December 2021 - ChimeraX-users - RBVI Mailing Lists

Color docking resulls by rank
by Visvaldas K. 17 Dec '21

17 Dec '21

Dear Users and Developers, I have a ViewdockX question (but I guess it's a more generic one, about coloring models/submodels): is there a trick to color docking results by rank, like rank was some sort of B-factor? Or even by docking energy (score), but that's maybe too much. I could color each "submodel" by hand, but I don't know how to obtain color gradients, say distributed at even distances between blue and red. Years ago I was able to do similar trick in Chimera, but I completely forgot how I did that :( Thank you, Vis On Friday, December 17, 2021, 05:24:30 PM GMT, chimerax-users-request(a)cgl.ucsf.edu <chimerax-users-request(a)cgl.ucsf.edu> wrote: Send ChimeraX-users mailing list submissions to chimerax-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users or, via email, send a message with subject or body 'help' to chimerax-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimerax-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of ChimeraX-users digest..." Today's Topics: 1. independent centers of rotation (Elaine Meng) 2. Change the directory for data fetched from databases (Guillaume Gaullier) 3. Re: Change the directory for data fetched from databases (Tom Goddard) 4. Re: Change the directory for data fetched from databases (Guillaume Gaullier) 5. Re: Change the directory for data fetched from databases (Tristan Croll) 6. Re: Change the directory for data fetched from databases (Guillaume Gaullier) 7. PDB: 7OVR (Veler, Hana (NIH/NCI) [F]) 8. Re: PDB: 7OVR (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Wed, 15 Dec 2021 12:51:58 -0800 From: Elaine Meng <meng(a)cgl.ucsf.edu> To: Abigail Jackson <ajackson(a)scripps.edu> Cc: "chimerax-users(a)cgl.ucsf.edu" <chimerax-users(a)cgl.ucsf.edu> Subject: [chimerax-users] independent centers of rotation Message-ID: <90DEEA37-1BF5-4F52-AF35-DF81F0B4F273(a)cgl.ucsf.edu> Content-Type: text/plain; charset=us-ascii Hi Abigail, Ah, you're referring to the "independent centers of rotation" mode in Chimera. By default, the "tile" command in Chimera automatically turns it on. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/tile.html> I agree that this mode is very useful, but unfortunately it does not yet exist in ChimeraX. It is listed in the missing features section of the ChimeraX download page. <https://www.rbvi.ucsf.edu/chimerax/download.html> Sorry about that, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 15, 2021, at 12:28 PM, Abigail Jackson via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Hi there, > I have a question regarding the tile function in ChimeraX. In the original Chimera, once multiple maps were tiled they would all rotate individually and the grid itself was fixed in space. In ChimeraX, however, once maps are tiled the entire grid rotates as a unit and the individual maps are fixed. Do you know if there is an option to have the maps spin individually instead, like in the original Chimera? > > Hopefully that description makes sense. Thank you in advance for your help! > Best, > Abigail Jackson > The Scripps Research Institute ------------------------------ Message: 2 Date: Thu, 16 Dec 2021 10:08:26 +0000 From: Guillaume Gaullier <guillaume.gaullier(a)icm.uu.se> To: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> Subject: [chimerax-users] Change the directory for data fetched from databases Message-ID: <7B64261E-92A8-45FF-BF14-0B597E14A98B(a)icm.uu.se> Content-Type: text/plain; charset="utf-8" Hello, The documentation for the open command says "Web-fetched data are stored locally in ~/Downloads/ChimeraX/ (where ~ indicates a user's home directory)". Is there a way to change this directory? I couldn?t find one in the settings window, but maybe a command could do that? (in that case I would simply need to add this command to the startup commands). The use case I have in mind is to share the ChimeraX cache between all accounts on a multi-user workstation (so, relocate the cache at some place like /data/ChimeraX). Thank you, Guillaume N?r du har kontakt med oss p? Uppsala universitet med e-post s? inneb?r det att vi behandlar dina personuppgifter. F?r att l?sa mer om hur vi g?r det kan du l?sa h?r: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy ------------------------------ Message: 3 Date: Thu, 16 Dec 2021 14:50:25 -0800 From: Tom Goddard <goddard(a)sonic.net> To: Guillaume Gaullier <guillaume.gaullier(a)icm.uu.se> Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> Subject: Re: [chimerax-users] Change the directory for data fetched from databases Message-ID: <8D292E49-13E7-4DF0-9B94-7EAC424DA7D0(a)sonic.net> Content-Type: text/plain; charset=utf-8 