- ChimeraX-users - RBVI Mailing Lists

best desk-top for Chimerax
by Homer Guy 21 Sep '20

21 Sep '20

What are the best desk-tops for Chimerax using Windows 10 64 bit? H. Robert Guy

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Registration of ChimeraX
by Raymond P. Cox 19 Sep '20

19 Sep '20

I would like to register ChimeraX but I cannot enter @ in the box for my email address. Instead, the @ appears on the command line. Best regards Raymond Cox University of Southern Denmark

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Hiding pivot in ChimeraX
by Mutum Yaikhomba 18 Sep '20

18 Sep '20

Hi Is there a way to hide the pivot in ChimeraX? The pivot automatically appeared when I started ISOLDE in ChimeraX. Screenshot of the pivot attached. I looked on how to hide this pivot up online - but could not find it. Thanks Yaikhomba

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Fwd: Unable to load --offscreen and --nogui options
by Sai Janani Ganesan 15 Sep '20

15 Sep '20

Hello All, I am unable to save images from the command line, I get an OpenGL error. I get openGL errors on both Mac and Linux. Any suggestions? ChimeraX --offscreen --nogui test.cxc Traceback (most recent call last): File "/opt/chimerax-1.0-1.fc32/lib/python3.7/runpy.py", line 193, in _run_module_as_main "__main__", mod_spec) File "/opt/chimerax-1.0-1.fc32/lib/python3.7/runpy.py", line 85, in _run_code exec(code, run_globals) File "/opt/chimerax-1.0-1.fc32/lib/python3.7/site-packages/ChimeraX_main.py", line 895, in <module> exit_code = init(sys.argv) File "/opt/chimerax-1.0-1.fc32/lib/python3.7/site-packages/ChimeraX_main.py", line 453, in init sess = session.Session(app_name, debug=opts.debug, silent=opts.silent) File "/opt/chimerax-1.0-1.fc32/lib/python3.7/site-packages/chimerax/core/session.py", line 441, in __init__ self.logger = logger.Logger(self) File "/opt/chimerax-1.0-1.fc32/lib/python3.7/site-packages/chimerax/core/session.py", line 501, in __setattr__ if not name.startswith('_') and self.snapshot_methods(value, base_type=StateManager) is not None: File "/opt/chimerax-1.0-1.fc32/lib/python3.7/site-packages/chimerax/core/session.py", line 535, in snapshot_methods from chimerax import graphics as gr File "/opt/chimerax-1.0-1.fc32/lib/python3.7/site-packages/chimerax/graphics/__init__.py", line 34, in <module> from .opengl import Texture, Lighting, Material File "/opt/chimerax-1.0-1.fc32/lib/python3.7/site-packages/chimerax/graphics/opengl.py", line 61, in <module> from OpenGL import GL File "/opt/chimerax-1.0-1.fc32/lib/python3.7/site-packages/PyOpenGL-3.1.5-py3.7.egg/OpenGL/GL/__init__.py", line 4, in <module> from OpenGL.GL.VERSION.GL_1_1 import * File "/opt/chimerax-1.0-1.fc32/lib/python3.7/site-packages/PyOpenGL-3.1.5-py3.7.egg/OpenGL/GL/VERSION/GL_1_1.py", line 14, in <module> from OpenGL.raw.GL.VERSION.GL_1_1 import * File "/opt/chimerax-1.0-1.fc32/lib/python3.7/site-packages/PyOpenGL-3.1.5-py3.7.egg/OpenGL/raw/GL/VERSION/GL_1_1.py", line 7, in <module> from OpenGL.raw.GL import _errors File "/opt/chimerax-1.0-1.fc32/lib/python3.7/site-packages/PyOpenGL-3.1.5-py3.7.egg/OpenGL/raw/GL/_errors.py", line 4, in <module> _error_checker = _ErrorChecker( _p, _p.GL.glGetError ) AttributeError: 'NoneType' object has no attribute 'glGetError'-- Thanks, Sai

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Loading OpenMM platform plugins
by Thomas Mulvaney 15 Sep '20

