December 2023 - ChimeraX-users - RBVI Mailing Lists

Re: [Chimera-users] Changing threshold value of attributes
by Eric Pettersen 04 Jan '24

04 Jan '24

Hi Abril, There are separate mailing list for Chimera and ChimeraX, so you should send ChimeraX questions to chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> . The problem you ran into has been fixed and the fix is in the 1.7 release candidate, so if you use that then things will work. --Eric Eric Pettersen UCSF Computer Graphics Lab > On Nov 28, 2023, at 10:25 AM, Abril Gijsbers via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear community, > > I want to render my model by attribute and change the thresholds (up and bottom limits). I want to change the 0.3 to 0.1 and the 2.6 to 2.7 (see the figure), this way I can compare the colour intensity with other conditions. > <image.png> > > When I do that, I get the following error. My ignorance in command use limits my understanding. Could someone help me out to understand this? I have a colleague that changes the up and bottom limit with no problem. Why? :( > > ui tool show <> "Render By Attribute" > Traceback (most recent call last): > File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py <http://chimerax-1.6.1.app/Contents/Library/Frameworks/Python.framework/Vers…>", line 759, in _set_value_cb > self._redraw_cb() > File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py <http://chimerax-1.6.1.app/Contents/Library/Frameworks/Python.framework/Vers…>", line 646, in _redraw_cb > self._bins = left + filled_bins + right > ValueError: operands could not be broadcast together with shapes (0,) (157,) > > ValueError: operands could not be broadcast together with shapes (0,) (157,) > > File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py <http://chimerax-1.6.1.app/Contents/Library/Frameworks/Python.framework/Vers…>", line 646, in _redraw_cb > self._bins = left + filled_bins + right > > See log for complete Python traceback. > > Traceback (most recent call last): > File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py <http://chimerax-1.6.1.app/Contents/Library/Frameworks/Python.framework/Vers…>", line 760, in _set_value_cb > self._move_cur_marker(v) > File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py <http://chimerax-1.6.1.app/Contents/Library/Frameworks/Python.framework/Vers…>", line 570, in _move_cur_marker > self._active_markers._update_plot() > File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py <http://chimerax-1.6.1.app/Contents/Library/Frameworks/Python.framework/Vers…>", line 1222, in _update_plot > self._update_marker_coordinates() > File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py <http://chimerax-1.6.1.app/Contents/Library/Frameworks/Python.framework/Vers…>", line 1207, in _update_marker_coordinates > x, y = self._scene_xy(m.xy) > File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py <http://chimerax-1.6.1.app/Contents/Library/Frameworks/Python.framework/Vers…>", line 1090, in _scene_xy > return self.histogram._scene_xy(abs_xy) > File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py <http://chimerax-1.6.1.app/Contents/Library/Frameworks/Python.framework/Vers…>", line 512, in _scene_xy > num_bins = len(self._bins) > TypeError: object of type 'function' has no len() > > TypeError: object of type 'function' has no len() > > File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py <http://chimerax-1.6.1.app/Contents/Library/Frameworks/Python.framework/Vers…>", line 512, in _scene_xy > num_bins = len(self._bins) > > See log for complete Python traceback. > _______________________________________________ > Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu > To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/

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volume amount estimation
by Jesse Hansen 04 Jan '24

04 Jan '24

dear ChimeraX users, We have a tomogram volume (.mrc) which we have segmented different components (stl files; surfaces). Is there any tool available to estimate the volume within each of the cellular components (within each surface)? Either some approximation of the cubic Angstrom/nanometers, or as a percentage of the total tomogram volume. thanks in advance! best Jesse Hansen

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Problems with installation
by Roger Cole 01 Jan '24

