December 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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Quest 2 Support?
by Blaine Hewitt 27 Dec '24

27 Dec '24

Hello, my name is Blaine Hewitt. Now I know that you have stated previously that you have no intention of bringing support to the Oculus Quest. Which is completely understandable since I know that not only would you have to develop around a completely new Operating System but another CPU architecture and much much more I assume. But with the soon release of the Oculus Quest 2 and it's new XR 2 chip-set makes a pretty good argument for it. As this would allow for much easier use in education (as is what I am attempting to do with it). I think it will be even easier now to push updates with SideQuest <https://sidequestvr.com/> being relatively simple to setup. I know that another (Naome <https://blog.matryx.ai/nanome-on-quest-public-beta-is-now-available-b546321…>) program is already available on the platform. But I do like your program a lot more since it is able to be used for free unlike Nanome Pricing <https://nanome.ai/pricing/> which is... as to say unappealing to public schools (such as mine). I was was also thinking (sorry if I am becoming annoying at this point) that if you do make a version of the Quest that you could make that GitHub branch available to the public. As for example while I may not be great at understanding complex protein structures I can help to make the whole experience more user friendly. Anyways if you read this far thank you for taking time from your day to read this. If you want to know who I am, my name is Blaine I am in my senior year of High School (Waynecsd <https://wh.waynecsd.org/>). I have to do a project by the end of the year where I have to present an area of study I want to pursue and I decided to research the effects of VR on the human's ability to learn and retain information. Budget..... None

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Bottleneck Large Surfaces
by Anderson, Jacob 04 Jan '21

04 Jan '21

With large colored surfaces of maps ~2.4GB, I experience a lag/delay of several seconds during rotation and translation. Is it obvious where the bottleneck might be that causes the lag? I am running ChimeraX on a 3090 gpu w/ 128gb ram, & 12 core CPU. Might there be ways to change other graphics settings to make the manipulations have a less observable delay? ~jacob

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Computing protein cavities
by Y. Mutum 29 Dec '20

29 Dec '20

Hi This question is on calculating empty cavities of large protein complexes (~2 MDa) For example, the pdb-id: 6J5K. I have tried a few webservers and they are ignoring to calculate such large protein-pdb files as a whole. Does ChimeraX have tools that can be installed from the 'More-Tools' or an inbuilt one to calculate protein cavities in ChimeraX? If you could suggest external programs for computing cavities, that are reliable for such large protein-inputs, it would be also of a great help. The cavities need not be sealed by proteins all around - they can still be open to the bulk solvent. Thanks Yaikhomba

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ChimeraX "color by conservation" tutorial
by Elaine Meng 29 Dec '20

29 Dec '20

In case anyone is interested, there's a new tutorial on coloring by sequence conservation using ChimeraX (requires version 1.1 or newer). It has click-to-execute links if you view it in the ChimeraX built-in browser. <https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/conservation-…> Happy holidays! Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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setting up mousemode - translate z - set pivot
by Helge Paternoga 22 Dec '20

22 Dec '20

Hi Elaine and Tom, Thanks for the explanations, that was very helpful. The build-in shift functionality indeed explains the translate/rotate behaviour! For me the shift button + "reversed" translate/rotate functions work perfectly, so I guess I will keep it that way. Is there anything else that speaks against it? For fitting, I am dealing with ribosomes and I have come to align the map I am fitting into in a way that makes the features clearly distinguishable (i. e. the straight solvent side of the large subunit viewed from the side), then I just move in my new map rotate to align the features and dump it using the z translate until it is in the other map, followed by fit in map. I was contemplating on how much I should stick to my old habits vs. trying new behaviours that might be more effcient in the long run. It is clear that ChimeraX offers many new opportunities for improving the workflow, but for now I like to keep my old logic (which cleary comes from using Chimera for a long time). I like to have three separate keys for rotating - xy translating - z translate that can be modified for the selected model (or dragged, will look into that). Therefore, I came up with the following setup: mousemode shift leftMode 'translate selected models' mousemode shift middleMode 'rotate selected models' mousemode shift wheel contour mousemode setting contour speed 0.1 mousemode control wheel 'translate selected models' mousemode setting zoom speed -1 fun F1 cofr sel camera ortho set bgColor grey lighting soft This actually leaves the right mouse button completely free and I was already wondering what could be a good function to map here! An unrelated observation that I had was that with grey background the selection rectangle while holding control is not visible on the background anymore (It works with white and black). Helge

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setting up mousemode - translate z - set pivot
by Helge Paternoga 21 Dec '20

21 Dec '20

Dear ChimeraX users, I am currently using the homeoffice time to finally get into ChimeraX, coming from Chimera. I just discovered "mousemode" and am trying to set up the controls to my liking. My goal is to make the fitting process of models and volumes into cryo-EM maps as smooth as possible. Currently, I use the following commands which are entered in the "execute these commands at startup" option in the settings => Is this the best way to permanently change the key-mapping? I could not find an .ini file, yet. mousemode shift leftMode 'translate selected models' mousemode shift middleMode 'rotate selected models' mousemode rightMode zoom mousemode shift wheel contour mousemode setting contour speed 0.1 My idea is to have the following set up: left mouse - turn all models (default) middle mouse - translate xy (default) right mouse - zoom shift left mouse - turn selected model shift middle mouse - translate xy selected model shift right mouse - translate z selected model scroll wheel - contour volume control right mouse - set pivot on selected model Turning and translating the models works well, also while holding shift for the selected model. As a side note, 'translate selected models' rotates the selected models in place whereas 'rotate selected models' translates in xy, is this intentional? => I would like to move the selected model in the z direction with the right mouse button while holding shift, is there an option for "translate z" ? => I am often re-setting the pivot point, therefore I would like to bind this function ("Set Pivot") to the mouse as well, does this option exist? I tried "pivot" but it did not work for cryo-EM volumes. Many thanks for reading, Helge

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Showing waters changes lighting
by Daniel Asarnow 18 Dec '20

18 Dec '20

Hi all, I have a few maps and models loaded, which have a couple hundred water molecules. When I display all the waters using 'show :HOH' the lighting changes. It makes "soft" look like "flat" and creates what looks like more ambient reflection in "full" or "simple." I embedded some screenshots below. My guess is something about a depth or lighting calculation is affected by all the waters, does anyone recognize what setting would need to change to correct this? Soft, shadows false: [image: image.png] Same after show :HOH [image: image.png] Full, shadows false [image: image.png] Same after show :HOH [image: image.png] Best, -da

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