December 2023 - ChimeraX-users - RBVI Mailing Lists

Determining Chirality
by steffen＠sthomas.de 20 Jun '25

20 Jun '25

4 5

Show side chain, main chain, and cartoon at the same time
by Zhang, Miao 27 Feb '25

27 Feb '25

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 24

Surface dust command in the .cxc script
by 李泽 24 Feb '25

24 Feb '25

Hi all: I'm trying to use the .cxc script to run the software, I found that the "surface dust" command has never been executed in it. Have anyone met the same problem? Any suggestions. Thank you all. Best, Ze

3 3

Get color code of a custom color
by Ahmad Khalifa 11 Feb '25

11 Feb '25

I created a custom color that I want to use in a different session. is there a way to do that besides trying to match colors by eye? Regards.

5 4

Double and Triple Bond Stick Style
by Smith, Chase 05 Feb '25

05 Feb '25

Dear ChimeraX, I was just wondering why there is no way to represent a double or triple bond in either the ligands or the protein amino acids when viewing as a Stick or Ball-and-Stick representation? I sometimes use Chimera or ChimeraX to make visuals for my lectures, and the students often have difficulty in understanding due to the absence of the multiple bonds. I would love to have the ability to represent the double or triple bonds with multiple lines between the atoms. Thank you, Chase Smith ... ChaseSmith, PhD Chair, Department of Pharmaceutical Sciences & Associate Professor of Medicinal Chemistry School of Pharmacy MCPHS University 19 Foster Street | WorcesterMA01608 T 508.373.5717F 508.890.5618C 978.855.7203 chase.smith(a)mcphs.edu www.mcphs.edu MCPHS University Confidentiality Note: This e-mail, and any attachment to it, is intended to be confidential and might be legally privileged. It is intended solely for the use of the addressee. If you are not the intended recipient, you are hereby notified that reading, copying, disseminating or distributing this email is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you.

5 5

Quest 2 Support?
by Blaine Hewitt 27 Dec '24

27 Dec '24

Hello, my name is Blaine Hewitt. Now I know that you have stated previously that you have no intention of bringing support to the Oculus Quest. Which is completely understandable since I know that not only would you have to develop around a completely new Operating System but another CPU architecture and much much more I assume. But with the soon release of the Oculus Quest 2 and it's new XR 2 chip-set makes a pretty good argument for it. As this would allow for much easier use in education (as is what I am attempting to do with it). I think it will be even easier now to push updates with SideQuest <https://sidequestvr.com/> being relatively simple to setup. I know that another (Naome <https://blog.matryx.ai/nanome-on-quest-public-beta-is-now-available-b546321…>) program is already available on the platform. But I do like your program a lot more since it is able to be used for free unlike Nanome Pricing <https://nanome.ai/pricing/> which is... as to say unappealing to public schools (such as mine). I was was also thinking (sorry if I am becoming annoying at this point) that if you do make a version of the Quest that you could make that GitHub branch available to the public. As for example while I may not be great at understanding complex protein structures I can help to make the whole experience more user friendly. Anyways if you read this far thank you for taking time from your day to read this. If you want to know who I am, my name is Blaine I am in my senior year of High School (Waynecsd <https://wh.waynecsd.org/>). I have to do a project by the end of the year where I have to present an area of study I want to pursue and I decided to research the effects of VR on the human's ability to learn and retain information. Budget..... None

4 3

Bundles with dependencies
by Vincent Mallet 24 Jun '24

24 Jun '24

Hello, Thanks for the tool and the tutorials. I have a machine learning tool based on pytorch to analyse cryo-EM data. I was hoping to package (bundle) it for Chimerax and started to follow tutorials, but I don't think you mention the right way to set up a code environment with depencies. I see a numpy import in the save_new_format tutorial, but it's not listed in the "dependencies" section of the xml file. I guess my question is : can I add arbitrary packages in a bundle ? Is there a way to install pip packages only ? Should I copy all source code in the folder and deal with my imports like that ? In particular, I am thinking of torch that is not so easy to replace... I am hoping you can help me, thanks in advance for the help ! Best, Vincent

2 8

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

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

3 2

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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ChimeraX Log File Question
by Bani Kaur 20 Dec '23

20 Dec '23

Hi, I hope you are doing well! My name is Bani Kaur and I am a ChimeraX user. I wanted to ask you how I would be able to download my log file - I am not able to figure out what line to put into the system. Thank you so much! Best, Bani kaur

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ChimeraX protein-protein binding site modeling question
by Parks, Ryssa 20 Dec '23

20 Dec '23

Hello, I work in a lab that researches biopesticides in the form of insect neuropeptides, which bind to receptor proteins. I am trying to use ChimeraX to model potential binding sites between peptide ligands and their corresponding receptor. Does ChimeraX have this capability? When I was trying to figure this out myself online through the ChimeraX Youtube tutorials and tutorials on the UCSF site, I came across a comment on a video that mentioned I could upload the sequences of my receptor and peptide ligand separated by a comma, and model it as a protein complex, and then I can get information on where the two molecules interact. I'm relatively new to protein research, and so I hadn't yet thought of ligand-protein interactions as a type of protein complex. My specific questions are: * When modeling a peptide ligand and a receptor as a protein complex, will ChimeraX accurately predict the relationship between the two molecules based on binding compatibility? Or is it based on something else, like similarity of sequence alignments...? * If multiple binding sites are possible, is there any way to view the different options for multiple binding sites? Or is there any way to restrict the area on the receptor to which my target peptide ligand is predicted to bind (i.e. the extracellular region only)? * The peptide ligands are only 7-9 amino acids in length and do not take very long to model, but the receptor is about 600 amino acids and takes a much longer time to model. Do I have to model protein complexes by re-modeling everything for each different receptor-ligand combination, or can I combine existing models somehow? I hope these questions aren't too troublesome, and I hope I haven't grossly misunderstood ChimeraX's capabilities. Thank you for your time, Ryssa Parks

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Problem with Snap Installation
by Stephen P. Molnar 20 Dec '23

20 Dec '23

I have had Chimerax.flatpack installed on by Debian Bookworm Platform. As a result of a system crash I was force to reinstall the OS. When I attempted a reinstallation on the New OS I got the following error: error: The application edu.ucsf.rbvi.ChimeraX/x86_64/master requires the runtime org.freedesktop.Platform/x86_64/22.08 which was not found Please advise. Thanks in advance. -- Stephen P. Molnar, Ph.D. https://insilicochemistry.net (614)312-7528 (c) Skype: smolnar1

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ISOLDE messes with view?
by Alexis Rohou 19 Dec '23

19 Dec '23

Hello, I've just noticed that the view command doesn't behave as expected after I have started ISOLDE. Specifically, if I save a view ("view name view1") and later try to restore it ("view view1"), it will get me back to the correct orientation of view1 but the zoom will not be restored. I assume ISOLDE is changing a setting under the hood. Is there some way to make ISOLDE play nicely with "view"? Right now my only workaround is to quit ChimeraX and start again front he beginning, without launching ISOLDE. Cheers, Alexis

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