01 Jan '24

Good Evening I wanted to asked about compatibility and installation issues. I am currently using a Chromebook with Linux Debian 11 (Bootstrap) and I am trying to get ChimeraX 1.7 installed onto it. I keep coming into errors when I try to run it by the way specified on the site. For info: " Download is a tarball of the chimerax application directory. Make symbolic link to executable in chimerax/bin/ChimeraX. Do not put on path. It may require additional libraries and/or older versions of libraries to be installed. More Info...built: 2023-12-19 02:49:21 PST committed: 2023-12-19 00:36:03 PST size: 584.1 MiB md5: d44f016e787d45621a077b04852ab66c sha256: 005bd0b6942b5e8c3a32ad39bb6ea1118da173217c2c0c51d3e0c665913e6c3a I used the Generic Linux download and with all i could look up with and try to figure out with ChatGPT, I get this when I try to run it: "NOTE: available bundle cache has not been initialized yet WARNING: Traceback (most recent call last): File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 376, in initialize api._api_caller.initialize(api, session, self) File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1294, in initialize return cls._get_func(api, "initialize")(session, bi) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site-packages/chimerax/dicom/__init__.py", line 31, in initialize from .ui.segmentation_mouse_mode import ( File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site-packages/chimerax/dicom/ui/segmentation_mouse_mode.py", line 20, in <module> from .segmentations import SegmentationTool File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site-packages/chimerax/dicom/ui/segmentations.py", line 55, in <module> from ..ui.orthoplanes import Axis File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site-packages/chimerax/dicom/ui/orthoplanes.py", line 51, in <module> from ..graphics import ( File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site-packages/chimerax/dicom/graphics/__init__.py", line 1, in <module> from .view import OrthoplaneView File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site-packages/chimerax/dicom/graphics/view.py", line 6, in <module> from chimerax.graphics import gllist File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site-packages/chimerax/graphics/gllist.py", line 71, in <module> wrap_opengl_routines(globals()) File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site-packages/chimerax/graphics/gllist.py", line 22, in wrap_opengl_routines from OpenGL import GL File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site-packages/OpenGL/GL/__init__.py", line 4, in <module> from OpenGL.GL.VERSION.GL_1_1 import * File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site-packages/OpenGL/GL/VERSION/GL_1_1.py", line 14, in <module> from OpenGL.raw.GL.VERSION.GL_1_1 import * File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site-packages/OpenGL/raw/GL/VERSION/GL_1_1.py", line 7, in <module> from OpenGL.raw.GL import _errors File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site-packages/OpenGL/raw/GL/_errors.py", line 4, in <module> _error_checker = _ErrorChecker( _p, _p.GL.glGetError ) ^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'glGetError' ERROR: Bundle 'ChimeraX-Dicom' custom initialization failed NOTE: Traceback (most recent call last): File "<frozen runpy>", line 198, in _run_module_as_main File "<frozen runpy>", line 88, in _run_code File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site- packages/chimerax/core/__main__.py", line 1069, in <module> exit_code = init(sys.argv) ^^^^^^^^^^^^^^ File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site- packages/chimerax/core/__main__.py", line 722, in init sess.ui.build() File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site- packages/chimerax/ui/gui.py", line 191, in build self.main_window = mw = MainWindow(self, self.session) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site- packages/chimerax/ui/gui.py", line 445, in __init__ self.graphics_window = g = GraphicsWindow(self._stack, ui, stereo) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site- packages/chimerax/ui/graphics.py", line 36, in __init__ oc = OpenGLContext(self, ui.primaryScreen(), use_stereo = stereo) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site- packages/chimerax/graphics/opengl.py", line 60, in __init__ _initialize_pyopengl() # Set global GL module. ^^^^^^^^^^^^^^^^^^^^^^ File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site- packages/chimerax/graphics/opengl.py", line 375, in _initialize_pyopengl import OpenGL.GL File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site- packages/OpenGL/GL/__init__.py", line 4, in <module> from OpenGL.GL.VERSION.GL_1_1 import * File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site- packages/OpenGL/GL/VERSION/GL_1_1.py", line 14, in <module> from OpenGL.raw.GL.VERSION.GL_1_1 import * File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site- packages/OpenGL/raw/GL/VERSION/GL_1_1.py", line 7, in <module> from OpenGL.raw.GL import _errors File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site- packages/OpenGL/raw/GL/_errors.py", line 4, in <module> _error_checker = _ErrorChecker( _p, _p.GL.glGetError ) ^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'glGetError' BUG: AttributeError: 'NoneType' object has no attribute 'glGetError' File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site- packages/OpenGL/raw/GL/_errors.py", line 4, in _error_checker = _ErrorChecker( _p, _p.GL.glGetError ) ^^^^^^^^^^^^^^^^ _See log for complete Python traceback._ NOTE: Exception ignored in: <function OpenGLContext.__del__ at 0x7e24611d5a80> Traceback (most recent call last): File "/home/rogercoleucf/chimerax-1.7/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 85, in __del__ if not self._deleted: ^^^^^^^^^^^^^ AttributeError: 'OpenGLContext' object has no attribute '_deleted'" This is as far as i could get I apologize about the lengthy message, and thank you for any assistance you can give -CJ

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Recover unsaved ChimeraX session?
by André Graça 29 Dec '23