15 Sep '20

Hi, I've been having fun developing a plugin for ChimeraX and want to firstly thank everyone involved for such a great platform to build upon. I'm starting to introduce a molecular dynamics component and was excited to see that ChimeraX ships with OpenMM support. Unfortunately, the OpenMM Platform plugins (which add CPU, CUDA, OpenCL etc) functionality, do not seem to be loaded by default at least in ChimeraX 1.1 on macOS. I couldn't see any documentation about how to load these plugins, but for anyone running into this issue, the following code got things working for me: ------ import chimerax openmm_plugins_dir = os.path.join(chimerax.app_lib_dir, 'plugins') Platform.loadPluginsFromDirectory(openmm_plugins_dir) ------ Kind regards, Tom

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headless chimerax is built in via --offscreen and --nogui
by Moth, Christopher W 14 Sep '20

14 Sep '20

For other longtime and unimaginative 🙂 legacy chimera users who might be googling/searching for 'headless chimerax', hopefully this note will be picked up by search engines The details you seek: http://www.rbvi.ucsf.edu/pipermail/chimerax-users/2019-April/000472.html No need to reply.

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Choosing solvent exposed residues automatically
by Mutum Yaikhomba 09 Sep '20

09 Sep '20

Hi I am working with a very big pdb model: pdb - 6g2j. I was wondering if there is a quick way to select all residues (surface residues) that are exposed to the solvent (including those facing the membrane)? This is instead of going over each residue one by one and selecting them. Additionally, say you have selected these solvent-exposed residues and now you want to filter them based on Hydrophobicity - is there a way to filter based on the standard Kyte-Doolittle Hydrophobicity index for these residues? If there is, it would be of great help and very much appreciated. Thanks Yaikhomba

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mousemode and ISOLDE
by Alexis Rohou 06 Sep '20

06 Sep '20

Hi all, Not sure whether this is a ChimeraX question, or an ISOLDE question, or a bit of both. I am using ChimeraX 1.0 (2020-06-04) and ISOLDE version ChimeraX_ISOLDE-1.0.1-cp37-cp37m-macosx_10_13_x86_64.whl. When I start ChimeraX, I get the following left mouse bindings, which I believe are default: - ctrl-left click = select - shift-ctrl-left click = select add When I just start ISOLDE via the GUI menu (no further action), this seems to clear the mousemode. Or, at least, ctrl-click does not select anymore, and shift-ctrl-click also doesn't seem to do anything. To remedy this, I issue the following commands: mousemode control left select mousemode control shift left 'select add' This restores ctrl-left to 'select' as expected, but shift-ctrl-left also triggers 'select', not 'select add'. Couple of questions: (1) Is ISOLDE intentionally overriding mousemode when it is launched? I'm 99.9% this didn't use to be the case pre-1.0... (2) How do I restore shift-ctrl-left to 'select add'? I assume I am getting the syntax wrong, but I did read the doc and thought I was following it, so I guess I need some help understanding the syntax. Cheers, Alexis

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Fit Map Question/Articles
by Luis José Castillo Valverde 03 Sep '20

03 Sep '20

Hello, I am currently working on my thesis work (this is why they have received many questions from me these days), this is why I am collecting information on biomolecular structures, and I wanted to know if you know of any article that comments on the pros and cons of its "Fit Map in Map" algorithm? This because I have been searching on this topic and have not been able to find anything. Sorry for the inconvenience and thanks in advance. Best regards, Luis -- Luis José Castillo Valverde Ingeniero en Computación, TEC Costa Rica Estudiante de maestría (MSc) académica en Computación, TEC Costa Rica Telegram: @LCastillo98 LinkedIn: luisjosecastillo98

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Re: [chimerax-users] [Chimera-users] User-defined graphics in chimera: NMR tensor plotting
by Tom Goddard 31 Aug '20

