG /B THR 32 CG2 -0.208 3.698
/A PHE 102 O /B CYS 23 CA -0.215 3.515
/A LEU 20 O /B PHE 17 CD2 -0.220 3.400
/B CYS 23 CA /A CYS 103 CB -0.221 3.981
/A PRO 35 CB /B PHE 17 CE2 -0.230 3.870
/A ASP 106 O /B HIS 22 CE1 -0.233 3.413
/B CYS 23 CB /A ARG 101 NE -0.234 3.754
/A ARG 21 CB /B ILE 15 O -0.234 3.534
/A ARG 101 CG /B GLU 26 O -0.245 3.545
/A GLU 175 CB /B ARG 11 CB -0.247 4.007
/B GLY 25 CA /A PHE 102 CB -0.247 4.007
/B CYS 23 SG /A ARG 101 CB -0.253 3.903
/A ARG 101 CG /B LEU 27 N -0.254 3.774
/B ILE 28 O /A ILE 100 N -0.256 2.916
/A LEU 59 CD1 /B LEU 30 CD2 -0.262 4.022
/B LEU 30 O /A LEU 95 N -0.262 2.922
/B THR 32 CG2 /A GLY 94 C -0.273 3.763
/A TYR 164 CD1 /B PHE 17 CE1 -0.279 3.799
/A ILE 100 O /B LEU 27 CA -0.280 3.580
/A TYR 164 CD1 /B ILE 15 CG2 -0.281 3.921
/B TYR 9 O /A ILE 177 N -0.289 2.949
/B ILE 28 O /A ILE 100 CG1 -0.294 3.594
/B PHE 17 CE2 /A PRO 35 CG -0.295 3.935
/B ASN 18 OD1 /A ARG 101 NH1 -0.295 2.955
/A ARG 101 CG /B LEU 27 CB -0.304 4.064
/B CYS 19 CB /A ALA 139 N -0.305 3.825
/A LEU 20 CD1 /B ASN 18 CA -0.310 4.070
/B THR 32 CG2 /A GLY 94 CA -0.318 4.078
/A LEU 20 CD1 /B ASN 18 OD1 -0.320 3.620
/B CYS 19 SG /A TYR 164 CD2 -0.325 3.855
/B THR 16 CA /A ARG 21 CB -0.326 4.086
/B CYS 23 CB /A ARG 101 CD -0.331 4.091
/B THR 31 CG2 /A GLN 93 NE2 -0.331 3.851
/A ARG 101 CB /B CYS 23 CB -0.341 4.101
/A ARG 101 CG /B GLU 26 C -0.343 3.833
/B LEU 30 CD2 /A ILE 100 CD1 -0.354 4.114
/A PHE 36 CE2 /B CYS 19 SG -0.354 3.884
/B CYS 23 SG /A CYS 103 SG -0.354 3.494
/B GLY 25 O /A ARG 101 CZ -0.354 3.384
/A CYS 103 SG /B HIS 22 CA -0.360 4.010
/B ARG 11 O /A GLU 175 CA -0.362 3.662
/A CYS 103 CA /B HIS 22 O -0.365 3.665
/B HIS 7 CE1 /A ALA 127 C -0.366 3.736
/A VAL 98 O /B LEU 30 N -0.368 3.028
/A ILE 100 CG1 /B ILE 28 CB -0.370 4.130
/B ILE 15 CD1 /A ARG 174 C -0.373 3.863
/A GLU 175 CD /B ARG 11 CD -0.377 4.137
/B THR 31 CB /A GLY 94 CA -0.378 4.138
/B PHE 17 CD1 /A TYR 164 CG -0.380 3.750
/A LEU 20 O /B PHE 17 CB -0.382 3.682
/A HIS 18 CE1 /B CYS 20 SG -0.385 3.915
/B PHE 17 CE2 /A CYS 173 CB -0.385 4.025
/A HIS 18 CB /B CYS 23 SG -0.386 4.036
/B ARG 11 O /A GLU 175 CB -0.399 3.699
136 contacts
> save
> /Users/bonellpatinoescobar/Downloads/fold_2025_09_26_gorasp2_golgin45_cd8tm-2/GORASP2-Golgin45-CD8TM.cxs
——— End of log from Thu Oct 2 11:18:21 2025 ———
> view name session-start
opened ChimeraX session
> ui tool show Boltz
> boltz predict protein /A protein /B name
> fold_2025_09_26_gorasp2_golgin45_cd8tm_model_0.cif_A resultsDirectory
> /Users/bonellpatinoescobar/Desktop/UCSF/Wiita Lab/AlphaFold
> 3/fold_2025_09_26_gorasp2_golgin45_cd8tm/Affinity prediction
Expected a keyword
> boltz predict protein /A protein /B name
> fold_2025_09_26_gorasp2_golgin45_cd8tm_model_0.cif_A resultsDirectory
> /Users/bonellpatinoescobar/Desktop/UCSF/Wiita Lab/AlphaFold
> 3/fold_2025_09_26_gorasp2_golgin45_cd8tm/Affinity prediction
Expected a keyword
> boltz predict protein /A protein /B name
> fold_2025_09_26_gorasp2_golgin45_cd8tm_model_0.cif_A resultsDirectory
> /Users/bonellpatinoescobar/Desktop/UCSF/Wiita Lab/AlphaFold
> 3/fold_2025_09_26_gorasp2_golgin45_cd8tm/Affinity prediction installLocation
> "/Users/bonellpatinoescobar/Desktop/UCSF/Wiita Lab/AlphaFold
> 3/fold_2025_09_26_gorasp2_golgin45_cd8tm"
Expected a keyword
> boltz predict protein /A protein /B name
> fold_2025_09_26_gorasp2_golgin45_cd8tm_model_0.cif_A resultsDirectory
> /Users/bonellpatinoescobar/Desktop/UCSF/Wiita Lab/AlphaFold
> 3/fold_2025_09_26_gorasp2_golgin45_cd8tm/Affinity prediction installLocation
> "/Users/bonellpatinoescobar/Desktop/UCSF/Wiita Lab/AlphaFold
> 3/fold_2025_09_26_gorasp2_golgin45_cd8tm"
Expected a keyword
