- ChimeraX-users - RBVI Mailing Lists

Error "Cannot determine format for"
by Karjalainen, Mikael 09 Oct '20

09 Oct '20

Hi! I am trying to get transparent background in png pictures, but it is not working and I get error "Cannot determine format for". Only way to get this is by using command line? I am writing something like: save C:\Users\a\Desktop\k [ format png ] [ supersample 4 ] [ transparentBackground true ] or save C:\Users\a\Desktop\k format png supersample 4 transparentBackground true Also, I have tried different variations. Regards, Mikael

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Exporting 3D models from ChimeraX?
by Karjalainen, Mikael 07 Oct '20

07 Oct '20

Hi! Is it possible to export 3D models from ChimeraX? Preferably in formats GLB (best for powerpoint), FBX, OBJ or 3MF? You can in old Chimera, but for powerpoint presentations it can only give STL files which do not have textures. Here are supported file formats for Office products: https://support.microsoft.com/en-us/office/3d-content-guidelines-for-micros… Regards, Mikael

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Request for access to ChimeraX GitHub repository
by Chen, Xiang 05 Oct '20

05 Oct '20

Dear Sir or Madam, I am a graduate student at the Memorial University of Newfoundland, and I am working on the development of virtual reality applications that can be used to visualize biological microscopic data. May I get access to the ChimeraX GitHub repository for further non-commercial research? Looking forward to your reply. Thank you very much! Best Regards, Xiang Chen --- Xiang Chen, Student # 201992538 Department of Computer Science Memorial University of Newfoundland St. John's, NL, Canada T (709) 219-2960 / E xiangc(a)mun.ca

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Access ChimeraX GitHub repository
by 唐翊国 05 Oct '20

05 Oct '20

Hi Dear, I'm learning Python 3 now, and I think one good way is to refer to a good application like ChimeraX, so please allow me to access ChimeraX repository, thanks a lot! BR, Eagle

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orientation
by Fabian Glaser 02 Oct '20

02 Oct '20

Dear chimerax experts, I have maybe a trivial question, I am willing to show a figure with several copies of the same protein, but when I move one copy of them using the "move x 10 model #1” etc command, they rotate upon probably the center of mass of all the models, such as when I separate all of them, they are rotated slightly different. I would like to show them in exactly the same orientation, is there a trick to move them in such a way that will be show in exactly the same orientation? Thanks a lot! 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/ <https://lokey.technion.ac.il/bioinformatic-knowledge-unit/> Tel +972 (0) 4 8293701 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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ensemble match; ensemble cluster; plotting RMSD
by Cristina Marino Buslje 25 Sep '20

25 Sep '20

Dear ChimeraX users, After a hole evening trying everything, reading every possible page, I can not do what I want that is superposing models of an NMR PDB (ej 20 models) all by all and compare their RMSD (a matrix if possible). And also compare this ensemble (NMR with 20 models) with another (let's say another NMR with 30-50 models). My chimeraX has not the option "Structure comparison" in the tools bars. The web manual doesn't give the commands needed to do so. Below is what is written in the manual but, as I said, structure comparison is not in my tools bar. " Ensemble Match, a tool in the Structure Comparison and MD/Ensemble Analysis categories". I know that there are tools to work with MD simulations (several conformers), but also can not find in the version install in my windows 10 computer. I know this is passible from chimeraX. Could you please help me find the solution? has anybody try this? Is very important for me to do it. Thank you very much in advanced, Cristina Cristina Marino Buslje MS, PhD Researcher, National Research Council (CONICET) Head of Bioinformatics Unit Fundación Instituto Leloir Av. Patricias Argentinas 435. Buenos Aires, Argentina Tel: +54(11)5238-7500 | Fax: +54(11)5238-7501 http://www.leloir.org.ar<http://www.leloir.org.ar/>

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Re: [chimerax-users] [Chimera-users] Is RTX support planned?
by Tom Goddard 25 Sep '20