31 Aug '20

Hi Albert, Not sure if you are talking about using a modified version that spherical Python code in Chimera or using it in ChimeraX. I'll assume ChimeraX. http://plato.cgl.ucsf.edu/trac/chimera/wiki/SphericalHarmonics <http://plato.cgl.ucsf.edu/trac/chimera/wiki/SphericalHarmonics> It is much easier to shift and rotate the vertices than your approach. Python numpy arrays make this very convenient. After the line of code that makes the numpy array of vertices va = array(vertices, float32) you could shift it to a new origin with just va += (32.5, 13, -24.1) Rotation is also easy. from chimerax.geometry import rotation r = rotation(axis = (0,1,0), angle = 45) va = r * va na = r * na Here I rotate the vertices and the normal vectors about 0,0,0. Then I could apply the translation after that. You might want to do a rotation given by a 3 by 3 rotation matrix and the translation in one step, like this from chimerax.geometry import Place t = Place(matrix = ((0,1,0, 32.5), (-1,0,0, 13), (0,0,1, -24.1))) t.transform_points(va, in_place = True) t.transform_vectors(na, in_place = True) Here I used a 3 by 4 matrix where the first 3 columns were the rotation and the 4th column is the translation. I'll update the example code to show this. These geometric transforms are described in the ChimeraX Python programming documentation: https://www.cgl.ucsf.edu/chimerax/docs/devel/bundles/geometry/src/geometry.… As for what went wrong with you np.array([x0,y0,z0]).T approach -- that transpose operation put the vertices in a non-standard memory order -- you created a 3 by N array and then did a transpose to get an N by 3 array but numpy is smart and does not allocate a new array and instead just adjusts the strides and uses the original array. My guess is the calculate_surface_normals() code has a bug in that it does not handle non-standard orders for the vertex array. So the normals were completely wrong and that effects the lighting. In the ChimeraX Python shell (menu Tools / General / Shell) the variable "session" is the ChimeraX session. Tom > On Aug 31, 2020, at 2:43 PM, Albert Smith-Penzel <Albert.Smith-Penzel(a)medizin.uni-leipzig.de> wrote: > > Dear all, > > Thanks for such quick replies and helpful answers. I had two follow-up questions on the approach that Tom suggested in ChimeraX. > > The first is maybe a glitch, or more likely something I don’t fully understand in python/chimera. > > In the code Tom links to (http://plato.cgl.ucsf.edu/trac/chimera/wiki/SphericalHarmonics <http://plato.cgl.ucsf.edu/trac/chimera/wiki/SphericalHarmonics>), a list of vertices (x,y,z tuples) is created. Suppose I want to shift the center of the spherical harmonic and/or rotate it. One way to do this is to extract x,y,z from the vertices list and modify them, then put them back in the list. My first step is to switch the tuple to a list in the code (switch xyz = (r*sp*ct, r*sp*st, r*cp) to xyz = [r*sp*ct, r*sp*st, r*cp] ). Then I extract the elements, do some editing, and then put them back into a list of vertices. > > x0,y0,z0=np.array(vertices).T > #Some editing of x0,y0,z0 - although editing is not required to produce the strange effects. > vertices=np.array([[x,y,z] for x,y,z in zip(x0,y0,z0)]) > #vertices=np.array([x0,y0,z0]).T > > Finally, I need to reconstruct the vertices list. The first approach (currently uncommented) works just fine. The second approach (commented) doesn’t create any errors, but the lighting is very strange, in that there are alternating dark and light areas on the surface of the harmonic. I would have claimed that the two approaches should produce practically identical numpy arrays, but clearly that’s not the case. > > Anyway, it’s not particularly important for me, since I can work around it, but it does take some time to figure out, because one would think the latter approach should also work. > > The second question is: is it possible to get the “session” object into an interactive python session? Usually, I work interactively with python, and have a number of functions that create various scripts and input files for chimera, and then launch chimera from a shell, calling some script on startup. While this works, it would be really nice if one could manipulate an existing chimera session (maybe a bit off of the original topic now). > > In any case, the new graphics with the tensors come out very nicely- thanks so much for your help. > > Cheers, > Albert > > > >> On 28. Aug 2020, at 20:58, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> WARNUNG: Diese E-Mail kam von außerhalb der Organisation. Klicken Sie nicht auf Links oder öffnen Sie keine Anhänge, es sei denn, Sie kennen den Absender und wissen, dass der Inhalt sicher ist. >> >> Hi Albert, >> >> You need finer phi and theta steps to get a smoother appearance. I found that 10 degree steps gives chunky appearance, while 3 degree steps givs smooth appearance. Chimera does not have code to make an arbitrary surface smoother. >> >> Maybe you are interested in making these surfaces all in Python instead of using BILD. Here is how it is done in our newer ChimeraX program. >> >> http://plato.cgl.ucsf.edu/trac/chimera/wiki/SphericalHarmonics <http://plato.cgl.ucsf.edu/trac/chimera/wiki/SphericalHarmonics> >> >> Tom >> >> <harmonics.png> >> >>> On Aug 28, 2020, at 1:54 AM, Albert Smith-Penzel <Albert.Smith-Penzel(a)medizin.uni-leipzig.de <mailto:Albert.Smith-Penzel@medizin.uni-leipzig.de>> wrote: >>> >>> Hello, >>> >>> I have a question about improving user defined graphics in Chimera. >>> >>> For background (maybe not necessary for answering): >>> I’m working with nuclear magnetic resonance and MD simulation, and so I want to plot dynamically averaged spin-spin (H–C) dipole tensors, obtained from MD, on top of the corresponding H–C bonds. I’ve been relatively successful, but while one has a very high-resolution picture of the molecule itself, the tensors themselves are visibly triangulated. >>> >>> How I get this plot: >>> Each tensor is expressed first in spherical coordinate (theta, phi, r). In python, I run Delauney from scipy.spatial on theta and phi to get a list of vertices that can be used for triangulation of the tensor. Then, for each tensor, I convert theta, phi, and r into cartesian coordinates, shift the center so that the tensor sits on top of the correct bond. Finally, I create a .bild file where I write out each triangle using the coordinates and vertices. Tensors have negative and positive values (red and blue in the plot), and so I only take triangles for which r for all vertices is positive, and then in a second step, take only triangles where all vertices are negative. This all gets written to the .bild file, and then opened in chimera on top of the molecule (see picture). >>> >>> The question: >>> The result is certainly acceptable, however, there is clearly a quality difference in the molecule rendering vs. the tensor rendering (obviously, because the tensors are just made of triangles that I’ve created in python). Is there a better way to bring the surface data describing the tensors into chimera that would then allow usage of some sort of smoothing within chimera for a nicer image? (And possibly with a relatively simple data format….) >>> >>> Thanks for your help! >>> >>> Cheers, >>> Albert Smith >>> >>> <example_triangulation.png> >>> _______________________________________________ >>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >>> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users> >> > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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Fit in Map - Overlap
by Luis José Castillo Valverde 28 Aug '20

