Changes between Initial Version and Version 1 of Ticket #17915, comment 7


Ignore:
Timestamp:
Jun 10, 2025, 10:33:45 AM (6 months ago)
Author:
Tom Goddard

Legend:

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  • Ticket #17915, comment 7

    initial v1  
    1 {{{
     1
    22Hi Tom,
    33
    44I re-installed twice. Problem persists. Here is the install log:
    55
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     6Successfully created Boltz Python virtual environment /Users/dobertr/boltz.
     7Now installing Boltz and required packages from PyPi. This may take tens of of minutes since Boltz uses many other packages totaling about 1 Gbyte of disk space including torch, scipy, rdkit, llvmlite, sympy, pandas, numpy, wandb, numba...
     8/Users/dobertr/boltz/bin/python -m pip install git+https://github.com/RBVI/boltz@chimerax
     9Collecting git+https://github.com/RBVI/boltz@chimerax
     10
     11Cloning https://github.com/RBVI/boltz (to revision chimerax) to /private/var/folders/7r/r953prcj6dv89f_b28f_4jyw0000gp/T/pip-req-build-3ab1m_29
     12
     13Running command git clone --filter=blob:none --quiet https://github.com/RBVI/boltz /private/var/folders/7r/r953prcj6dv89f_b28f_4jyw0000gp/T/pip-req-build-3ab1m_29
     14
     15Running command git checkout -b chimerax --track origin/chimerax
     16
     17Switched to a new branch 'chimerax'
     18
     19branch 'chimerax' set up to track 'origin/chimerax'.
     20
     21Resolved https://github.com/RBVI/boltz to commit ca6c444937381392e979c1c26db72dce7963e480
     22
     23Installing build dependencies: started
     24
     25Installing build dependencies: finished with status 'done'
     26
     27Getting requirements to build wheel: started
     28
     29Getting requirements to build wheel: finished with status 'done'
     30
     31Preparing metadata (pyproject.toml): started
     32
     33Preparing metadata (pyproject.toml): finished with status 'done'
     34
     35Collecting torch>=2.2 (from boltz==1.0.0)
     36
     37Using cached torch-2.7.1-cp311-none-macosx_11_0_arm64.whl (68.6 MB)
     38
     39Requirement already satisfied: numpy<2.0,>=1.26 in /Applications/ChimeraX-1.10-rc2025.06.04.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from boltz==1.0.0) (1.26.4)
     40
     41Collecting hydra-core==1.3.2 (from boltz==1.0.0)
     42
     43Using cached hydra_core-1.3.2-py3-none-any.whl (154 kB)
     44
     45Collecting pytorch-lightning==2.4.0 (from boltz==1.0.0)
     46
     47Using cached pytorch_lightning-2.4.0-py3-none-any.whl (815 kB)
     48
     49Collecting rdkit>=2024.3.2 (from boltz==1.0.0)
     50
     51Using cached rdkit-2025.3.2-cp311-cp311-macosx_11_0_arm64.whl (28.0 MB)
     52
     53Collecting dm-tree==0.1.8 (from boltz==1.0.0)
     54
     55Using cached dm_tree-0.1.8-cp311-cp311-macosx_11_0_arm64.whl (110 kB)
     56
     57Requirement already satisfied: requests==2.32.3 in /Applications/ChimeraX-1.10-rc2025.06.04.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from boltz==1.0.0) (2.32.3)
     58
     59Collecting pandas>=2.2.2 (from boltz==1.0.0)
     60
     61Using cached pandas-2.3.0-cp311-cp311-macosx_11_0_arm64.whl (10.8 MB)
     62
     63Collecting types-requests (from boltz==1.0.0)
     64
     65Using cached types_requests-2.32.0.20250602-py3-none-any.whl (20 kB)
     66
     67Collecting einops==0.8.0 (from boltz==1.0.0)
     68
     69Using cached einops-0.8.0-py3-none-any.whl (43 kB)
     70
     71Collecting einx==0.3.0 (from boltz==1.0.0)
     72
     73Using cached einx-0.3.0-py3-none-any.whl (102 kB)
     74
     75Collecting fairscale==0.4.13 (from boltz==1.0.0)
     76
