September 2020 - ChimeraX-users - RBVI Mailing Lists

Surface dust command in the .cxc script
by 李泽 24 Feb '25

24 Feb '25

Hi all: I'm trying to use the .cxc script to run the software, I found that the "surface dust" command has never been executed in it. Have anyone met the same problem? Any suggestions. Thank you all. Best, Ze

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Get color code of a custom color
by Ahmad Khalifa 11 Feb '25

11 Feb '25

I created a custom color that I want to use in a different session. is there a way to do that besides trying to match colors by eye? Regards.

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Double and Triple Bond Stick Style
by Smith, Chase 05 Feb '25

05 Feb '25

Dear ChimeraX, I was just wondering why there is no way to represent a double or triple bond in either the ligands or the protein amino acids when viewing as a Stick or Ball-and-Stick representation? I sometimes use Chimera or ChimeraX to make visuals for my lectures, and the students often have difficulty in understanding due to the absence of the multiple bonds. I would love to have the ability to represent the double or triple bonds with multiple lines between the atoms. Thank you, Chase Smith ... ChaseSmith, PhD Chair, Department of Pharmaceutical Sciences & Associate Professor of Medicinal Chemistry School of Pharmacy MCPHS University 19 Foster Street | WorcesterMA01608 T 508.373.5717F 508.890.5618C 978.855.7203 chase.smith(a)mcphs.edu www.mcphs.edu MCPHS University Confidentiality Note: This e-mail, and any attachment to it, is intended to be confidential and might be legally privileged. It is intended solely for the use of the addressee. If you are not the intended recipient, you are hereby notified that reading, copying, disseminating or distributing this email is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you.

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Re: [chimerax-users] [Chimera-users] color by zone in chimeraX
by Elaine Meng 20 Nov '20

20 Nov '20

Hi Pranav, I’m Cc'ing the chimerax-users(a)cgl.ucsf.edu list (recommended for ChimeraX questions). I believe the problem is that when coloring the chains you are using “target c” which means to color only cartoons, whereas coloring by zone uses the atom colors. Since you only colored the cartoons, the atoms probably still had heteroatom color-coding. If you use “target ac” instead (even if the atoms aren’t shown), then as long as the color zone distance is big enough, I think you will get the color zones you expect. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#simple> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone> 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 20, 2019, at 10:54 AM, Pranav Shah <p.shah.lab(a)gmail.com> wrote: > > Hi Elaine and Co., > > I am trying to color a virus map with the relevant pdb file, the > series of commands I am running are as follows, > open virus.mrc > open virus.pdb > color /A plum target c > color /B lightgreen target c > color /C dodger blue target c > color zone #1 near #2 dist 3 > However, the resultant surface is rendered in splotches of red and > blue, which leads me to think the it is coloring the surface using > atom type. Could you tell me how I can get Chimera X to color the > surface using the colors of the chains only? FYI, color by zone works > flawlessly in chimera. > > Cheers, > Pranav

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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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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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