28 Aug '20

Hi, As I understand it, the overlay resulting from the "Fit in Map" command corresponds to the sum over the fit map grid points of the product of the fit map value and the reference map value at that point, determined by trilinear interpolation. I want to calculate the percentage of overlap of two maps, it would be as simple as calculating the formula "min ((sum of the grid points of map 1), (sum of the grid points of map 2)) / (overlap obtained from the fit ) "the problem I have that I do not know how to obtain those values (" sum of the grid points of map 1 "," sum of the grid points of map 2 "); I tried to do "Fit in Map" of map 1 with map 1 and use the overlap that returns as the sum of the points of map 1 but it didn't work. So I wanted to know if you can tell me how to get the sum of the grid points of a given map. Regards, Luis -- Luis José Castillo Valverde Ingeniero en Computación, TEC Costa Rica Estudiante de maestría (MSc) académica en Computación, TEC Costa Rica Telegram: @LCastillo98 LinkedIn: luisjosecastillo98

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MD trajectories in ChimeraX
by David Slochower 24 Aug '20

24 Aug '20

Hi, are there any plans to implement a "metafile" interface (e.g., http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#…) for loading trajectories with ChimeraX? In particular, it would be great to be able to load `prmtop` and `nc` trajectories, even if it were available only through the command line and without a GUI. (This can be considered a follow up to this message: http://www.rbvi.ucsf.edu/pipermail/chimerax-users/2019-December/000773.html) I'm aware of the Molecular Dynamics Viewer in the Toolshed, but that appears to be geared for multi-PDB trajectories. Thanks.

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Stack sidebar tools as tabs
by Sean Connell 22 Aug '20

22 Aug '20

Hello, I was wondering if there is a command to automatically stack the tools (i.e. log, volume viewer) in the sidebar as TABs? For example to put in the preferences so it starts this way or to make an alias so it can be done quickly. Thanks in advance for any tips you have. Sean

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ChimeraX depthCue
by Gokhan Tolun 18 Aug '20

18 Aug '20

Hi, Based on here: https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/lighting.html I am trying to adjust the depth cue using the depthCue true | false depthCueColor color-spec depthCueStart start depthCueEnd end commands, but I get the error Unknown command: Any suggestions? Thanks, Gökhan PS: ChimeraX 1.0

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Oculus quest for chimeraX?
by Miriam Díaz Galicia 18 Aug '20