> boltz predict protein /A protein /B name
> fold_2025_09_26_gorasp2_golgin45_cd8tm_model_0.cif_A resultsDirectory
> /Users/bonellpatinoescobar/Desktop/UCSF/Wiita Lab/AlphaFold
> 3/fold_2025_09_26_gorasp2_golgin45_cd8tm/Affinity prediction installLocation
> "/Users/bonellpatinoescobar/Desktop/UCSF/Wiita Lab/AlphaFold
> 3/fold_2025_09_26_gorasp2_golgin45_cd8tm"
Expected a keyword
> boltz predict protein /A protein /B name
> fold_2025_09_26_gorasp2_golgin45_cd8tm_model_0.cif_A resultsDirectory
> /Users/bonellpatinoescobar/Desktop/UCSF/Wiita Lab/AlphaFold
> 3/fold_2025_09_26_gorasp2_golgin45_cd8tm/Affinity prediction device cpu
> installLocation "/Users/bonellpatinoescobar/Desktop/UCSF/Wiita Lab/AlphaFold
> 3/fold_2025_09_26_gorasp2_golgin45_cd8tm"
Expected a keyword
> boltz predict protein /A protein /B name
> fold_2025_09_26_gorasp2_golgin45_cd8tm_model_0.cif_A device cpu
Running Boltz prediction of 2 proteins with 551 residues on cpu
Using multiple sequence alignment server https://api.colabfold.com
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/boltz_gui.py", line 511, in _predict
self._run_prediction(options = ' '.join(options))
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/boltz_gui.py", line 528, in _run_prediction
br = run(self.session, cmd)
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 63, in boltz_predict
br.start(results_directory)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 217, in start
self._run_boltz_local()
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 373, in _run_boltz_local
p = Popen(command, cwd = self._results_directory,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py",
line 1026, in __init__
self._execute_child(args, executable, preexec_fn, close_fds,
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py",
line 1950, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory:
'/Users/bonellpatinoescobar/Desktop/UCSF/Wiita Lab/AlphaFold
3/fold_2025_09_26_gorasp2_golgin45_cd8tm/bin/boltz'
FileNotFoundError: [Errno 2] No such file or directory:
'/Users/bonellpatinoescobar/Desktop/UCSF/Wiita Lab/AlphaFold
3/fold_2025_09_26_gorasp2_golgin45_cd8tm/bin/boltz'
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py",
line 1950, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M4
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac16,1
Model Number: MW2U3LL/A
Chip: Apple M4
Total Number of Cores: 10 (4 performance and 6 efficiency)
Memory: 16 GB
System Firmware Version: 11881.81.4
OS Loader Version: 11881.81.4
Software:
System Software Overview:
System Version: macOS 15.3.2 (24D81)
Kernel Version: Darwin 24.3.0
Time since boot: 16 days, 23 hours, 39 minutes
Graphics/Displays:
Apple M4:
Chipset Model: Apple M4
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.6.1
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.19
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.3
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.10.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.15
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.59.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.3.2
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.1
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
Change History (2)
comment:1 by , 4 weeks ago
| Component: | Unassigned → Structure Prediction |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → boltz predict: cannot execute Boltz |
comment:2 by , 4 weeks ago
| Resolution: | → not a bug |
|---|---|
| Status: | assigned → closed |
Note:
See TracTickets
for help on using tickets.
Seems that the user set the Boltz installation directory to some AlphaFold 3 directory that does not have Boltz installed.