25 Sep '20

Hi Gökhan, We haven't considered working on raytracing in ChimeraX yet. What advantage do you think it would have? One that I can think of is that having multiples models with transparency could work correctly with raytracing. ChimeraX uses the same material for all surfaces now which defines how light bounces off it, how shiny it is. The ChimeraX material command controls those settings https://www.cgl.ucsf.edu/chimerax/docs/user/commands/material.html <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/material.html> We may in the future allow different models to use different materials. ChimeraX also allows using textures on surfaces with the "color image" command, although good use cases are hard to come by: https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#image <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#image> Generic 3D modeling packages like Blender, Cinema4d, Maya, ... work poorly or not at all with vertex colors which ChimeraX uses for multi-color surfaces like coloring a molecule surface by electrostatic potential. But sometimes people want to export those colorings from ChimeraX, for instance to print a 3D color surface and so they want the colors in a texture. So I have been looking at that use and will probably try to allow electrostatic and hydrophobic coloring to use a texture and to export as GLTF, OBJ, Collada or other 3D formats using texture colors in the next several months. Tom > On Sep 25, 2020, at 1:42 AM, Gokhan Tolun <gokhan(a)uow.edu.au> wrote: > > Hi Tom, > > Are there any plans to implement RTX (real-time ray tracing) support to ChimeraX (and even better, allow the use of physically modelled materials and textures)? > > Thanks, > > Gökhan > > > Gökhan Tolun <https://scholars.uow.edu.au/display/gokhan_tolun>, M.S., Ph.D. > Senior Lecturer > School of Chemistry and Molecular Bioscience <https://www.uow.edu.au/science-medicine-health/schools-entities/school-of-c…> | Faculty of Science, Medicine and Health (SMAH) <https://smah.uow.edu.au/index.html> | Room 125 / Building 18 > Molecular Horizons Research Institute <https://www.uow.edu.au/molecular-horizons/index.html> > Illawarra Health and Medical Research Institute <https://www.ihmri.org.au/researchers/gokhan-tolun/> > University of Wollongong NSW 2522 Australia > T +61 2 4221 3365 > uow.edu.au <http://uow.edu.au/> | Facebook <https://www.facebook.com/UOW> | Twitter <https://twitter.com/uow> | Instagram <https://www.instagram.com/uow/> | LinkedIn <http://www.linkedin.com/edu/school?id=10255> > > NOTICE: This email is intended for the addressee name and may contain confidential information. If you are not the intended recipient, please delete it and notify the sender. Please consider the environment before printing this email. > > _______________________________________________ > 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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Center of cube in mrc
by Luis José Castillo Valverde 24 Sep '20

24 Sep '20

Hello, I want to move a mrc near another mrc from terminal controlled, the problem is that I don't know how ChimeraX defines the center point of movement when loading a mrc file. So I wanted to know if you can explain to me that ChimeraX defines the X, Y, Z coordinates in which it will load the center of the cube? 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] Exporting image in 300 DPI
by Fabian Glaser 22 Sep '20

22 Sep '20

Dear all, I saw Elaine mail regarding the 300 DPI question, but I am not able to get more than 72, I played with the width and heigh as follows: save /Users/fglaser/test2.tiff pixelsize 0.1 save /Users/fglaser/test2.tiff width 900 But I am not able to get more than 72. Could you please help me to get 300 DPI? Thanks! 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/ <https://lokey.technion.ac.il/bioinformatic-knowledge-unit/> Tel +972 (0) 4 8293701 Elaine Meng meng at cgl.ucsf.edu <mailto:chimerax-users%40cgl.ucsf.edu?Subject=Re:%20Re%3A%20%5Bchimerax-users%5D%20Exporting%20image%20in%20300%20DPI&In-Reply-To=%3C439F4072-9421-4196-8095-5824C8FB5DB4%40cgl.ucsf.edu%3E> Tue Jan 21 08:17:48 PST 2020 Previous message: [chimerax-users] Exporting image in 300 DPI <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-January/000813.html> Next message: [chimerax-users] silhouettes on mesh in ChimeraX <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-January/000819.html> Messages sorted by: [ date ] <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-January/date.html#816> [ thread ] <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-January/thread.html#…> [ subject ] <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-January/subject.html…> [ author ] <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-January/author.html#…> Hi Ahmed, Currently the saving dialog does not show many options, but the “save” command includes all of these controls. Use the “save” command with “width” and/or “height” option, where the values are numbers of pixels. You would just calculate the pixels by multiplying the desired size in inches by the dpi. E.g. 3 inches wide X 300 dpi = 900 pixels wide. See: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#image <http://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#image>> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Keep mouse or pointer active in recorded movies
by Sarah Piper 21 Sep '20

21 Sep '20

Hi ChimeraX team, I was wondering whether there is an option to make a mouse/cursor (or some sort of other pointer) visible when movies are recorded? E.g. When I want to point to my model or run simulations in Isolde and move atoms around, my mouse/cursor is not visible in the recording. Is it possible to keep the cursor visible in the recording, so that it becomes clear what was moved/pointed at in a movie recording? I hope the question make sense! Many thanks for all your work on this, awesome piece of software! Regards, Sarah

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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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