     77Using cached fairscale-0.4.13-py3-none-any.whl
     78
     79Collecting mashumaro==3.14 (from boltz==1.0.0)
     80
     81Using cached mashumaro-3.14-py3-none-any.whl (92 kB)
     82
     83Collecting modelcif==1.2 (from boltz==1.0.0)
     84
     85Using cached modelcif-1.2-py3-none-any.whl
     86
     87Collecting wandb==0.18.7 (from boltz==1.0.0)
     88
     89Using cached wandb-0.18.7-py3-none-macosx_11_0_arm64.whl (15.2 MB)
     90
     91Collecting click==8.1.7 (from boltz==1.0.0)
     92
     93Using cached click-8.1.7-py3-none-any.whl (97 kB)
     94
     95Collecting pyyaml==6.0.2 (from boltz==1.0.0)
     96
     97Using cached PyYAML-6.0.2-cp311-cp311-macosx_11_0_arm64.whl (172 kB)
     98
     99Collecting biopython==1.84 (from boltz==1.0.0)
     100
     101Using cached biopython-1.84-cp311-cp311-macosx_11_0_arm64.whl (2.7 MB)
     102
     103Collecting scipy==1.13.1 (from boltz==1.0.0)
     104
     105Using cached scipy-1.13.1-cp311-cp311-macosx_12_0_arm64.whl (30.3 MB)
     106
     107Collecting numba==0.61.0 (from boltz==1.0.0)
     108
     109Using cached numba-0.61.0-cp311-cp311-macosx_11_0_arm64.whl (2.8 MB)
     110
     111Collecting sympy (from einx==0.3.0->boltz==1.0.0)
     112
     113Using cached sympy-1.14.0-py3-none-any.whl (6.3 MB)
     114
     115Collecting frozendict (from einx==0.3.0->boltz==1.0.0)
     116
     117Using cached frozendict-2.4.6-py311-none-any.whl (16 kB)
     118
     119Collecting omegaconf<2.4,>=2.2 (from hydra-core==1.3.2->boltz==1.0.0)
     120
     121Using cached omegaconf-2.3.0-py3-none-any.whl (79 kB)
     122
     123Collecting antlr4-python3-runtime==4.9.* (from hydra-core==1.3.2->boltz==1.0.0)
     124
     125Using cached antlr4_python3_runtime-4.9.3-py3-none-any.whl
     126
     127Requirement already satisfied: packaging in /Applications/ChimeraX-1.10-rc2025.06.04.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from hydra-core==1.3.2->boltz==1.0.0) (24.2)
     128
     129Requirement already satisfied: typing-extensions>=4.1.0 in /Applications/ChimeraX-1.10-rc2025.06.04.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from mashumaro==3.14->boltz==1.0.0) (4.14.0)
     130
     131Requirement already satisfied: ihm>=1.7 in /Applications/ChimeraX-1.10-rc2025.06.04.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from modelcif==1.2->boltz==1.0.0) (2.2)
     132
     133Collecting llvmlite<0.45,>=0.44.0dev0 (from numba==0.61.0->boltz==1.0.0)
     134
     135Using cached llvmlite-0.44.0-cp311-cp311-macosx_11_0_arm64.whl (26.2 MB)
     136
     137Collecting tqdm>=4.57.0 (from pytorch-lightning==2.4.0->boltz==1.0.0)
     138
     139Using cached tqdm-4.67.1-py3-none-any.whl (78 kB)
     140
     141Collecting fsspec[http]>=2022.5.0 (from pytorch-lightning==2.4.0->boltz==1.0.0)
     142
     143Using cached fsspec-2025.5.1-py3-none-any.whl (199 kB)
     144
     145Collecting torchmetrics>=0.7.0 (from pytorch-lightning==2.4.0->boltz==1.0.0)
     146
     147Using cached torchmetrics-1.7.2-py3-none-any.whl (962 kB)
     148
     149Collecting lightning-utilities>=0.10.0 (from pytorch-lightning==2.4.0->boltz==1.0.0)
     150
     151Using cached lightning_utilities-0.14.3-py3-none-any.whl (28 kB)
     152
     153Requirement already satisfied: charset-normalizer<4,>=2 in /Applications/ChimeraX-1.10-rc2025.06.04.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from requests==2.32.3->boltz==1.0.0) (3.4.2)
     154
     155Requirement already satisfied: idna<4,>=2.5 in /Applications/ChimeraX-1.10-rc2025.06.04.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from requests==2.32.3->boltz==1.0.0) (3.10)
     156