29 Dec '23

Dear all, happy Holidays! I am not very optimistic about this one, but I will just drop the question here and it may simply be that I am unaware of this function: I had a ChimeraX session crashing just when I was about to save it for the first time... is there any way to recover unsaved ChimeraX session, such as temporarily saved files? Thank you, André

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PDB Conversion to Mol2 File Inquiry
by Joel Subach 28 Dec '23

28 Dec '23

Hello Chimerax, I hope you're well:). Towards the above subject, SwissParam has recommended UCSF Chimera to convert my pdb to a Mol2 File for SwissParam subsequent parameterization, however, I could not discover this webpage within your UCSF Chimerax Website? Thanks if you can clarify how I may generate this Mol2 via yout Chimera if able. Best, Joel 🚀

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Error in using alphafold by ChimeraX
by Ping-Hung Chen 陳炳宏 25 Dec '23

25 Dec '23

Hi, I tried to run Alphafold prediction by ChieraX, and it appears below Error. Please cite ColabFold: Making protein folding accessible to all. Nature Methods (2022) if you use these predictions. INFO:__main__:Starting prediction on 2023-12-26 UTC time INFO:__main__:Installing ColabFold on Google Colab virtual machine. --------------------------------------------------------------------------- ImportError Traceback (most recent call last) <ipython-input-8-1833a07b73e1> in <cell line: 329>() 327 remove_from_list(seq_list, 'prokaryote') # Obsolete "prokaryote" flag 328 --> 329 run_prediction(seq_list, use_templates = use_templates, energy_minimize = not dont_minimize) 7 frames /usr/local/lib/python3.10/dist-packages/alphafold/data/mmcif_parsing.py in <module> 22 from absl import logging 23 from Bio import PDB ---> 24 from Bio.Data import SCOPData 25 26 # Type aliases: ImportError: cannot import name 'SCOPData' from 'Bio.Data' (/usr/local/lib/python3.10/dist-packages/Bio/Data/__init__.py) --------------------------------------------------------------------------- Would you like to help me with it? Thank you. Sincerely, PH Ping-Hung Chen, Ph.D., Assistant Professor Institute of Biochemistry and Molecular Biology College of Medicine, National Taiwan University Address: R913, No.1, Sec.1, Ren-Ai Rd., Zhongzheng Dist., Taipei 10051, Taiwan (R.O.C.) E-mail: pinghungchen(a)ntu.edu.tw; phcrose(a)gmail.com Phone: +886 2-23123456 Ext. 88864

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Re: How to save a sequence in an mmCIF file?
by Greg Couch 22 Dec '23

22 Dec '23

To answer the general question, ChimeraX doesn't yet have a way to set the full sequence for a mmCIF entity. See https://www.wwpdb.org/deposition/preparing-pdbx-mmcif-files for how to fix the mmCIF output from various refinement packages. For example, the Phenix has "mmtbx.prepare_pdb_deposition program to create a mmCIF file with the sequence". In this particular case, where the starting structure is an Alphafold prediction with atoms for every residue in the full sequence, you can get the correct sequence into the mmCIF output with the "bestGuess" option. See https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html#mmcif. I'd also recommend, in your case, using the computedSheets option. In older ChimeraX's, you need to run dssp before using computedSheets to get the helix information. In recent ChimeraX's (daily build and 1.7 release candidate), computedSheets will also output the helix information if it wasn't present in the input. Adding a sequence with bestGuess can be deceiving of because missing leading or trailing residues, or gaps of indeterminate length. But in this case, you should be fine. -- Greg On 11/29/23 02:45, Guillaume Gaullier wrote: > *From: *Guillaume Gaullier via ChimeraX-users > <chimerax-users(a)cgl.ucsf.edu> > *Subject: **[chimerax-users] How to save a sequence in an mmCIF file?* > *Date: *November 29, 2023 at 2:45:31 AM PST > *To: *"chimerax-users(a)cgl.ucsf.edu" <chimerax-users(a)cgl.ucsf.edu> > *Reply-To: *Guillaume Gaullier <guillaume.gaullier(a)kemi.uu.se> > > Hello, > > Starting from an AlphaFold prediction, I refined a model against a map > with ISOLDE. I trimmed the segments not supported by any density. The > resulting mmCIF file that I saved now opens with this warning: > > Unknown polymer entity '1' near line 187 > Missing or incomplete entity_poly_seq table. Inferred polymer > connectivity. > > Displaying the sequence of this chain shows the correct numbering > (with jumps in numbering according to missing segments in the > structure), but the sequence of the missing structure segments is not > displayed. > > When I open the fasta file containing the full-length sequence, the > sequence gets automatically associated to the structure, and the > sequence viewer annotates the segments with missing structure > correctly. I would like to save this full-length sequence in my mmCIF > file so the full-length sequence with annotated missing structure > segments shows up next time I open this file. But when I try to save > at this point, I get the following notice: > > Not saving entity_poly_seq for non-authoritative sequences > > The documentation for "save" and "sequence" didn't help. How can I > make this sequence "authoritative" and save it into my mmCIF file? > > Thank you in advance, > > Guillaume > > > > > > > > > > När du har kontakt med oss på Uppsala universitet med e-post så > innebär det att vi behandlar dina personuppgifter. För att läsa mer om > hur vi gör det kan du läsa > här:http://www.uu.se/om-uu/dataskydd-personuppgifter/ > > E-mailing Uppsala University means that we will process your personal > data. For more information on how this is performed, please read > here:http://www.uu.se/en/about-uu/data-protection-policy_______________________________________________ > ChimeraX-users mailing list --chimerax-users(a)cgl.ucsf.edu > To unsubscribe send an email tochimerax-users-leave(a)cgl.ucsf.edu > Archives:https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl… >

