- ChimeraX-users - RBVI Mailing Lists

Re: [chimerax-users] Assistance: ChimeraX save scene
by Guillaume Gaullier 19 Oct '20

19 Oct '20

Hi Priyanka, Sorry for this late reply. I am copying the chimerax-users list (if you had sent your last email to the list, somebody else would maybe have answered you earlier; also a good idea to communicate through the list because all emails are archived and that sometimes enables people to find answers to their questions directly by searching the archives). Regarding you question about colors: in ChimeraX, the command "color list" will print in the log a list of colors with their names. Color names made of more than one word are listed twice: spelled with and without a space. I just checked that if you spell color names as they are listed by this command, it works. So, in your case, try spelling it "royalblue" with no space. Regarding your second question, I think this should work, but I am not quite sure what you are trying to do: volume zone #1 nearAtoms sel range 2 newMap true minimalBounds false in which #1 is your main map (so not necessarily #1 in your session, use the correct model number for your map as seen in the model panel) and sel is a selection of the atoms of interest (in your case "/A" for chain A), "range 2" is how many angstroms away from the model atoms you want to perform the map cut-out (I put 2 arbitrarily; try different values and use what you think is best for what you are trying to do), "newMap true" tells it to generate a new object for this map cut-out (it should show up in the model panel after you run the command) and "minimalBounds false" tells it to keep the same box size as your original map (if set to true instead, it will choose the minimal box size that encloses your map cut-out; not sure which one you need, but keeping the same box size should be safe). Once you have this, you can write this map cut-out to a file with the following command: save /path/to/your/new/map.mrc models #2 (replace #2 by the correct object identifier for your new map, as reported in the model panel). I hope this helps, Guillaume > On 16 Oct 2020, at 03:31, Priyanka Abeyrathne <pabeyrat(a)gmail.com> wrote: > > Hi Guillaume, > > Thank you so much for your assistance. I am going to use it soon and if I happened to have questions I will let you know. > > I have two other questions to clarify with you. > > 1. I used the following commands to color the pdb > seq chain /A > Then I highlighted the chain A > color sel blue > > I can see the chain A color is blue. Now ChimeraX has really nice color scheme. I tried to color chain A to royal blue (#4169E1 26,41,88). When I use the above commands > seq chain /A > highlighted the chain A > color sel royal blue > Didn't change the color blue to royal blue. Cod you please assist me how to fix theis? > > 2. pdb of the protein has three chains (A, B and C). I have a cryo-EM structure of the same protein. How can I extract only chain A density from cryo-EM structure. I think I have to use a segment map command. Could you please assist me how to do this in ChimeraX. > > Thank you so much. > Kind regards, > Priyanka > > > > On Mon, Oct 12, 2020 at 3:41 AM Guillaume Gaullier <guillaume(a)gaullier.org <mailto:guillaume@gaullier.org>> wrote: > Hi Priyanka, > > If what you need is a command that can restore the camera’s position to a previously saved state after you moved it, then this should be helpful: > > 1. set the scene the way you want it > 2. run command "view name myview" ("myview" can be any name); what this does is assign a name to the current view (camera settings) > 3. rotate or translate, move around, etc. > 4. run command "view myview", which should reset the camera settings to what they were when you did step 2 above > > I believe named views are saved with the session, so you should be able to use them even after you save and close, then reopen your .cxs file. > > You will find more details in the documentation, with command "help view". Also here: https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name> > > I hope this helps, > > Guillaume > > >> On 11 Oct 2020, at 22:10, Priyanka Abeyrathne <pabeyrat(a)gmail.com <mailto:pabeyrat@gmail.com>> wrote: >> >> Hi All, >> >> Is there a save scene command in ChimeraX? >> >> Thanks, >> Priyanka >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> >

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Set transparency on DNA stubs
by Siyu Chen 16 Oct '20

