- ChimeraX-users - RBVI Mailing Lists

Re: [Chimera-users] Changing threshold value of attributes
by Eric Pettersen 05 Jan '24

05 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 05 Jan '24

05 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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looking glass technology for chimerax,
by Krishnan Raman 05 Jan '24

05 Jan '24

Hi guys, Happy new year. I came across this https://www.schrodinger.com/3d-visualization-looking-glass-holographic-disp… . Can we look forward to having this compatible for chimerax since we are having difficulty finding 3D stereo displays for structural biology. Regards Krish Krishnan Raman Executive Director, Structural Biology BioCryst Pharmaceuticals CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

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Tile behavior in Chimera vs ChimeraX - different behavior of independent rotation?
by Oliver Clarke 04 Jan '24

04 Jan '24

Hi all, Happy new year! I have some observations/queries regarding the "tile models" command in Chimera vs ChimeraX. In Chimera, the rotation mode is not linked to a specific mouse mode - so if I change it from "front center" to "independent", this will affect rotation of models regardless of how I do it - whether using the mouse, the trackpad, or using the rock, roll or turn commands on the command line. In ChimeraX, independent rotation is now a separate mousemode - so it only applies to whatever mouse mode (e.g. left mouse) one has it applied to, and does not apply to the trackpad or command line. Is there any prospect of altering this behavior, or mimicking the old behavior? When tiling many models (or maps) for comparison, I like to view them with a rocking motion to give better 3D perception, but now I can't do this (it just rocks the entire "plane" of dispersed models, rather than each independently). Cheers Oli

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Error when trying to run previously working script
by Alexander Hung Lee 04 Jan '24

04 Jan '24

I have a .py script that successfully works on 400 pdb's. I tried using the same script to open a single pdb containing several thousand models. ChimeraX quit and sent me this error message in terminal "Release of profile requested but webenginepage still not deleted" Alex Lee PhD Student Woods Research Group<https://woodsgroup.franklinresearch.uga.edu/> Department of Biochemistry & Molecular Biology Complex Carbohydrate Research Center University of Georgia 315 Riverbend Rd. Athens, GA 30602 Email: ahl63010(a)uga.edu Mobile: (470) 641-3884

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ChimeraX Inquiry
by ‍강유은[학생](대학원 생명공학원) 03 Jan '24

03 Jan '24

Hello I would like to purchase the premium GPU A100 to predict large proteins. How can I get access to the purchasing page? Regards, Yoo Kang

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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 26 Dec '23

26 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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