- ChimeraX-users - RBVI Mailing Lists

Chimerax background color gradient
by hu.qi＠mayo.edu 12 Jan '24

12 Jan '24

Hello, Is there a way to set a gradient for the Chimerax background color, or use an image? I know Chimerax can do that but not sure how to do it in Chimerax. Any information is appreciated. QH

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Re: [Chimera-users] how to play trajectory frames ?
by Elaine Meng 11 Jan '24

11 Jan '24

Hi Mitch, What program are you using? It looks like you may be reading the ChimeraX help, but ChimeraX is a different program than Chimera. If you are using ChimeraX, you may want to ask questions on the chimerax-users(a)cgl.ucsf.edu list and not chimera-users(a)cgl.ucsf.edu ... We try to keep them separate so that people don't get confused. Also if you are actually using ChimeraX, the "coordsets" option of "open" is only for opening PDB or mmCIF files, not XTC. Just leave it out, and simply open both the PSF and XTC with the "coords" option similar to the third example in the ChimeraX help section linked below, except that your trajectory file is XTC and not DCD: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#traj-options> That just opens the trajectory, it does not play it. To play the trajectory in ChimeraX, you would use the slider GUI and/or the "coordset" command, as mentioned in the help section linked above. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Jan 11, 2024, at 3:57 PM, Mitch Murphy via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > i tried "open 3ft6.psf coordsets true coords 3ft6.xtc" > but i get "'coordsets' has no suffix" error message. > > and with "open 3ft6.psf coords 3ft6.xtc coordsets true" i get "Expected a keyword". > > how do i play frames of a trajectory. i have the psf and xtc or dcd trajectory files available.

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Angular distribution plot in ChimeraX
by Rayees Mattoo 10 Jan '24

10 Jan '24

Hi, I was trying to make an angular distribution plot using .bild file. I want to show the map inside the plot as in the attachment. Few questions: -My map needs to be flipped to get the correct handedness, I think I need to flip the angular distribution plot as well, how to do that? or do I have to go back and get the .bild file for the flipped map? -How can I change the colors and transparency of the angular distribution plot? -Can I get the particle count for each cylinder in the plot? Wanted to show a scale bar for particle distribution around the sphere of the plot. Best Rayees

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Question regarding gaussian filtering
by Dennis Dannecker 09 Jan '24

09 Jan '24

Hello, I would like to ask a question regarding the gaussian filtering. I filtered a given map (downloaded from the emdb with the "open" command from chimerax) in chimerax using the following command: vop gaussian #1 sDev X with X taking different values ranging from 0.25 to 20 with different steps. Now I would like to know the resolutions these maps actually correspond to after this gaussian filtering. The originally loaded map is stated to have nominal resolution of 2 Angstroms (GSFSC). sDev defines the standard deviation in Angstrom of the 3D Gaussian function that is used for the filtering. How can one now calculate the resolution these filtered maps correspond to? Is it possible to calculate or state a resolution for these maps that is related to the resolution given for the original map (here 2 Angstroms). Thank you very much. Kind regards Dennis Dennis Dannecker Master Student of Biochemistry Department of Chemistry Faculty of Mathematics and Natural Sciences University of Cologne Albertus-Magnus-Platz 50923 Cologne, Germany

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Question about Cylinder Representation
by Bi, Maxine 09 Jan '24

09 Jan '24

Hi there, I've been stuck trying to make my cylinder representation straight instead of curved as the default. I've tried many commands that I can find in the documentation. Could you please guide me if there is a way to just make the cylinders straight? There is a command like that in Pymol as an example (see link: https://urldefense.proofpoint.com/v2/url?u=https-3A__urldefense.com_v3_-5F-… ). Thank you so much, Maxine

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retrieve the sequence of an atom selection
by Engeholm, Maik 09 Jan '24

09 Jan '24

Hi there, I'm looking for a neat way to retrieve the sequence of an atom selection (in this case part of a double-stranded DNA molecule) from within a python script. I've been playing around with: selection = run (session, 'select #1/A:2-4|#1/B:6-9') for a in selection.atoms.unique_residues: print(a) which gives me: 151 atoms, 169 bonds, 7 residues, 1 model selected /A DG 2 /A DG 3 /A DG 4 /B G 6 /B G 7 /B A 8 /B T 9 This is a good start, but ideally I'd like to get back a contiguous sequence string for each chain (like (('A', 'GGG'), ('B', GGAT'))). Also, I do not really understand, why residue names are reported as 'DG' for strand A, but 'G' for strand B, which makes extracting a sequence string from the above output quite difficult. I've also tried: selection = run (session, 'select #1/A:2-4|#1/B:6-9') for a in selection.atoms.by_chain: print(a[1]) print(a[2].unique_residues.unique_sequences[0][1]) which gives me: 151 atoms, 169 bonds, 7 residues, 1 model selected A AGGGAGTAATCCCCTTG B CAAGGGGATTACTCCCT This is obviously also not what I want since it returns the entire sequence of each chain. I guess I could take the residue numbers from the first command and use those to slice the strings returned by the second, but that feels a little awkward, and so I was wondering if there was a better, more direct way to achieve this seemingly simple task. Your help would be much appreciated. Cheers, Maik

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ChimeraX : Cannot recommend to my class until minimization with vital cofactors such as FAD, NADH is built in. Returning to Chimera.
by Anne-Frances Miller 09 Jan '24