16 Oct '20

Dear chimerax developers, I am writing to ask about an issue regarding to the transparency of DNA bases. I set the double strand DNA as stubs and colored cyan, and I wanted to set it as transparent (trans 70 tar c). However, it looks like only the DNA backbones become transparent, and the bases are still bright and solid. I even tried to throw in all possible targets into the 'trans' command (acrsbpfl) and got the same looking images. I am just wondering if this is because of the style or color that makes the bases look solid? Also, do you have other suggestions to get around this issue? Thanks in advance for your time and help! Best, Siyu Chen

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Chnage Chain IDs
by Kazan Ramy (M.) 13 Oct '20

13 Oct '20

Greetings to all, In UCSF Chimera tools, there's an option to change chains ID/names. Unfortunately, I can't save my model under a cif format. While in Chimera X , I can save a model under a cif format but can't change the name of my chains, or at least I'm not able to find the command for that. My main goal is to have my model under a cif format with my new naming system, any idea on how I can solve this problem? Ramy Kazan PhD Student

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Assistance: ChimeraX save scene
by Priyanka Abeyrathne 12 Oct '20

12 Oct '20

Hi All, Is there a save scene command in ChimeraX? Thanks, Priyanka

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Resources to get started with toolshed development
by Florian Wernert 12 Oct '20

12 Oct '20

Hi there, I'm looking forward to integrate a processing algorithm I coded into a toolshed for ChimeraX. Are there any available resources in order to get started with plugin/toolshed development for ChimeraX ? Thanks, Florian Wernert

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Measure Motion / Blob Detection
by Scott, Brandon L. 09 Oct '20

09 Oct '20

Hello all, I had two questions: 1) I see there is now the option in measure area to ignore dusted objects, is it possible to have this feature in the measure motion as well? 2) For measure and mark blobs, Is there any way to use the output of the measure motion function to link the blobs since the triangle number changes in each frame, but following measure motion we know where it goes in the next frame. Thanks, Brandon Scott, PhD CZI Imaging Scientist, Research Assistant Professor Nanoscience & Nanoengineering South Dakota Mines 501 E. Saint Joseph St., Rapid City, SD 57701 724.510.1253 | Brandon.Scott(a)sdsmt.edu<mailto:Brandon.Scott@sdsmt.edu> [South Dakota Mines]<https://www.sdsmt.edu/> [South Dakota Mines on Facebook]<https://www.facebook.com/SouthDakotaMines/>[South Dakota Mines on Instagram]<https://www.instagram.com/southdakotamines/>[South Dakota Mines on Twitter]<https://twitter.com/sdsmt>[South Dakota Mines on Snapchat]<https://www.snapchat.com/add/sdsmt>

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Option Include non-water HETATM in Modeller Comparative
by Marta Martinez 09 Oct '20

09 Oct '20

Hi all, I am running a very simple example in Modeller Comparative (a small alignment including the template structure and the target sequence to model). Since the template harbors a HEME group, I decided to select the Advanced option "Include non-water molecules HETATM residues from template". However, no one of the retrieved models contains the HEME group. Does anyone know what could be happening? Thanks in advance: MARTA -- Marta Martinez Gonzalez Biocomputing Unit (Lab B13) National Center for Biotechnology-CSIC Darwin, 3. Campus de la Universidad Autonoma de Madrid 28049 Madrid. Spain Tel:+34 915854510 Fax:+34 913720112 E-mail: mmmtnez(a)cnb.csic.es

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right mouse zone selection labels
by Sarah Piper 09 Oct '20

09 Oct '20

HI ChimeraX team, I really like the feature in ChimeraX that creates a map clipping zone in the right mouse tools - zone with automatic labelling. However, the default labels are black background and yellow text, and only the residue 3 letter code and number. Is it possible to change these labels to a white bg and customise the labels to include e.g. the one letter code and chain ID? I tried to do this with the selection - labels tool but it did not seem to change it for the zone labels. Many thanks and keep up the great work :) Sarah

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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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