April 2024 - ChimeraX-users - RBVI Mailing Lists

NICE DCV graphics error
by georg.kempf＠fmi.ch 28 Jun '24

28 Jun '24

Dear ChimeraX developers and users, we would like to use ChimeraX in a virtual session using the “NICE DCV” software. We verified that OpenGL hardware rendering is working in the virtual session (glxinfo, glxgears, nvidia-smi) but when opening a structure in ChimeraX, we get the below error. We tried it with different versions of ChimeraX (1.8.dev202311220127, 1.6.1 stable) on Ubuntu 20.04.6 LTS. Since the error doesn’t appear when using ChimeraX on the physical display of the same workstation(s) (where the DCV server is running) it must be related to the virtual session context. I was wondering if anyone knows what could be the cause of the error and in which direction to look regarding debugging? This is the traceback from ChimeraX: An error occurred in drawing the scene. Redrawing graphics is now stopped to avoid a continuous stream of error messages. To restart graphics use the command "graphics restart" after changing the settings that caused the error. GLError( err = 1282, description = b'invalid operation', baseOperation = glDrawBuffer, cArguments = (GL_NONE,) ) Traceback (most recent call last): File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 84, in draw_new_frame view.draw(check_for_changes = False) File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/view.py", line 188, in draw self._draw_scene(camera, drawings) File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/view.py", line 226, in _draw_scene shadow, multishadow = self._compute_shadowmaps(opaque_drawings, transparent_drawings, camera) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/view.py", line 626, in _compute_shadowmaps multishadow_enabled = r.multishadow.use_multishadow_map(shadow_drawings) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 1628, in use_multishadow_map self._start_rendering_multishadowmap(center, radius, size) File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 1711, in _start_rendering_multishadowmap fb = r.start_depth_render(self._multishadow_map_framebuffer, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 1356, in start_depth_render if not fb.activate(): ^^^^^^^^^^^^^ File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 2309, in activate fbo = self.framebuffer_id ^^^^^^^^^^^^^^^^^^^ File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 2305, in framebuffer_id self._fbo = fbo = self._create_framebuffer() ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 2141, in _create_framebuffer fbo = self._create_fbo(self.color_texture or self._color_rb, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 2169, in _create_fbo GL.glDrawBuffer(GL.GL_NONE) File "src/errorchecker.pyx", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1282, description = b'invalid operation', baseOperation = glDrawBuffer, cArguments = (GL_NONE,) ) Many thanks! Kind regards, Georg

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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

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Cinematographic effects in MD movie recording
by Enrico Martinez 17 May '24

17 May '24

Dear Chimera-X users ! I would like to add some cinematographic effects such as changing the camera angle back and forth during a short recording time of MD movies. Could you suggest some scripting tricks that I could add to the following coordset routine: # start recording movie record size 3840,2160 supersample 1 ## play movie from beginning to the end coordset #1 1,1000,1 wait 1000 etc Would it be possible to bend the camera automatically e.g. during the first 250 steps of recording ? Any other possibilities ? Yours with thanks Enrico

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Alphafold
by Chang, Jufang 06 May '24

06 May '24

Dear Sir Recently I can not use the ChimerX to do the alphafold prediction. The error message is some connection to the colab is broken sine March 2024. I am wondering when this feature of ChimeraX will come back? Thank you Ju-Fang ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Problem visualizing hydrogen bonds during a trajectory
by Ute Roehrig 02 May '24

02 May '24

Hello, I'm trying to visualize the hydrogen bonds of a small molecule in water over the trajectory of a molecular dynamics simulation, using the following commands: alias evalhb hide solvent; hb :LIG reveal true coordsets false makePseudobonds true ; view perframe evalhb; coordset #1 1,20 holdsteady :LIG; wait 20; ~perframe However, this does not work as expected. Could you please help me with this issue? Thank you, Ute

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Visualizing PAE contact lines between more than two peptides
by David S. Fay 30 Apr '24

30 Apr '24

Greetings, Was wondering if it’s possible to simultaneously display PAE contact lines for more than two peptides? For example, all contacts between A and B AND B and C etc. Couldn’t find anything on it and have already made the obvious attempts such as "alphafold contacts /A to /C AND /B to /C distance 6” Thanks! David

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Schematic
by Das, Abhinaba 30 Apr '24

30 Apr '24

Hi all, I don’t think it is possible to draw this kind of schematic representation (panel b) in ChimeraX, is it? [cid:image001.png@01DA9A41.C6E2E040] Thanks, Abhi

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Alphafold predicton using ChimeraX
by Chang, Jufang 29 Apr '24

29 Apr '24

Dear Sir, When I tried to use alphafold prediction with ChimeraX, I got this error message. I alreday download the latest version 1.7.1 (2024-01-23). But I still got the same error message. Could you please suggest me what to do the next to fix this? Thank you Ju-Fang AlphaFold Prediction Requires Newer ChimeraX Alphafold prediction requires a ChimeraX daily build from March 19, 2024 or later. The ChimeraX AlphaFold prediction service was broken by an update on Google Colab on March 14, 2024. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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running AlphaFold predictions in ChimeraX
by Elaine Meng 29 Apr '24

29 Apr '24

> On Apr 29, 2024, at 9:31 AM, Chang, Jufang via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear Greg > > Recently I can not use the ChimerX to do the alphafold prediction. The error message is some connection to the colab is broken sine March 2024. I am wondering when this feature of ChimeraX will come back? > > Thank you > > Ju-Fang Hello Ju-Fang, As Greg said, you should use the address chimerax-users(a)cgl.ucsf.edu for ChimeraX questions, not chimera-users(a)cgl.ucsf.edu which is for Chimera, and put some description of the current issue in the email subject line. If you get an error running the AlphaFold prediction in ChimeraX and you think it is a bug, please use ChimeraX menu Help... Report a Bug and include a description and your email address. As far as I knew it was working, so we wouldn't know what the problem is for you without more information. Also here are some common issues and limitations of running these predictions: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#caveats> 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

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Unroll radius?
by Ricardo Righetto 29 Apr '24

29 Apr '24

Hi, We've been using the 'volume unroll' command on a cylindrical structure, and while we do get some very decent results with the defaults, we want to do a systematic comparison with values entered manually for the inner and outer radius. Specifically, I'd like to know if I can get ChimeraX to report what minimum and maximum radii it is currently using for unrolling the volume? Currently, all I get in the reply log is this: volume unroll #1 Opened unrolled SPA_density.mrc as #2, grid size 68,697,492, pixel 1.22,1.2,1.2, shown at step 1, values float32 https://www.cgl.ucsf.edu/chimera/data/downloads/1.8/docs/UsersGuide/midas/v… From the help here it says: > (...) and inner and outer radii *r1* and *r2* (defaults are 90% of the > smallest radius and 110% of the largest radius of the displayed isosurface, > respectively, given the cylinder center and axis direction). Since this is a high-resolution cryo-EM map with many intricate features, it's hard to visually find exactly what are the smallest and largest radii currently displayed at the isosurface. So we'd like to know what ChimeraX is finding by itself and compare it to our measurements. Any tips are appreciated. Thank you! -- Ricardo Diogo Righetto

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