09 Jan '24

Dear Sir or Madam, After devoting several days to updating three weeks of my course to use ChimeraX instead of Chimera, I am returning to Chimera. ChimeraX may be a great cutting-edge tool, but it is not ready for a wider audience until it can make ‘common’ tasks easy. Please do not distance research from science. We desperately need science to be exciting and accessible to a wide audience. Chimera does that. ChimeraX does the opposite, sending the clear message that only an elite few are deemed worthy. Please please please, open the door to wider use, for the sake of science, and for the sake of the citizens of our country (who fund your agencies via taxes). Very Helpful - To make images with transparent backgrounds, members of my class as not going to type out ’transparentbackground true’ (even my emailer wants to spell the first string as two words). CRUCIAL - in-program minimization that includes critical cofactors (present in >40% of all enzymes and the actual source of their activities often!!) FAD, FMN, NAD(H), how is this anything more than structural biology if the sources of activity are not included? (‘biology’ implies life. Life REQUIRES chemical reactivity.) CRUCIAL - in-program trajectory analysis that can tabulate (for example) a distance, frame-by-frame and allow export in tabular form. Very Helpful - worms with thicknesses that can represent an attribute. These provide a critical orthogonal way to add a second attribute when color is already in use for a first. Very Helpful - Lighting/effects/side view GUI that allows easy optimization of figure reflectivity, special effects, all in one place and does not require users to remember what Cartesian coordinates they gave their first light. It is so much faster and delivers much better results than ChimeraX. This email records the current worst applicability gaps only, I see others have reported more. I would like to like ChimeraX, but as a person trying to bring science to wide audiences, ChimeraX is the best argument for Pymol I have seen in a while. Do not stop supporting Chimera until ChimeraX can serve real humans, please! Sincerely, and thanks to the team, Anne-Frances Novel Meritorious Research (and teaching) —•—•—•—•—•—•—•—•—•—•—•—•—•— A.-F. Miller, Ph. D. (she/elle/sie) University Research Professor Professor of Chemistry University of Kentucky https://www.uky.edu/~afm/ Visiting Fellow, Einstein Foundation of Berlin

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Depth cueing
by Paul Miller 09 Jan '24

09 Jan '24

Hi How do I depth cue in ChimeraX? In Chimera I used to be able to precisely control this from the side view window but I cannot find any way of controlling depth cueing in ChimeraX. Thank you. Cheers, Paul Paul Miller (he/him), PhD University Lecturer in Pharmacology Department of Pharmacology University of Cambridge Tennis Court Road Cambridge CB2 1PD +44 1223 761267 https://www.phar.cam.ac.uk/research/miller

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Hydrophobic comparison
by M.J. 08 Jan '24

08 Jan '24

Hi Dear ChimeraX developers, I met a problem and cannot find a solution on the website. I have a protein that has two conformations, in those two conformations the hydrophobic character is different, I can show them clearly by the command of mlp in Chimerax, super convenient! My question is that is there a way to show the difference quantitatively? or can be shown in one molecule and color the different on one molecule? (What I means is, for conformation A each residue has a parameter for hydrophobic, so as conformation B, can I get the numbers and do a subtraction correspondingly and know which conformation is more hydrophobic quantitatively, and even I can color one of the conformation by the subtraction). Thanks! Best regards! MJ (Mingliang Jin) Postdoc in Yifan Cheng Lab, UCSF 415-2835-171

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Subscribe
by Hernando J Sosa 05 Jan '24

05 Jan '24

How do I subscribe to this (ChimeraX users) list? When I click the subscribe link in: file:///C:/Program Files/ChimeraX/bin/share/docs/contact.html I get an error message (Page not found). Thanks Hernando ___________________________________ Hernando Sosa, PhD. Dept. of Biochemistry Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 emai: hernando.sosa@einsteinmed.<mailto:hernando.sosa@einsteinmed.org>edu ___________________________________ ________________________________ From: chimerax-users-bounces(a)cgl.ucsf.edu <chimerax-users-bounces(a)cgl.ucsf.edu> Sent: Friday, January 5, 2024 12:42 PM To: Hernando J Sosa <hernando.sosa(a)einsteinmed.edu> Subject: Your message to chimerax-users(a)cgl.ucsf.edu awaits moderator approval CAUTION: This email comes from an external source; the attachments and/or links may compromise our secure environment. Do not open or click on suspicious emails. Please click on the “Phish Alert” button on the top right of the Outlook dashboard to report any suspicious emails. Your mail to 'chimerax-users(a)cgl.ucsf.edu' with the subject Python IDE Is being held until the list moderator can review it for approval. The message is being held because: The message is not from a list member Either the message will get posted to the list, or you will receive notification of the moderator's decision.

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Re: Python IDE
by sette＠uniroma2.it 05 Jan '24

05 Jan '24

Yes. Tools --> General -- Shell Best regards, Marco Il 05/01/2024 18:42, Hernando J Sosa via ChimeraX-users ha scritto: > Dear ChimeraX, > > Does chimera-X come with an IDE to edit and run python scripts?, > something like IDLE in Chimera? > > Thanks > Hernando > > ___________________________________ > Hernando Sosa, PhD. > Dept. of Biochemistry > Albert Einstein College of Medicine > 1300 Morris Park Av. > Bronx NY 10461 > phone (718) 430-3456 > emai: hernando.sosa@einsteinmed. <mailto:hernando.sosa@einsteinmed.org>edu > ___________________________________ > > > > _______________________________________________ > 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… -- Dr Marco Sette, PhD. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail:sette@uniroma2.it Tel.: +39-0672594424

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Python IDE
by Hernando J Sosa 05 Jan '24

05 Jan '24

Dear ChimeraX, Does chimera-X come with an IDE to edit and run python scripts?, something like IDLE in Chimera? Thanks Hernando ___________________________________ Hernando Sosa, PhD. Dept. of Biochemistry Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 emai: hernando.sosa@einsteinmed.<mailto:hernando.sosa@einsteinmed.org>edu ___________________________________

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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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looking glass technology for chimerax,
by Krishnan Raman 04 Jan '24

04 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 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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