Hi Guillaume, There is no setting to change the location where ChimeraX caches fetched files. It is always ~/Downloads/ChimeraX On a multi-user workstation is the idea that every person would change the ChimeraX setting to point to a common cache directory? Will people cooperate with that? Each person of course has their own ChimeraX settings. Everyone will also need write access to that directory. There are no site-wide settings in ChimeraX. You could modify the ChimeraX application file, a file in the distribution (here's the path for Linux) chimerax/lib/python3.9/site-packages/chimerax/core/fetch.py making _cache_dirs = ['/usr/local/chimerax_fetch'] near the top would I think change to use that directory. Of course each time you install a new ChimeraX it would need such a change, and if individual users install their own ChimeraX version it will use ~/Downloads/ChimeraX. Tom > On Dec 16, 2021, at 2:08 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Hello, > > The documentation for the open command says "Web-fetched data are stored locally in ~/Downloads/ChimeraX/ (where ~ indicates a user's home directory)". Is there a way to change this directory? I couldn?t find one in the settings window, but maybe a command could do that? (in that case I would simply need to add this command to the startup commands). > > The use case I have in mind is to share the ChimeraX cache between all accounts on a multi-user workstation (so, relocate the cache at some place like /data/ChimeraX). > > Thank you, > > Guillaume > > > > > > > > > > N?r du har kontakt med oss p? Uppsala universitet med e-post s? inneb?r det att vi behandlar dina personuppgifter. F?r att l?sa mer om hur vi g?r det kan du l?sa h?r: http://www.uu.se/om-uu/dataskydd-personuppgifter/ > > E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy > > _______________________________________________ > ChimeraX-users mailing list > ChimeraX-users(a)cgl.ucsf.edu > Manage subscription: > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users > ------------------------------ Message: 4 Date: Fri, 17 Dec 2021 08:40:06 +0000 From: Guillaume Gaullier <guillaume.gaullier(a)icm.uu.se> To: Tom Goddard <goddard(a)sonic.net> Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> Subject: Re: [chimerax-users] Change the directory for data fetched from databases Message-ID: <ED531B0A-5F66-4E86-920E-565966A5D8A3(a)icm.uu.se> Content-Type: text/plain; charset="utf-8" Hi Tom, This is the use case I had in mind indeed. Model files are small enough that duplication doesn?t matter, but a shared cache for maps could be convenient. I was simply asking in case there was a supported way to achieve this that I had missed in the documentation, but I can absolutely live with the current default. Thank you for your answer. Cheers, Guillaume On 16 Dec 2021, at 23:50, Tom Goddard <goddard(a)sonic.net<mailto:goddard@sonic.net>> wrote: Hi Guillaume, There is no setting to change the location where ChimeraX caches fetched files. It is always ~/Downloads/ChimeraX On a multi-user workstation is the idea that every person would change the ChimeraX setting to point to a common cache directory? Will people cooperate with that? Each person of course has their own ChimeraX settings. Everyone will also need write access to that directory. There are no site-wide settings in ChimeraX. You could modify the ChimeraX application file, a file in the distribution (here's the path for Linux) chimerax/lib/python3.9/site-packages/chimerax/core/fetch.py making _cache_dirs = ['/usr/local/chimerax_fetch'] near the top would I think change to use that directory. Of course each time you install a new ChimeraX it would need such a change, and if individual users install their own ChimeraX version it will use ~/Downloads/ChimeraX. Tom On Dec 16, 2021, at 2:08 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Hello, The documentation for the open command says "Web-fetched data are stored locally in ~/Downloads/ChimeraX/ (where ~ indicates a user's home directory)". Is there a way to change this directory? I couldn?t find one in the settings window, but maybe a command could do that? (in that case I would simply need to add this command to the startup commands). The use case I have in mind is to share the ChimeraX cache between all accounts on a multi-user workstation (so, relocate the cache at some place like /data/ChimeraX). Thank you, Guillaume N?r du har kontakt med oss p? Uppsala universitet med e-post s? inneb?r det att vi behandlar dina personuppgifter. F?r att l?sa mer om hur vi g?r det kan du l?sa h?r: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy _______________________________________________ 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