18 Aug '20

Dear chimeraX users I would like to buy my first VR headset to use with ChimeraX. I am considering buying the Oculus quest but I would like to confirm that it will properly work for ChimeraX. Has anyone used it? or is there a better low-cost VR headset (preferably but not limited to all-in-one devices) that you can recommend to me? Thank you very much in advance, Escarlet -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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Draw a circle
by Andrea Dallapè 18 Aug '20

18 Aug '20

Hi, I would like to highlight a hole in a protein -the exit tunnel of a ribosome, to be more specific. I tried the command shape tube in order to draw three tubes passing through three residues, but the result doesn't suit at best my need and expectations. Is possible to draw a circle, passing through three points -or residues-? Do you have any suggestions? Thank you for your attention. Have a great week end. Greetings, Andrea

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Re: [chimerax-users] [Chimera-users] [External] Re: The command like volume zone in X
by Tom Goddard 14 Aug '20

14 Aug '20

Hi Fengwei, I added the "wobble" command to ChimeraX today that makes a figure 8 motion. It will be in tonight's ChimeraX builds -- nightly builds are listed at the bottom of the downloads web page. The wobble command is just a shorthand for the turn command and the turn command now has two new options: wobble that controls speed and is the number of frames for a complete figure 8, and wobbleAspect that controls the amplitude of the bobbing motion as a fraction of the side to side motion (default 0.3). The wobble command uses a default cycle of 136 frames per second which at 60 frames/second rendering is a little more than 2 seconds per figure 8. The wobble command makes the default amplitude 15 degrees. Tom > On Aug 14, 2020, at 9:37 AM, Zheng, Fengwei wrote: > > Dear Elaine, > > Got it, Thank you so much for your kind explanation! Stay safe and Have a great weekend! > > Best, > Fengwei > From: Elaine Meng > Sent: Friday, August 14, 2020 12:34 > To: Zheng, Fengwei > Cc: chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> > Subject: [External] Re: [Chimera-users] The command like volume zone in X > > Hi Fengwei, > There is a "vop zone" command in Chimera similar to "volume zone" in ChimeraX. Same function, but the keywords and syntax are different, see > > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#zone <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#zone>> > > E.g. something like: > > vop zone #2 #0:.a 2 > > As for your other question, Chimera has a "precessionTilt" option to the "roll" command, but ChimeraX does not have this option currently. Looking at this kind of motion makes me feel seasick, so I don't use it in my own work. > > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/roll.html <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/roll.html>> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Aug 14, 2020, at 8:43 AM, Zheng, Fengwei wrote: > > > > Dear Developer, > > I am wodering if there is a command of Chimera can achieve the same function like "volume zone" in ChimeraX? I tried the command "vol zone #2 near #0:.a range 2", but the chimera always said "unknow keyword #2"~ > > Another thing is that I wonder if there is a command of ChimeraX can achieve the same function like "turn z 2 360 precess 20" in Chimera (to achieve the Wobble motion / "wiggle-rock" motion, like nutation in pymol)~ > > The I tried 1.14, 1.15 and the latest daily built versions of Chimera. > > The ChimeraX version I used is 1.0, Many thanks! > > Best, > > Fengwei > > CAUTION: This email was sent from outside of the organization (meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>). Do not click links or open attachments unless you recognize the sender and know the content is safe. If you have any questions, please contact ServiceDesk(a)vai.org <mailto:ServiceDesk@vai.org> <mailto:servicedesk@vai.org <mailto:servicedesk@vai.org>>. > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users>

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Discrete coloring and secondary structure assignment.
by Reza Khayat 13 Aug '20

13 Aug '20

Hi, I'm trying to generate a ribbons diagram where the secondary structures are defined by user and colored by user. I'm running into a problem where half of the amino acid is assigned the secondary structure and the entire residue is assigned the color. This makes for a strange image. Attached is an image. Notice how the coloring starts before the secondary structure. Any help is appreciated.? Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031

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Limits on movies
by mailman-bounces＠cgl.ucsf.edu 13 Aug '20

13 Aug '20

From: Maria Maldonado <mmaldo(a)ucdavis.edu <mailto:mmaldo@ucdavis.edu>> Subject: Limits on movies Date: August 9, 2020 at 7:23:21 PM PDT Hi! I have a question about movies and thought you might be able to help. Is there a limit to the length of the movies other than the limit maxframes? I’ve made scripts for movies with several steps. All the motions/commands show in the ChimeraX window while it is rendering, the script gets to the end and says “movie encoded”. However, when I open the movie file, the movie is missing several frames/steps. This happens even though I increased the limit maxframes (and my movies should be shorter than 15000 to begin with). If I split the original movie into shorter chunks that works fine, but I’ll have to edit the steps together in a different programme. I was wondering if this has to do with ChimeraX, or whether maybe it could be a computer memory issue or something else outside of the programme? It seems to be worse (ie the movie file stops earlier) for larger volumes and models than for smaller ones. Thank you very much for your help! Best, Maria