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autodock Vina
by Michael Sacher 22 Dec '23

22 Dec '23

I am running Chimera X. I downloaded autodock Vina. It should show as a tool>surface binding analysis but it is not there. How do I get the surface binding analysis option to show and to display Vina? Thanks. Michael

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Cannot launch ChimeraX 1.7 GUI on Red Hat Enterprise Linux 9.3
by Wen 21 Dec '23

21 Dec '23

Dear Elaine, I tried to install ChimeraX 1.7 on Red Hat Enterprise Linux 9.3. yum install mesa-libOSMesa-21.3.4-2.el9.x86_64.rpm yum install ucsf-chimerax-1.7-1.el9.x86_64.rpm Everything went well. However, when I tried to launch ChimeraX, I met the following errors: [wenliu@localhost Downloads]# chimerax QStandardPaths: runtime directory '/run/user/800' is not owned by UID 0, but a directory permissions 0700 owned by UID 800 GID 800 QStandardPaths: runtime directory '/run/user/800' is not owned by UID 0, but a directory permissions 0700 owned by UID 800 GID 800 NOTE: available bundle cache has not been initialized yet NOTE: Traceback (most recent call last): File "<frozen runpy>", line 198, in _run_module_as_main File "<frozen runpy>", line 88, in _run_code File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/__main__.py", line 1069, in <module> exit_code = init(sys.argv) ^^^^^^^^^^^^^^ File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/__main__.py", line 664, in init toolshed.init(sess.logger, debug=sess.debug, File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/toolshed/__init__.py", line 1389, in init _toolshed = Toolshed(*args, **kw) ^^^^^^^^^^^^^^^^^^^^^ File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/toolshed/__init__.py", line 396, in __init__ settings.toolshed_last_check = now.isoformat() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/settings.py", line 199, in __setattr__ ConfigFile.__setattr__(self, name, value) File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/configfile.py", line 386, in __setattr__ ConfigFile.save(self) File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/configfile.py", line 335, in save with SaveTextFile(self._filename) as f: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/safesave.py", line 191, in __init__ SaveFile.__init__(self, filename, open=open_text, critical=critical) File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/safesave.py", line 80, in __init__ raise OSError(errno.ENOTDIR, os.strerror(errno.ENOTDIR), save_dir) NotADirectoryError: [Errno 20] Not a directory: '/do/not/run/as/root/.config/ChimeraX' BUG: NotADirectoryError: [Errno 20] Not a directory: '/do/not/run/as/root/.config/ChimeraX' File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/safesave.py", line 80, in __init__ raise OSError(errno.ENOTDIR, os.strerror(errno.ENOTDIR), save_dir) _See log for complete Python traceback._ ChimeraX did not launch. Could you advise me on how to proceed? Thanks in advance. Wen Liu @ UCHC

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ISOLDE 1.7 released
by Tristan Croll 21 Dec '23

21 Dec '23

Hi all, To follow the recent announcement of the ChimeraX 1.7 release, I'm happy to announce the matching release of ISOLDE 1.7. Should now be available for installation from the ToolShed. I've also put up a new build of the QScore plugin compatible with Python, allowing it to be used with recent ChimeraX versions. Happy holidays (and happy modelling)! Best, Tristan -- Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT

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