December 2023 - ChimeraX-users - RBVI Mailing Lists

Show side chain, main chain, and cartoon at the same time
by Zhang, Miao 22 Apr '24

22 Apr '24

Dear colleagues I am new to ChimeraX. I am trying to figure out how to show side chain, main chain, and cartoon at the same time in a protein structure. Like the one below made in other software. Could you please help? [cid:image001.png@01D9D154.CE3D4440] Best, - - - - - - - - - - - - - - - - - Miao Zhang Ph.D. Associate Professor Chapman University School of Pharmacy 9401 Jeronimo Rd, Suite 297W Irvine, CA 92618 Phone: 714-516-5478 http://www.chapman.edu/our-faculty/miao-zhang

2 18

Missing Vina on ChimeraX
by Luigi Marongiu 03 Apr '24

03 Apr '24

Dear sir or madam, I am using UCSF ChimeraX version 1.5 (2022-11-24). I have been trying to use AutoDock Vina but there is no such command in my version. How do I install it into ChimeraX (as shown in many tutorials, Vina is part of Chimera)? Thank you. Best regards, Luigi Marongiu Ph.D., B.Sc. (Hons.)

4 6

Feature request; sort by last time file was modified in save window
by m.c.feasey2＠newcastle.ac.uk 12 Feb '24

12 Feb '24

The content of this message was lost. It was probably cross-posted to multiple lists and previously handled on another list.

4 7

Re: [Chimera-users] Chimera X menu "View" vs. "Focus"
by Eric Pettersen 23 Jan '24

23 Jan '24

Hi Christian, We named it “View” instead of “Focus” because it issues a “view” command, but your points have merit — “Focus” is more evocative of what the action actually does, and is less confusable with hide/show, so after some discussion we have renamed the menu item to “Focus” and the change will be in the next daily build. The menu item item still issues/logs a “view” command to do its work. We are aware that the direct equivalent of the “Fetch By ID” dialog is missing in ChimeraX and we intend to add it. It’s just a matter of implementation priorities, so it could still be a little while — but it’s useful to know that it’s definitely missed, which will make it more likely to get worked on sooner. Also, there is a list specifically for ChimeraX user issues — chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>, (cc’ed here), which would be better to discuss ChimeraX topics on than chimera-users… --Eric Eric Pettersen UCSF Computer Graphics Lab > On Sep 25, 2023, at 12:47 AM, C. Klein via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear Chimera Team > > first of all, thank you very much for your important and good work on the Chimera software. > > Two comments: > > I did some recent work with Chimera X. The menu item "Focus" was changed to "View", which I find less suitable. The term "View" is often applied in other contexts, in particular if a certain residue should be shown vs. not shown. In contrast, "Focus" is not ambiguous, it is not related to showing vs. hiding certain parts of the molecular representation but exactly indicates what is done by the command. > > The direct pdb download from rcsb or whatever repository is a highly useful tool which is more difficult to access than it used to be. Ok I know it is there, I type "open xxxx" and I use the command line quite a lot anyway, but for others who start with the menus it does not appear to be accessible. Perhaps I also missed something, but then others may not find it as well. > > Thank you and best wishes > Christian Klein > _______________________________________________ > 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/

5 5

Colouring clipping plane
by GOVAERTS Cédric 20 Jan '24

20 Jan '24

Hi ChimeraX team. I’m trying to get an image of a protein whose surface is colored by electrostatic properties but clipped halfway. I would like the clipping plane to be white, not red/blue according to the electrostativ properties of the residues insides the protein. However, I don’t’ seem to be able to do that. -If I color everything white and then click on Molecular-Display “electrostatic”, the clipping plane also gets the electrostatic coloring [Graphical user interface Description automatically generated] -If I color everything white and then click on Molecular-Display “hydrophobic” or “rainbow” it works, the clipping plane remains white. [cid:image002.png@01D94092.6E8A2390] Can you help me getting the white clipping plane with electrostatic surface ? Thanks a bunch Cedric — Prof. Cedric Govaerts, Ph.D. Universite Libre de Bruxelles Campus Plaine. Phone :+32 2 650 53 77 Building BC, Room 1C4 203 Boulevard du Triomphe, Acces 2 1050 Brussels Belgium http://govaertslab.ulb.ac.be/

2 5

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/

5 7

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

3 4

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

2 1

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

2 2

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 🚀

2 6

ChimeraX-users December 2023