     157Requirement already satisfied: urllib3<3,>=1.21.1 in /Applications/ChimeraX-1.10-rc2025.06.04.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from requests==2.32.3->boltz==1.0.0) (2.4.0)
     158
     159Requirement already satisfied: certifi>=2017.4.17 in /Applications/ChimeraX-1.10-rc2025.06.04.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from requests==2.32.3->boltz==1.0.0) (2023.11.17)
     160
     161Collecting docker-pycreds>=0.4.0 (from wandb==0.18.7->boltz==1.0.0)
     162
     163Using cached docker_pycreds-0.4.0-py2.py3-none-any.whl (9.0 kB)
     164
     165Collecting gitpython!=3.1.29,>=1.0.0 (from wandb==0.18.7->boltz==1.0.0)
     166
     167Using cached GitPython-3.1.44-py3-none-any.whl (207 kB)
     168
     169Requirement already satisfied: platformdirs in /Applications/ChimeraX-1.10-rc2025.06.04.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from wandb==0.18.7->boltz==1.0.0) (4.3.8)
     170
     171Collecting protobuf!=4.21.0,!=5.28.0,<6,>=3.19.0 (from wandb==0.18.7->boltz==1.0.0)
     172
     173Using cached protobuf-5.29.5-cp38-abi3-macosx_10_9_universal2.whl (418 kB)
     174
     175Requirement already satisfied: psutil>=5.0.0 in /Applications/ChimeraX-1.10-rc2025.06.04.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from wandb==0.18.7->boltz==1.0.0) (7.0.0)
     176
     177Collecting sentry-sdk>=2.0.0 (from wandb==0.18.7->boltz==1.0.0)
     178
     179Using cached sentry_sdk-2.29.1-py2.py3-none-any.whl (341 kB)
     180
     181Collecting setproctitle (from wandb==0.18.7->boltz==1.0.0)
     182
     183Using cached setproctitle-1.3.6-cp311-cp311-macosx_11_0_arm64.whl (11 kB)
     184
     185Requirement already satisfied: setuptools in /Users/dobertr/boltz/lib/python3.11/site-packages (from wandb==0.18.7->boltz==1.0.0) (65.5.0)
     186
     187Requirement already satisfied: python-dateutil>=2.8.2 in /Applications/ChimeraX-1.10-rc2025.06.04.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from pandas>=2.2.2->boltz==1.0.0) (2.9.0.post0)
     188
     189Requirement already satisfied: pytz>=2020.1 in /Applications/ChimeraX-1.10-rc2025.06.04.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from pandas>=2.2.2->boltz==1.0.0) (2025.2)
     190
     191Requirement already satisfied: tzdata>=2022.7 in /Applications/ChimeraX-1.10-rc2025.06.04.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from pandas>=2.2.2->boltz==1.0.0) (2025.2)
     192
     193Requirement already satisfied: Pillow in /Applications/ChimeraX-1.10-rc2025.06.04.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from rdkit>=2024.3.2->boltz==1.0.0) (10.4.0)
     194
     195Requirement already satisfied: filelock in /Applications/ChimeraX-1.10-rc2025.06.04.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from torch>=2.2->boltz==1.0.0) (3.18.0)
     196
     197Requirement already satisfied: networkx in /Applications/ChimeraX-1.10-rc2025.06.04.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from torch>=2.2->boltz==1.0.0) (3.3)
     198
     199Requirement already satisfied: jinja2 in /Applications/ChimeraX-1.10-rc2025.06.04.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from torch>=2.2->boltz==1.0.0) (3.1.6)
     200
     201Requirement already satisfied: six>=1.4.0 in /Applications/ChimeraX-1.10-rc2025.06.04.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from docker-pycreds>=0.4.0->wandb==0.18.7->boltz==1.0.0) (1.16.0)
     202
     203Collecting aiohttp!=4.0.0a0,!=4.0.0a1 (from fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz==1.0.0)
     204
     205Using cached aiohttp-3.12.12-cp311-cp311-macosx_11_0_arm64.whl (469 kB)
     206
     207Collecting gitdb<5,>=4.0.1 (from gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz==1.0.0)