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chimerax amino acid sequence
by Peter Steinhagen 09 Aug '20

09 Aug '20

Hello, I am new to chimerax. For my protein of interest, there is no PDB available, thus, I chose a similar protein. However, the amino acid sequence is different. Is it possible to change the amino acid structure in chimerax? Will this change the 3D conformation? If this does not work what would be a good solution for my problem? Thanks, Peter

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Command line utility for .cmap
by Daniel Asarnow 06 Aug '20

06 Aug '20

Hi all, I have only been able to load volume series data using the .cmap format (using a daily from this week on OS X). Is there a command-line utility, perhaps ChimeraX itself, that can generate a .cmap file from a number .mrc volumes? It would be nice to generate these on my processing machine and then only download the .cmaps to my laptop. Best, -da

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Server maintenance
by Eric Pettersen 06 Aug '20

06 Aug '20

Hi all, The servers that usually host the Chimera web site and web services will be undergoing maintenance Monday and Tuesday of next week (August 10/11), but we have jury-rigged a temporary solution that should allow the web site and services to continue to function through the maintenance window. Nonetheless, do not be shocked if the site/services wind up being down on those days. Also, mail to the Chimera mailing lists and Chimera bug reports will be not be fully processed until the servers fully come back up on Wednesday. Such mail/reports will be accepted but spooled during the maintenance window, and delivered afterward. So you probably will not get any responses until Wednesday/Thursday. --Eric Eric Pettersen UCSF Computer Graphics Lab

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ChimeraX Toolshed will be down 10-11 August 2020
by Greg Couch 05 Aug '20

05 Aug '20

Hello everyone, The ChimeraX Toolshed will be down for two days starting Monday, August 10th, 2020. This is due to a major infrastructure upgrade. We are planning to keep the regular ChimeraX web site up during that time, but there's a small chance that it will be down too. Everything should be back to normal by Wednesday, August 13th. If not, we will be frantically working on getting it back up :-). -- Greg

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Fit map in map and save result map
by Luis José Castillo Valverde 05 Aug '20

05 Aug '20

Hello, I know that the ones I am going to ask maybe a recurring question but I have not managed to solve it. I know that maps as such do not have location or rotation information, but I want to generate a new map (with a new cube I imagine) which represents the current position and rotation for a given map. I am working with "fitmap (map # 1) inmap (map # 2)" the idea is to generate the new map from the optimized map, to be able to load that new "result" map without the need to perform any other transformation. If this is possible, I wanted to know if you can give me the command list to be able to do it? I already appreciate the attention provided. Best regards, Luis -- Luis José Castillo Valverde Ingeniero en Computación, TEC Costa Rica Estudiante de maestría (MSc) académica en Computación, TEC Costa Rica Telegram: @LCastillo98 LinkedIn: luisjosecastillo98

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OpenGL error with nogui?
by Fabian Glaser 01 Aug '20

01 Aug '20

Dear gurus, I am trying to produce a series of figures on the fly with chimeraX, using a python script of the following format (this is only a simple demo): test.py: #!/usr/bin/env python3 import sys from chimerax.core.commands import run run(session, "open 1d66") run(session, "color red") run (session, "save fig1.png”) == This works like a charm with the gui, but without the gui it gives the following error, stops and no figure is produced, we tried both in Mac and linux. We are interest in the —nogui option: .../MacOS/ChimeraX --script "test.py 1d66" —nogui Executing: surface sel-residues enclose sel-residues Executing: transparency 0 ribbons Set transparency of 542 residues Executing: ~select Nothing selected Nothing selected Executing: save fig1.jpg Unable to save images because OpenGL rendering is not available So is this solvable? How? We tried also with the —offscreen, no luck either. Best, Fabian Fabian Glaser PhD Bioinformatics Knowledge Unit - BKU The Lorry I. Lokey Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa, Israel Web https://lokey.technion.ac.il/bioinformatic-knowledge-unit/ Tel +972 (0) 4 8293701

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