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PDB: 7OVR
by Veler, Hana (NIH/NCI) [F] 17 Dec '21

17 Dec '21

To whom it may concern, The command “show sel atoms’ does not work in the 7OVR structure and I was wondering how can I fix this? I wanted to show certain residues as atoms in the structure. When I open other structures, e.g. 5FMM, the command works perfectly fine. Would you know what could be the cause? Thanks, Hana

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Change the directory for data fetched from databases
by Guillaume Gaullier 17 Dec '21

17 Dec '21

Hello, The documentation for the open command says "Web-fetched data are stored locally in ~/Downloads/ChimeraX/ (where ~ indicates a user's home directory)". Is there a way to change this directory? I couldn’t find one in the settings window, but maybe a command could do that? (in that case I would simply need to add this command to the startup commands). The use case I have in mind is to share the ChimeraX cache between all accounts on a multi-user workstation (so, relocate the cache at some place like /data/ChimeraX). Thank you, Guillaume När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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ChimeraX Question
by Abigail Jackson 15 Dec '21

15 Dec '21

Hi there, I have a question regarding the tile function in ChimeraX. In the original Chimera, once multiple maps were tiled they would all rotate individually and the grid itself was fixed in space. In ChimeraX, however, once maps are tiled the entire grid rotates as a unit and the individual maps are fixed. Do you know if there is an option to have the maps spin individually instead, like in the original Chimera? Hopefully that description makes sense. Thank you in advance for your help! Best, Abigail Jackson The Scripps Research Institute

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Fwd: ChimeraX VR question or suggestions
by Elaine Meng 14 Dec '21

14 Dec '21

> > From: Alejandro Villalta Cásares <alejandrovillaltac(a)gmail.com> > Subject: ChimeraX VR question or suggestions > Date: December 13, 2021 at 4:36:03 AM PST > To: chimerax(a)cgl.ucsf.edu > > Dear ChimeraX staff, > > I tested the ChimeraX VR mode today. I was very happy on how it looks and how easy it was to move and see some parts of the structure compared to the flat screen version. Nevertheless, the function that I think it will very useful the VR is to segment and select different segments to save them later. That I couldn't manage to do it after some time I managed to be able to select one region but no more than one at time. It should be nice to add the ability to select multiple regions or at least as in the flat screen that it tells you the name of the models that you are pointing, like that we could pass through command lines. Also it should be nice that a keyboard appears on the headset in order to type on the command lines, but it is true that is a minor point, if it can be written directly on the PC. > > Thank you very much for this amazing function, > > I hope that this constructive mail could help you to improve it more. > > Sincerely yours, > > Alejandro Villalta >

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Analog command to reinit & create?
by Eric Pettersen 13 Dec '21