     208
     209Using cached gitdb-4.0.12-py3-none-any.whl (62 kB)
     210
     211Requirement already satisfied: msgpack in /Applications/ChimeraX-1.10-rc2025.06.04.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from ihm>=1.7->modelcif==1.2->boltz==1.0.0) (1.1.0)
     212
     213Collecting mpmath<1.4,>=1.1.0 (from sympy->einx==0.3.0->boltz==1.0.0)
     214
     215Using cached mpmath-1.3.0-py3-none-any.whl (536 kB)
     216
     217Requirement already satisfied: MarkupSafe>=2.0 in /Applications/ChimeraX-1.10-rc2025.06.04.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from jinja2->torch>=2.2->boltz==1.0.0) (3.0.2)
     218
     219Collecting aiohappyeyeballs>=2.5.0 (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz==1.0.0)
     220
     221Using cached aiohappyeyeballs-2.6.1-py3-none-any.whl (15 kB)
     222
     223Collecting aiosignal>=1.1.2 (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz==1.0.0)
     224
     225Using cached aiosignal-1.3.2-py2.py3-none-any.whl (7.6 kB)
     226
     227Collecting attrs>=17.3.0 (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz==1.0.0)
     228
     229Using cached attrs-25.3.0-py3-none-any.whl (63 kB)
     230
     231Collecting frozenlist>=1.1.1 (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz==1.0.0)
     232
     233Using cached frozenlist-1.7.0-cp311-cp311-macosx_11_0_arm64.whl (47 kB)
     234
     235Collecting multidict<7.0,>=4.5 (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz==1.0.0)
     236
     237Using cached multidict-6.4.4-cp311-cp311-macosx_11_0_arm64.whl (37 kB)
     238
     239Collecting propcache>=0.2.0 (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz==1.0.0)
     240
     241Using cached propcache-0.3.2-cp311-cp311-macosx_11_0_arm64.whl (43 kB)
     242
     243Collecting yarl<2.0,>=1.17.0 (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz==1.0.0)
     244
     245Using cached yarl-1.20.1-cp311-cp311-macosx_11_0_arm64.whl (89 kB)
     246
     247Collecting smmap<6,>=3.0.1 (from gitdb<5,>=4.0.1->gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz==1.0.0)
     248
     249Using cached smmap-5.0.2-py3-none-any.whl (24 kB)
     250
     251Building wheels for collected packages: boltz
     252
     253Building wheel for boltz (pyproject.toml): started
     254
     255Building wheel for boltz (pyproject.toml): finished with status 'done'
     256
     257Created wheel for boltz: filename=boltz-1.0.0-py3-none-any.whl size=150846 sha256=4bff148c95022886ca643c7269c3efbd835ed0d5920a108075583370fbdd8bb5
     258
     259Stored in directory: /private/var/folders/7r/r953prcj6dv89f_b28f_4jyw0000gp/T/pip-ephem-wheel-cache-npc7eg89/wheels/cf/72/1c/bb985c095c0d1f3b385f30452dcb2ac8f404a8439c7b383eef
     260
     261Successfully built boltz
     262
     263Installing collected packages: mpmath, dm-tree, antlr4-python3-runtime, types-requests, tqdm, sympy, smmap, setproctitle, sentry-sdk, scipy, rdkit, pyyaml, protobuf, propcache, multidict, mashumaro, llvmlite, lightning-utilities, fsspec, frozenlist, frozendict, einops, docker-pycreds, click, biopython, attrs, aiohappyeyeballs, yarl, torch, pandas, omegaconf, numba, modelcif, gitdb, einx, aiosignal, torchmetrics, hydra-core, gitpython, fairscale, aiohttp, wandb, pytorch-lightning, boltz
     264
     265Attempting uninstall: scipy
     266
     267Found existing installation: scipy 1.14.0
     268
     269Not uninstalling scipy at /Applications/ChimeraX-1.10-rc2025.06.04.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages, outside environment /Users/dobertr/boltz
     270
     271Can't uninstall 'scipy'. No files were found to uninstall.
     272
     273Successfully installed aiohappyeyeballs-2.6.1 aiohttp-3.12.12 aiosignal-1.3.2 antlr4-python3-runtime-4.9.3 attrs-25.3.0 biopython-1.84 boltz-1.0.0 click-8.1.7 dm-tree-0.1.8 docker-pycreds-0.4.0 einops-0.8.0 einx-0.3.0 fairscale-0.4.13 frozendict-2.4.6 frozenlist-1.7.0 fsspec-2025.5.1 gitdb-4.0.12 gitpython-3.1.44 hydra-core-1.3.2 lightning-utilities-0.14.3 llvmlite-0.44.0 mashumaro-3.14 modelcif-1.2 mpmath-1.3.0 multidict-6.4.4 numba-0.61.0 omegaconf-2.3.0 pandas-2.3.0 propcache-0.3.2 protobuf-5.29.5 pytorch-lightning-2.4.0 pyyaml-6.0.2 rdkit-2025.3.2 scipy-1.13.1 sentry-sdk-2.29.1 setproctitle-1.3.6 smmap-5.0.2 sympy-1.14.0 torch-2.7.1 torchmetrics-1.7.2 tqdm-4.67.1 types-requests-2.32.0.20250602 wandb-0.18.7 yarl-1.20.1
     274
     275
     276
     277[notice] A new release of pip is available: 23.1.2 -> 25.1.1
     278
     279[notice] To update, run: /Users/dobertr/boltz/bin/python -m pip install --upgrade pip
     280
     281Successfully installed Boltz.
     282Downloading Boltz model parameters (3.3 GB) and chemical component database (330 MB) to ~/.boltz
     283/Users/dobertr/boltz/bin/python /Applications/ChimeraX-1.10-rc2025.06.04.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/boltz/download_weights_and_ccd.py
     284Downloading the CCD dictionary to /Users/dobertr/.boltz/ccd.pkl. You may change the cache directory with the --cache flag.
     285
     286Downloading the model weights to /Users/dobertr/.boltz/boltz1_conf.ckpt. You may change the cache directory with the --cache flag.
     287
     288Boltz model parameters and CCD database are installed in ~/.boltz
     289Successfully installed Boltz.
     290
    145291Dominik
    146 
    147 On 10.06.25 10:44, Dominik Oberthuer wrote:
    148 >
    149 >
    150 >
    151 >
    152 >> #17915: Boltz structures distorted
    153 >> -------------------------------------------+-------------------------
    154 >>            Reporter:  dominik.oberthuer@\u2026   |      Owner:  Tom Goddard
    155 >>                Type:  defect                |     Status: assigned
    156 >>            Priority:  normal                |  Milestone:
    157 >>           Component:  Structure Prediction  |    Version:
    158 >>          Resolution:                        |   Keywords:
    159 >>          Blocked By:                        |   Blocking:
    160 >> Notify when closed:                        |   Platform:  all
    161 >>             Project:  ChimeraX              |
    162 >> -------------------------------------------+-------------------------
    163 >> Comment (by Tom Goddard):
    164 >>
    165 >>   Hi Dominik,
    166 >>
    167 >>     Thanks for the files.  My Mac M2 machine predicts your
    168 >> protein1.fasta
    169 >>   sequence producing a very reasonable looking protein with ChimeraX
    170 >> Boltz.
    171 >>   Your protein1_chimera.cif has all the residues within a few
    172 >> Angstroms of
    173 >>   the origin. I'll attach the correct prediction.
    174 >>
    175 >>     So something is probably broken with your Boltz installation. 
    176 >> Maybe the
    177 >>   Boltz network parameters (in ~/.boltz) are corrupted.  I suggest you
    178 >>   reinstall Boltz.  Delete directories ~/boltz and ~/.boltz that
    179 >> ChimeraX
    180 >>   created, then start the ChimeraX Boltz tool (menu Tools / Structure
    181 >>   Prediction / Boltz) and press the "Install Boltz" button that should
    182 >>   appear at the bottom of the Boltz panel.  After it has installed
    183 >> Boltz try
    184 >>   your protein1.fasta prediction again.
    185 >>
    186 >>     Let me know if that fixes the problem.
    187 >>
    188 >>       Tom
    189 >
    190 }}}