13 Dec '21

> Begin forwarded message: > > From: "Jan Gebauer" <jan.gebauer(a)uni-koeln.de <mailto:jan.gebauer@uni-koeln.de>> > Subject: Analog command to reinit & create? > Date: December 13, 2021 at 7:11:40 AM PST > To: ChimeraX-users <chimerax-users-bounces(a)cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> > Reply-To: "Jan Gebauer" <jan.gebauer(a)uni-koeln.de <mailto:jan.gebauer@uni-koeln.de>> > > > Hi everyone, > > I am currently teaching a crystallographic course and this year I am introducing ChimeraX for the first time (previous years we have used PyMol). > I still am in the middle of my personal transiston from PyMol to ChimeraX and potentially I am still stuck too much in the "PyMol"-way to do it, but I still miss a couple of commands. Could anyone help with that? > > 1) Analog to Reinit > I generate all my publication figures with scripts (now cxc). The Reinit command in Pymol, always gave me a fresh enviroment, however the closest analog I found "Close" only closes the current model. All other settings (Lightning etc.) are kept and only reset after closing ChimeraX. Therefore, I do not get the same results from my script, if I run it multiple times... > > 2) Create object > Is there a way to copy a selection of atoms into a new molecule - for complicated visualisations? > > Thanks so far to the developers - I love more things on ChimeraX than I miss 👍 > Best, > Jan > > -- > Dr. Jan Gebauer > AG Baumann / Biochemistry Cologne > Zülpicher Str. 47 / 50764 Köln > +49 - 221 - 470 - 3212

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ViewDockX for Autodock Vina error
by Visvaldas K. 13 Dec '21

13 Dec '21

Dear colleagues, for some reason ChimeraX does not recognize pdbqt from Autodock Vina 1.1.2 as a "docking file", even though it opens pdbqt file just fine (The message: No suitable models found for ViewDockX). The documentation says that Autodock Vina is supported. Perhaps it's the version of Vina (I use 1.1.2, or preferably its fork Smina, while the newest version is 1.2)? If I knew what the file that ChimeraX recognizes as a "model" looks like, I'd write a script to reformat my pdbqt, but at the moment I'm in the dark... Not too bad since I still can view the structures, but perhaps I'm missing some cool features... Thank you in advance, Vis

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Save ribbons and surfaces with minimal amount of vertices/faces
by Sarah Piper 13 Dec '21

13 Dec '21

Hi ChimeraX team and others, I got a bit of an unusual question and am interested to see whether it is possible! I am trying to use a short helix in ribbon style from ChimeraX into Blender, and use it to create a 'skeleton' for animations. For this, it would be most useful to have as few vertices as possible for the helix (basically only the 'invisible' coordinates themselves as 'line', instead of having it as a 3D view/thick helix. When I export a helix even with a very thin ribbon style through the command line (e.g. width and thickness to 0.1), this is unfortunately still too thick and creates too many vertices/faces. Setting these values to 0 gives errors. I have looked at the ribbon style editor in Chimera as well, and unfortunately the minimum settings are 0.05. Would it be possible to somehow set any of these parameters to 0 and save this as a file format suitable for 3D softwares (e.g. .glb)? Would it work through a python script potentially? (I'm not familiar with python in chimera yet but happy to learn more about this). And if so, would this be also applicable for surfaces, to reduce the numbers of vertices/faces that are exported? On another note, I was wondering whether it would be possible to set the chimaera scene 'world origin' to a particular coordinate set; I think in Pymol this is possible with resetting the camera view: cmd.set_view([ 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 40.0, 100.0, -20.0]) Sorry for these unusual question but looking forward to hearing back from anyone who might have any suggestions! Cheers, Sarah

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Showing long coiled coil alpha helices as tubes
by Huiskonen, Juha T 13 Dec '21

13 Dec '21

Hi all, I am trying to render two long alpha helices forming a coiled coil as tubes instead of ribbons. The tubes rendered with default settings do not however follow the paths of the helices. Instead, the tubes become almost straight. Any suggestions? Best wishes, Juha

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rotation parameters of the map
by Dmitry Semchonok 13 Dec '21

13 Dec '21

Dear colleagues, When I align one map to the other (either manually or by using the Fit option), I would like to know the applied rotation parameters. How to find them our when a) using just Fit option b) rotation manually and then using the Fit option? Thank you Sincerely, Dmitry

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ChimeraX-users December 2021